Daily Papers

Sequence labelling tasks like Dialog Act and Emotion/Sentiment identification are a key component of spoken dialog systems. In this work, we propose a new approach to learn generic representations adapted to spoken dialog, which we evaluate on a new benchmark we call Sequence labellIng evaLuatIon benChmark fOr spoken laNguagE benchmark (SILICONE). SILICONE is model-agnostic and contains 10 different datasets of various sizes. We obtain our representations with a hierarchical encoder based on transformer architectures, for which we extend two well-known pre-training objectives. Pre-training is performed on OpenSubtitles: a large corpus of spoken dialog containing over 2.3 billion of tokens. We demonstrate how hierarchical encoders achieve competitive results with consistently fewer parameters compared to state-of-the-art models and we show their importance for both pre-training and fine-tuning.

Zero-resource cross-lingual transfer approaches aim to apply supervised models from a source language to unlabelled target languages. In this paper we perform an in-depth study of the two main techniques employed so far for cross-lingual zero-resource sequence labelling, based either on data or model transfer. Although previous research has proposed translation and annotation projection (data-based cross-lingual transfer) as an effective technique for cross-lingual sequence labelling, in this paper we experimentally demonstrate that high capacity multilingual language models applied in a zero-shot (model-based cross-lingual transfer) setting consistently outperform data-based cross-lingual transfer approaches. A detailed analysis of our results suggests that this might be due to important differences in language use. More specifically, machine translation often generates a textual signal which is different to what the models are exposed to when using gold standard data, which affects both the fine-tuning and evaluation processes. Our results also indicate that data-based cross-lingual transfer approaches remain a competitive option when high-capacity multilingual language models are not available.

Recent research on sequence labelling has been exploring different strategies to mitigate the lack of manually annotated data for the large majority of the world languages. Among others, the most successful approaches have been based on (i) the cross-lingual transfer capabilities of multilingual pre-trained language models (model-transfer), (ii) data translation and label projection (data-transfer) and (iii), prompt-based learning by reusing the mask objective to exploit the few-shot capabilities of pre-trained language models (few-shot). Previous work seems to conclude that model-transfer outperforms data-transfer methods and that few-shot techniques based on prompting are superior to updating the model's weights via fine-tuning. In this paper, we empirically demonstrate that, for Argument Mining, a sequence labelling task which requires the detection of long and complex discourse structures, previous insights on cross-lingual transfer or few-shot learning do not apply. Contrary to previous work, we show that for Argument Mining data transfer obtains better results than model-transfer and that fine-tuning outperforms few-shot methods. Regarding the former, the domain of the dataset used for data-transfer seems to be a deciding factor, while, for few-shot, the type of task (length and complexity of the sequence spans) and sampling method prove to be crucial.

Modelling persuasion strategies as predictors of task outcome has several real-world applications and has received considerable attention from the computational linguistics community. However, previous research has failed to account for the resisting strategies employed by an individual to foil such persuasion attempts. Grounded in prior literature in cognitive and social psychology, we propose a generalised framework for identifying resisting strategies in persuasive conversations. We instantiate our framework on two distinct datasets comprising persuasion and negotiation conversations. We also leverage a hierarchical sequence-labelling neural architecture to infer the aforementioned resisting strategies automatically. Our experiments reveal the asymmetry of power roles in non-collaborative goal-directed conversations and the benefits accrued from incorporating resisting strategies on the final conversation outcome. We also investigate the role of different resisting strategies on the conversation outcome and glean insights that corroborate with past findings. We also make the code and the dataset of this work publicly available at https://github.com/americast/resper.

In this paper we address the challenge of extracting scientific references from patents. We approach the problem as a sequence labelling task and investigate the merits of BERT models to the extraction of these long sequences. References in patents to scientific literature are relevant to study the connection between science and industry. Most prior work only uses the front-page citations for this analysis, which are provided in the metadata of patent archives. In this paper we build on prior work using Conditional Random Fields (CRF) and Flair for reference extraction. We improve the quality of the training data and train three BERT-based models on the labelled data (BERT, bioBERT, sciBERT). We find that the improved training data leads to a large improvement in the quality of the trained models. In addition, the BERT models beat CRF and Flair, with recall scores around 97% obtained with cross validation. With the best model we label a large collection of 33 thousand patents, extract the citations, and match them to publications in the Web of Science database. We extract 50% more references than with the old training data and methods: 735 thousand references in total. With these patent-publication links, follow-up research will further analyze which types of scientific work lead to inventions.

Named Entity Recognition (NER) is a foundational NLP task that aims to provide class labels like Person, Location, Organisation, Time, and Number to words in free text. Named Entities can also be multi-word expressions where the additional I-O-B annotation information helps label them during the NER annotation process. While English and European languages have considerable annotated data for the NER task, Indian languages lack on that front -- both in terms of quantity and following annotation standards. This paper releases a significantly sized standard-abiding Hindi NER dataset containing 109,146 sentences and 2,220,856 tokens, annotated with 11 tags. We discuss the dataset statistics in all their essential detail and provide an in-depth analysis of the NER tag-set used with our data. The statistics of tag-set in our dataset show a healthy per-tag distribution, especially for prominent classes like Person, Location and Organisation. Since the proof of resource-effectiveness is in building models with the resource and testing the model on benchmark data and against the leader-board entries in shared tasks, we do the same with the aforesaid data. We use different language models to perform the sequence labelling task for NER and show the efficacy of our data by performing a comparative evaluation with models trained on another dataset available for the Hindi NER task. Our dataset helps achieve a weighted F1 score of 88.78 with all the tags and 92.22 when we collapse the tag-set, as discussed in the paper. To the best of our knowledge, no available dataset meets the standards of volume (amount) and variability (diversity), as far as Hindi NER is concerned. We fill this gap through this work, which we hope will significantly help NLP for Hindi. We release this dataset with our code and models at https://github.com/cfiltnlp/HiNER

Idiomatic expressions have always been a bottleneck for language comprehension and natural language understanding, specifically for tasks like Machine Translation(MT). MT systems predominantly produce literal translations of idiomatic expressions as they do not exhibit generic and linguistically deterministic patterns which can be exploited for comprehension of the non-compositional meaning of the expressions. These expressions occur in parallel corpora used for training, but due to the comparatively high occurrences of the constituent words of idiomatic expressions in literal context, the idiomatic meaning gets overpowered by the compositional meaning of the expression. State of the art Metaphor Detection Systems are able to detect non-compositional usage at word level but miss out on idiosyncratic phrasal idiomatic expressions. This creates a dire need for a dataset with a wider coverage and higher occurrence of commonly occurring idiomatic expressions, the spans of which can be used for Metaphor Detection. With this in mind, we present our English Possible Idiomatic Expressions(EPIE) corpus containing 25206 sentences labelled with lexical instances of 717 idiomatic expressions. These spans also cover literal usages for the given set of idiomatic expressions. We also present the utility of our dataset by using it to train a sequence labelling module and testing on three independent datasets with high accuracy, precision and recall scores.

The automatic annotation of direct speech (AADS) in written text has been often used in computational narrative understanding. Methods based on either rules or deep neural networks have been explored, in particular for English or German languages. Yet, for French, our target language, not many works exist. Our goal is to create a unified framework to design and evaluate AADS models in French. For this, we consolidated the largest-to-date French narrative dataset annotated with DS per word; we adapted various baselines for sequence labelling or from AADS in other languages; and we designed and conducted an extensive evaluation focused on generalisation. Results show that the task still requires substantial efforts and emphasise characteristics of each baseline. Although this framework could be improved, it is a step further to encourage more research on the topic.

The incremental sequence labeling task involves continuously learning new classes over time while retaining knowledge of the previous ones. Our investigation identifies two significant semantic shifts: E2O (where the model mislabels an old entity as a non-entity) and O2E (where the model labels a non-entity or old entity as a new entity). Previous research has predominantly focused on addressing the E2O problem, neglecting the O2E issue. This negligence results in a model bias towards classifying new data samples as belonging to the new class during the learning process. To address these challenges, we propose a novel framework, Incremental Sequential Labeling without Semantic Shifts (IS3). Motivated by the identified semantic shifts (E2O and O2E), IS3 aims to mitigate catastrophic forgetting in models. As for the E2O problem, we use knowledge distillation to maintain the model's discriminative ability for old entities. Simultaneously, to tackle the O2E problem, we alleviate the model's bias towards new entities through debiased loss and optimization levels. Our experimental evaluation, conducted on three datasets with various incremental settings, demonstrates the superior performance of IS3 compared to the previous state-of-the-art method by a significant margin.The data, code, and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

Recent advances in multimodal pre-trained models have significantly improved information extraction from visually-rich documents (VrDs), in which named entity recognition (NER) is treated as a sequence-labeling task of predicting the BIO entity tags for tokens, following the typical setting of NLP. However, BIO-tagging scheme relies on the correct order of model inputs, which is not guaranteed in real-world NER on scanned VrDs where text are recognized and arranged by OCR systems. Such reading order issue hinders the accurate marking of entities by BIO-tagging scheme, making it impossible for sequence-labeling methods to predict correct named entities. To address the reading order issue, we introduce Token Path Prediction (TPP), a simple prediction head to predict entity mentions as token sequences within documents. Alternative to token classification, TPP models the document layout as a complete directed graph of tokens, and predicts token paths within the graph as entities. For better evaluation of VrD-NER systems, we also propose two revised benchmark datasets of NER on scanned documents which can reflect real-world scenarios. Experiment results demonstrate the effectiveness of our method, and suggest its potential to be a universal solution to various information extraction tasks on documents.

Extreme multi-label text classification (XMTC) is the task of finding the most relevant subset labels from an extremely large-scale label collection. Recently, some deep learning models have achieved state-of-the-art results in XMTC tasks. These models commonly predict scores for all labels by a fully connected layer as the last layer of the model. However, such models can't predict a relatively complete and variable-length label subset for each document, because they select positive labels relevant to the document by a fixed threshold or take top k labels in descending order of scores. A less popular type of deep learning models called sequence-to-sequence (Seq2Seq) focus on predicting variable-length positive labels in sequence style. However, the labels in XMTC tasks are essentially an unordered set rather than an ordered sequence, the default order of labels restrains Seq2Seq models in training. To address this limitation in Seq2Seq, we propose an autoregressive sequence-to-set model for XMTC tasks named OTSeq2Set. Our model generates predictions in student-forcing scheme and is trained by a loss function based on bipartite matching which enables permutation-invariance. Meanwhile, we use the optimal transport distance as a measurement to force the model to focus on the closest labels in semantic label space. Experiments show that OTSeq2Set outperforms other competitive baselines on 4 benchmark datasets. Especially, on the Wikipedia dataset with 31k labels, it outperforms the state-of-the-art Seq2Seq method by 16.34% in micro-F1 score. The code is available at https://github.com/caojie54/OTSeq2Set.

This paper presents a neural architecture for Vietnamese sequence labeling tasks including part-of-speech (POS) tagging and named entity recognition (NER). We applied the model described in lample-EtAl:2016:N16-1 that is a combination of bidirectional Long-Short Term Memory and Conditional Random Fields, which rely on two sources of information about words: character-based word representations learned from the supervised corpus and pre-trained word embeddings learned from other unannotated corpora. Experiments on benchmark datasets show that this work achieves state-of-the-art performances on both tasks - 93.52\% accuracy for POS tagging and 94.88\% F1 for NER. Our sourcecode is available at here.

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

Pre-trained language models based on masked language modeling (MLM) objective excel in natural language understanding (NLU) tasks. While fine-tuned MLM-based encoders consistently outperform causal language modeling decoders of comparable size, a recent trend of scaling decoder models to multiple billion parameters resulted in large language models (LLMs), making them competitive with MLM-based encoders. Although scale amplifies their prowess in NLU tasks, LLMs fall short of SOTA results in information extraction (IE) tasks, many framed as sequence labeling (SL). However, whether this is an intrinsic limitation of LLMs or whether their SL performance can be improved remains unclear. To address this, we explore strategies to enhance the SL performance of "open" LLMs (Llama2 and Mistral) on IE tasks. We investigate bidirectional information flow within groups of decoder blocks, applying layer-wise removal or enforcement of the causal mask (CM) during LLM fine-tuning. This approach yields performance gains competitive with SOTA SL models, matching or outperforming the results of CM removal from all blocks. Our findings hold for diverse SL tasks, proving that "open" LLMs with layer-dependent CM removal outperform strong MLM-based encoders and instruction-tuned LLMs. However, we observe no effect from CM removal on a small scale when maintaining an equivalent model size, pre-training steps, and pre-training and fine-tuning data.

Named entity recognition is a fundamental task in natural language processing, identifying the span and category of entities in unstructured texts. The traditional sequence labeling methodology ignores the nested entities, i.e. entities included in other entity mentions. Many approaches attempt to address this scenario, most of which rely on complex structures or have high computation complexity. The representation learning of the heterogeneous star graph containing text nodes and type nodes is investigated in this paper. In addition, we revise the graph attention mechanism into a hybrid form to address its unreasonableness in specific topologies. The model performs the type-supervised sequence labeling after updating nodes in the graph. The annotation scheme is an extension of the single-layer sequence labeling and is able to cope with the vast majority of nested entities. Extensive experiments on public NER datasets reveal the effectiveness of our model in extracting both flat and nested entities. The method achieved state-of-the-art performance on both flat and nested datasets. The significant improvement in accuracy reflects the superiority of the multi-layer labeling strategy.

Word emphasis in textual content aims at conveying the desired intention by changing the size, color, typeface, style (bold, italic, etc.), and other typographical features. The emphasized words are extremely helpful in drawing the readers' attention to specific information that the authors wish to emphasize. However, performing such emphasis using a soft keyboard for social media interactions is time-consuming and has an associated learning curve. In this paper, we propose a novel approach to automate the emphasis word detection on short written texts. To the best of our knowledge, this work presents the first lightweight deep learning approach for smartphone deployment of emphasis selection. Experimental results show that our approach achieves comparable accuracy at a much lower model size than existing models. Our best lightweight model has a memory footprint of 2.82 MB with a matching score of 0.716 on SemEval-2020 public benchmark dataset.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Dialogue Act recognition associate dialogue acts (i.e., semantic labels) to utterances in a conversation. The problem of associating semantic labels to utterances can be treated as a sequence labeling problem. In this work, we build a hierarchical recurrent neural network using bidirectional LSTM as a base unit and the conditional random field (CRF) as the top layer to classify each utterance into its corresponding dialogue act. The hierarchical network learns representations at multiple levels, i.e., word level, utterance level, and conversation level. The conversation level representations are input to the CRF layer, which takes into account not only all previous utterances but also their dialogue acts, thus modeling the dependency among both, labels and utterances, an important consideration of natural dialogue. We validate our approach on two different benchmark data sets, Switchboard and Meeting Recorder Dialogue Act, and show performance improvement over the state-of-the-art methods by 2.2% and 4.1% absolute points, respectively. It is worth noting that the inter-annotator agreement on Switchboard data set is 84%, and our method is able to achieve the accuracy of about 79% despite being trained on the noisy data.

State-of-the-art sequence labeling systems traditionally require large amounts of task-specific knowledge in the form of hand-crafted features and data pre-processing. In this paper, we introduce a novel neutral network architecture that benefits from both word- and character-level representations automatically, by using combination of bidirectional LSTM, CNN and CRF. Our system is truly end-to-end, requiring no feature engineering or data pre-processing, thus making it applicable to a wide range of sequence labeling tasks. We evaluate our system on two data sets for two sequence labeling tasks --- Penn Treebank WSJ corpus for part-of-speech (POS) tagging and CoNLL 2003 corpus for named entity recognition (NER). We obtain state-of-the-art performance on both the two data --- 97.55\% accuracy for POS tagging and 91.21\% F1 for NER.

In the absence of readily available labeled data for a given sequence labeling task and language, annotation projection has been proposed as one of the possible strategies to automatically generate annotated data. Annotation projection has often been formulated as the task of transporting, on parallel corpora, the labels pertaining to a given span in the source language into its corresponding span in the target language. In this paper we present T-Projection, a novel approach for annotation projection that leverages large pretrained text-to-text language models and state-of-the-art machine translation technology. T-Projection decomposes the label projection task into two subtasks: (i) A candidate generation step, in which a set of projection candidates using a multilingual T5 model is generated and, (ii) a candidate selection step, in which the generated candidates are ranked based on translation probabilities. We conducted experiments on intrinsic and extrinsic tasks in 5 Indo-European and 8 low-resource African languages. We demostrate that T-projection outperforms previous annotation projection methods by a wide margin. We believe that T-Projection can help to automatically alleviate the lack of high-quality training data for sequence labeling tasks. Code and data are publicly available.

Global sentence information is crucial for sequence labeling tasks, where each word in a sentence must be assigned a label. While BiLSTM models are widely used, they often fail to capture sufficient global context for inner words. Previous work has proposed various RNN variants to integrate global sentence information into word representations. However, these approaches suffer from three key limitations: (1) they are slower in both inference and training compared to the original BiLSTM, (2) they cannot effectively supplement global information for transformer-based models, and (3) the high time cost associated with reimplementing and integrating these customized RNNs into existing architectures. In this study, we introduce a simple yet effective mechanism that addresses these limitations. Our approach efficiently supplements global sentence information for both BiLSTM and transformer-based models, with minimal degradation in inference and training speed, and is easily pluggable into current architectures. We demonstrate significant improvements in F1 scores across seven popular benchmarks, including Named Entity Recognition (NER) tasks such as Conll2003, Wnut2017 , and the Chinese named-entity recognition task Weibo, as well as End-to-End Aspect-Based Sentiment Analysis (E2E-ABSA) benchmarks such as Laptop14, Restaurant14, Restaurant15, and Restaurant16. With out any extra strategy, we achieve third highest score on weibo NER benchmark. Compared to CRF, one of the most popular frameworks for sequence labeling, our mechanism achieves competitive F1 scores while offering superior inference and training speed. Code is available at: https://github.com/conglei2XU/Global-Context-Mechanism

In this paper, we formulate keyphrase extraction from scholarly articles as a sequence labeling task solved using a BiLSTM-CRF, where the words in the input text are represented using deep contextualized embeddings. We evaluate the proposed architecture using both contextualized and fixed word embedding models on three different benchmark datasets (Inspec, SemEval 2010, SemEval 2017) and compare with existing popular unsupervised and supervised techniques. Our results quantify the benefits of (a) using contextualized embeddings (e.g. BERT) over fixed word embeddings (e.g. Glove); (b) using a BiLSTM-CRF architecture with contextualized word embeddings over fine-tuning the contextualized word embedding model directly, and (c) using genre-specific contextualized embeddings (SciBERT). Through error analysis, we also provide some insights into why particular models work better than others. Lastly, we present a case study where we analyze different self-attention layers of the two best models (BERT and SciBERT) to better understand the predictions made by each for the task of keyphrase extraction.

Prompt-based methods have been successfully applied to multilingual pretrained language models for zero-shot cross-lingual understanding. However, most previous studies primarily focused on sentence-level classification tasks, and only a few considered token-level labeling tasks such as Named Entity Recognition (NER) and Part-of-Speech (POS) tagging. In this paper, we propose Token-Level Prompt Decomposition (ToPro), which facilitates the prompt-based method for token-level sequence labeling tasks. The ToPro method decomposes an input sentence into single tokens and applies one prompt template to each token. Our experiments on multilingual NER and POS tagging datasets demonstrate that ToPro-based fine-tuning outperforms Vanilla fine-tuning and Prompt-Tuning in zero-shot cross-lingual transfer, especially for languages that are typologically different from the source language English. Our method also attains state-of-the-art performance when employed with the mT5 model. Besides, our exploratory study in multilingual large language models shows that ToPro performs much better than the current in-context learning method. Overall, the performance improvements show that ToPro could potentially serve as a novel and simple benchmarking method for sequence labeling tasks.

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning.

Ordinal regression refers to classifying object instances into ordinal categories. It has been widely studied in many scenarios, such as medical disease grading, movie rating, etc. Known methods focused only on learning inter-class ordinal relationships, but still incur limitations in distinguishing adjacent categories thus far. In this paper, we propose a simple sequence prediction framework for ordinal regression called Ord2Seq, which, for the first time, transforms each ordinal category label into a special label sequence and thus regards an ordinal regression task as a sequence prediction process. In this way, we decompose an ordinal regression task into a series of recursive binary classification steps, so as to subtly distinguish adjacent categories. Comprehensive experiments show the effectiveness of distinguishing adjacent categories for performance improvement and our new approach exceeds state-of-the-art performances in four different scenarios. Codes are available at https://github.com/wjh892521292/Ord2Seq.

This work proposes a novel adaptation of a pretrained sequence-to-sequence model to the task of document ranking. Our approach is fundamentally different from a commonly-adopted classification-based formulation of ranking, based on encoder-only pretrained transformer architectures such as BERT. We show how a sequence-to-sequence model can be trained to generate relevance labels as "target words", and how the underlying logits of these target words can be interpreted as relevance probabilities for ranking. On the popular MS MARCO passage ranking task, experimental results show that our approach is at least on par with previous classification-based models and can surpass them with larger, more-recent models. On the test collection from the TREC 2004 Robust Track, we demonstrate a zero-shot transfer-based approach that outperforms previous state-of-the-art models requiring in-dataset cross-validation. Furthermore, we find that our approach significantly outperforms an encoder-only model in a data-poor regime (i.e., with few training examples). We investigate this observation further by varying target words to probe the model's use of latent knowledge.

Prevalent models based on artificial neural network (ANN) for sentence classification often classify sentences in isolation without considering the context in which sentences appear. This hampers the traditional sentence classification approaches to the problem of sequential sentence classification, where structured prediction is needed for better overall classification performance. In this work, we present a hierarchical sequential labeling network to make use of the contextual information within surrounding sentences to help classify the current sentence. Our model outperforms the state-of-the-art results by 2%-3% on two benchmarking datasets for sequential sentence classification in medical scientific abstracts.

Natural Language Processing (NLP) has seen remarkable advances in recent years, particularly with the emergence of Large Language Models that have achieved unprecedented performance across many tasks. However, these developments have mainly benefited a small number of high-resource languages such as English. The majority of languages still face significant challenges due to the scarcity of training data and computational resources. To address this issue, this thesis focuses on cross-lingual transfer learning, a research area aimed at leveraging data and models from high-resource languages to improve NLP performance for low-resource languages. Specifically, we focus on Sequence Labeling tasks such as Named Entity Recognition, Opinion Target Extraction, and Argument Mining. The research is structured around three main objectives: (1) advancing data-based cross-lingual transfer learning methods through improved translation and annotation projection techniques, (2) developing enhanced model-based transfer learning approaches utilizing state-of-the-art multilingual models, and (3) applying these methods to real-world problems while creating open-source resources that facilitate future research in low-resource NLP. More specifically, this thesis presents a new method to improve data-based transfer with T-Projection, a state-of-the-art annotation projection method that leverages text-to-text multilingual models and machine translation systems. T-Projection significantly outperforms previous annotation projection methods by a wide margin. For model-based transfer, we introduce a constrained decoding algorithm that enhances cross-lingual Sequence Labeling in zero-shot settings using text-to-text models. Finally, we develop Medical mT5, the first multilingual text-to-text medical model, demonstrating the practical impact of our research on real-world applications.

Sequence-to-sequence models are commonly trained via maximum likelihood estimation (MLE). However, standard MLE training considers a word-level objective, predicting the next word given the previous ground-truth partial sentence. This procedure focuses on modeling local syntactic patterns, and may fail to capture long-range semantic structure. We present a novel solution to alleviate these issues. Our approach imposes global sequence-level guidance via new supervision based on optimal transport, enabling the overall characterization and preservation of semantic features. We further show that this method can be understood as a Wasserstein gradient flow trying to match our model to the ground truth sequence distribution. Extensive experiments are conducted to validate the utility of the proposed approach, showing consistent improvements over a wide variety of NLP tasks, including machine translation, abstractive text summarization, and image captioning.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

We present an elegant and effective approach for addressing limitations in existing multi-label classification models by incorporating interaction matching, a concept shown to be useful for ad-hoc search result ranking. By performing soft n-gram interaction matching, we match labels with natural language descriptions (which are common to have in most multi-labeling tasks). Our approach can be used to enhance existing multi-label classification approaches, which are biased toward frequently-occurring labels. We evaluate our approach on two challenging tasks: automatic medical coding of clinical notes and automatic labeling of entities from software tutorial text. Our results show that our method can yield up to an 11% relative improvement in macro performance, with most of the gains stemming labels that appear infrequently in the training set (i.e., the long tail of labels).

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

In this study, we tackle the challenge of limited labeled data for low-resource languages in ASR, focusing on Hindi. Specifically, we explore pseudo-labeling, by proposing a generic framework combining multiple ideas from existing works. Our framework integrates multiple base models for transcription and evaluators for assessing audio-transcript pairs, resulting in robust pseudo-labeling for low resource languages. We validate our approach with a new benchmark, IndicYT, comprising diverse YouTube audio files from multiple content categories. Our findings show that augmenting pseudo labeled data from YouTube with existing training data leads to significant performance improvements on IndicYT, without affecting performance on out-of-domain benchmarks, demonstrating the efficacy of pseudo-labeled data in enhancing ASR capabilities for low-resource languages. The benchmark, code and models developed as a part of this work will be made publicly available.

A central goal of sequence modeling is designing a single principled model that can address sequence data across a range of modalities and tasks, particularly on long-range dependencies. Although conventional models including RNNs, CNNs, and Transformers have specialized variants for capturing long dependencies, they still struggle to scale to very long sequences of 10000 or more steps. A promising recent approach proposed modeling sequences by simulating the fundamental state space model (SSM) \( x'(t) = Ax(t) + Bu(t), y(t) = Cx(t) + Du(t) \), and showed that for appropriate choices of the state matrix \( A \), this system could handle long-range dependencies mathematically and empirically. However, this method has prohibitive computation and memory requirements, rendering it infeasible as a general sequence modeling solution. We propose the Structured State Space sequence model (S4) based on a new parameterization for the SSM, and show that it can be computed much more efficiently than prior approaches while preserving their theoretical strengths. Our technique involves conditioning \( A \) with a low-rank correction, allowing it to be diagonalized stably and reducing the SSM to the well-studied computation of a Cauchy kernel. S4 achieves strong empirical results across a diverse range of established benchmarks, including (i) 91\% accuracy on sequential CIFAR-10 with no data augmentation or auxiliary losses, on par with a larger 2-D ResNet, (ii) substantially closing the gap to Transformers on image and language modeling tasks, while performing generation 60times faster (iii) SoTA on every task from the Long Range Arena benchmark, including solving the challenging Path-X task of length 16k that all prior work fails on, while being as efficient as all competitors.

Weak supervision (WS) frameworks are a popular way to bypass hand-labeling large datasets for training data-hungry models. These approaches synthesize multiple noisy but cheaply-acquired estimates of labels into a set of high-quality pseudolabels for downstream training. However, the synthesis technique is specific to a particular kind of label, such as binary labels or sequences, and each new label type requires manually designing a new synthesis algorithm. Instead, we propose a universal technique that enables weak supervision over any label type while still offering desirable properties, including practical flexibility, computational efficiency, and theoretical guarantees. We apply this technique to important problems previously not tackled by WS frameworks including learning to rank, regression, and learning in hyperbolic space. Theoretically, our synthesis approach produces a consistent estimators for learning some challenging but important generalizations of the exponential family model. Experimentally, we validate our framework and show improvement over baselines in diverse settings including real-world learning-to-rank and regression problems along with learning on hyperbolic manifolds.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

This paper introduces a novel model for semantic role labeling that makes use of neural sequence modeling techniques. Our approach is motivated by the observation that complex syntactic structures and related phenomena, such as nested subordinations and nominal predicates, are not handled well by existing models. Our model treats such instances as sub-sequences of lexicalized dependency paths and learns suitable embedding representations. We experimentally demonstrate that such embeddings can improve results over previous state-of-the-art semantic role labelers, and showcase qualitative improvements obtained by our method.

Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream tasks. Despite these advancements, the performance of Large Language Models (LLMs) in information extraction tasks like Named Entity Recognition (NER), using prompts or instructions, still falls short of supervised baselines. The reason for this performance gap can be attributed to the fundamental disparity between NER and LLMs. NER is inherently a sequence labeling task, where the model must assign entity-type labels to individual tokens within a sentence. In contrast, LLMs are designed as a text generation task. This distinction between semantic labeling and text generation leads to subpar performance. In this paper, we transform the NER task into a text-generation task that can be readily adapted by LLMs. This involves enhancing source sentences with task-specific instructions and answer choices, allowing for the identification of entities and their types within natural language. We harness the strength of LLMs by integrating supervised learning within them. The goal of this combined strategy is to boost the performance of LLMs in extraction tasks like NER while simultaneously addressing hallucination issues often observed in LLM-generated content. A novel corpus Contract NER comprising seven frequently observed contract categories, encompassing named entities associated with 18 distinct legal entity types is released along with our baseline models. Our models and dataset are available to the community for future research * .

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Effective training of today's large language models (LLMs) depends on large batches and long sequences for throughput and accuracy. To handle variable-length sequences on hardware accelerators, it is common practice to introduce padding tokens, so that all sequences in a batch have the same length. We show in this paper that the variation in sequence lengths in common NLP datasets is such that up to 50% of all tokens can be padding. In less common, but not extreme, cases (e.g. GLUE-cola with sequence length 128), the ratio is up to 89%. Existing methods to address the resulting inefficiency are complicated by the need to avoid cross-contamination in self-attention, by a reduction in accuracy when sequence ordering information is lost, or by customized kernel implementations only valid for specific accelerators. This paper introduces a new formalization of sequence packing in the context of the well-studied bin packing problem, and presents new algorithms based on this formulation which, for example, confer a 2x speedup for phase 2 pre-training in BERT. We show how existing models can be adapted to ensure mathematical equivalence between the original and packed models, meaning that packed models can be trained with existing pre-training and fine-tuning practices.

This paper describes our study on using mutilingual BERT embeddings and some new neural models for improving sequence tagging tasks for the Vietnamese language. We propose new model architectures and evaluate them extensively on two named entity recognition datasets of VLSP 2016 and VLSP 2018, and on two part-of-speech tagging datasets of VLSP 2010 and VLSP 2013. Our proposed models outperform existing methods and achieve new state-of-the-art results. In particular, we have pushed the accuracy of part-of-speech tagging to 95.40% on the VLSP 2010 corpus, to 96.77% on the VLSP 2013 corpus; and the F1 score of named entity recognition to 94.07% on the VLSP 2016 corpus, to 90.31% on the VLSP 2018 corpus. Our code and pre-trained models viBERT and vELECTRA are released as open source to facilitate adoption and further research.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.

We present an approach for assessing how multilingual large language models (LLMs) learn syntax in terms of multi-formalism syntactic structures. We aim to recover constituent and dependency structures by casting parsing as sequence labeling. To do so, we select a few LLMs and study them on 13 diverse UD treebanks for dependency parsing and 10 treebanks for constituent parsing. Our results show that: (i) the framework is consistent across encodings, (ii) pre-trained word vectors do not favor constituency representations of syntax over dependencies, (iii) sub-word tokenization is needed to represent syntax, in contrast to character-based models, and (iv) occurrence of a language in the pretraining data is more important than the amount of task data when recovering syntax from the word vectors.

We present a neural transducer model with visual attention that learns to generate LaTeX markup of a real-world math formula given its image. Applying sequence modeling and transduction techniques that have been very successful across modalities such as natural language, image, handwriting, speech and audio; we construct an image-to-markup model that learns to produce syntactically and semantically correct LaTeX markup code over 150 words long and achieves a BLEU score of 89%; improving upon the previous state-of-art for the Im2Latex problem. We also demonstrate with heat-map visualization how attention helps in interpreting the model and can pinpoint (detect and localize) symbols on the image accurately despite having been trained without any bounding box data.

The Yunshan Cup 2020 track focused on creating a framework for evaluating different methods of part-of-speech (POS). There were two tasks for this track: (1) POS tagging for the Indonesian language, and (2) POS tagging for the Lao tagging. The Indonesian dataset is comprised of 10000 sentences from Indonesian news within 29 tags. And the Lao dataset consists of 8000 sentences within 27 tags. 25 teams registered for the task. The methods of participants ranged from feature-based to neural networks using either classical machine learning techniques or ensemble methods. The best performing results achieve an accuracy of 95.82% for Indonesian and 93.03%, showing that neural sequence labeling models significantly outperform classic feature-based methods and rule-based methods.

Textual label names (descriptions) are typically semantically rich in many natural language understanding (NLU) tasks. In this paper, we incorporate the prompting methodology, which is widely used to enrich model input, into the label side for the first time. Specifically, we propose a Mask Matching method, which equips an input with a prompt and its label with another, and then makes predictions by matching their mask representations. We evaluate our method extensively on 8 NLU tasks with 14 datasets. The experimental results show that Mask Matching significantly outperforms its counterparts of fine-tuning and conventional prompt-tuning, setting up state-of-the-art performances in several datasets. Mask Matching is particularly good at handling NLU tasks with large label counts and informative label names. As pioneering efforts that investigate the label-side prompt, we also discuss open issues for future study.

While contrastive learning is proven to be an effective training strategy in computer vision, Natural Language Processing (NLP) is only recently adopting it as a self-supervised alternative to Masked Language Modeling (MLM) for improving sequence representations. This paper introduces SupCL-Seq, which extends the supervised contrastive learning from computer vision to the optimization of sequence representations in NLP. By altering the dropout mask probability in standard Transformer architectures, for every representation (anchor), we generate augmented altered views. A supervised contrastive loss is then utilized to maximize the system's capability of pulling together similar samples (e.g., anchors and their altered views) and pushing apart the samples belonging to the other classes. Despite its simplicity, SupCLSeq leads to large gains in many sequence classification tasks on the GLUE benchmark compared to a standard BERTbase, including 6% absolute improvement on CoLA, 5.4% on MRPC, 4.7% on RTE and 2.6% on STSB. We also show consistent gains over self supervised contrastively learned representations, especially in non-semantic tasks. Finally we show that these gains are not solely due to augmentation, but rather to a downstream optimized sequence representation. Code: https://github.com/hooman650/SupCL-Seq

Large language models (LLMs) have become the cornerstone of modern AI. However, the existing paradigm of next-token prediction fundamentally limits their ability to form coherent, high-level concepts, making it a critical barrier to human-like understanding and reasoning. Take the phrase "ribonucleic acid" as an example: an LLM will first decompose it into tokens, i.e., artificial text fragments ("rib", "on", ...), then learn each token sequentially, rather than grasping the phrase as a unified, coherent semantic entity. This fragmented representation hinders deeper conceptual understanding and, ultimately, the development of truly intelligent systems. In response, we introduce Concept-Aware Fine-Tuning (CAFT), a novel multi-token training method that redefines how LLMs are fine-tuned. By enabling the learning of sequences that span multiple tokens, this method fosters stronger concept-aware learning. Our experiments demonstrate significant improvements compared to conventional next-token finetuning methods across diverse tasks, including traditional applications like text summarization and domain-specific ones like de novo protein design. Multi-token prediction was previously only possible in the prohibitively expensive pretraining phase; CAFT, to our knowledge, is the first to bring the multi-token setting to the post-training phase, thus effectively democratizing its benefits for the broader community of practitioners and researchers. Finally, the unexpected effectiveness of our proposed method suggests wider implications for the machine learning research community. All code and data are available at https://github.com/michaelchen-lab/caft-llm

The task of Grammatical Error Correction (GEC) has received remarkable attention with wide applications in Natural Language Processing (NLP) in recent years. While one of the key principles of GEC is to keep the correct parts unchanged and avoid over-correction, previous sequence-to-sequence (seq2seq) models generate results from scratch, which are not guaranteed to follow the original sentence structure and may suffer from the over-correction problem. In the meantime, the recently proposed sequence tagging models can overcome the over-correction problem by only generating edit operations, but are conditioned on human designed language-specific tagging labels. In this paper, we combine the pros and alleviate the cons of both models by proposing a novel Sequence-to-Action~(S2A) module. The S2A module jointly takes the source and target sentences as input, and is able to automatically generate a token-level action sequence before predicting each token, where each action is generated from three choices named SKIP, COPY and GENerate. Then the actions are fused with the basic seq2seq framework to provide final predictions. We conduct experiments on the benchmark datasets of both English and Chinese GEC tasks. Our model consistently outperforms the seq2seq baselines, while being able to significantly alleviate the over-correction problem as well as holding better generality and diversity in the generation results compared to the sequence tagging models.

When applying automated speech recognition (ASR) for Belgian Dutch (Van Dyck et al. 2021), the output consists of an unsegmented stream of words, without any punctuation. A next step is to perform segmentation and insert punctuation, making the ASR output more readable and easy to manually correct. As far as we know there is no publicly available punctuation insertion system for Dutch that functions at a usable level. The model we present here is an extension of the models of Guhr et al. (2021) for Dutch and is made publicly available. We trained a sequence classification model, based on the Dutch language model RobBERT (Delobelle et al. 2020). For every word in the input sequence, the models predicts a punctuation marker that follows the word. We have also extended a multilingual model, for cases where the language is unknown or where code switching applies. When performing the task of segmentation, the application of the best models onto out of domain test data, a sliding window of 200 words of the ASR output stream is sent to the classifier, and segmentation is applied when the system predicts a segmenting punctuation sign with a ratio above threshold. Results show to be much better than a machine translation baseline approach.

In this paper, we propose a variety of Long Short-Term Memory (LSTM) based models for sequence tagging. These models include LSTM networks, bidirectional LSTM (BI-LSTM) networks, LSTM with a Conditional Random Field (CRF) layer (LSTM-CRF) and bidirectional LSTM with a CRF layer (BI-LSTM-CRF). Our work is the first to apply a bidirectional LSTM CRF (denoted as BI-LSTM-CRF) model to NLP benchmark sequence tagging data sets. We show that the BI-LSTM-CRF model can efficiently use both past and future input features thanks to a bidirectional LSTM component. It can also use sentence level tag information thanks to a CRF layer. The BI-LSTM-CRF model can produce state of the art (or close to) accuracy on POS, chunking and NER data sets. In addition, it is robust and has less dependence on word embedding as compared to previous observations.

Automatically classifying electronic health records (EHRs) into diagnostic codes has been challenging to the NLP community. State-of-the-art methods treated this problem as a multilabel classification problem and proposed various architectures to model this problem. However, these systems did not leverage the superb performance of pretrained language models, which achieved superb performance on natural language understanding tasks. Prior work has shown that pretrained language models underperformed on this task with the regular finetuning scheme. Therefore, this paper aims at analyzing the causes of the underperformance and developing a framework for automatic ICD coding with pretrained language models. We spotted three main issues through the experiments: 1) large label space, 2) long input sequences, and 3) domain mismatch between pretraining and fine-tuning. We propose PLMICD, a framework that tackles the challenges with various strategies. The experimental results show that our proposed framework can overcome the challenges and achieves state-of-the-art performance in terms of multiple metrics on the benchmark MIMIC data. The source code is available at https://github.com/MiuLab/PLM-ICD

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Annotated data has become the most important bottleneck in training accurate machine learning models, especially for areas that require domain expertise. A recent approach to deal with the above issue proposes using natural language explanations instead of labeling individual data points, thereby increasing human annotators' efficiency as well as decreasing costs substantially. This paper focuses on the task of turning these natural language descriptions into Python labeling functions by following a novel approach to semantic parsing with pre-trained text-to-text Transformers. In a series of experiments our approach achieves a new state of the art on the semantic parsing benchmark CoNaLa, surpassing the previous best approach by 3.7 BLEU points. Furthermore, on a manually constructed dataset of natural language descriptions-labeling functions pairs we achieve a BLEU of 0.39. Our approach can be regarded as a stepping stone towards models that are taught how to label in natural language, instead of being provided specific labeled samples. Our code, constructed dataset and models are available at https://github.com/ypapanik/t5-for-code-generation.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

This paper presents NorNE, a manually annotated corpus of named entities which extends the annotation of the existing Norwegian Dependency Treebank. Comprising both of the official standards of written Norwegian (Bokm{\aa}l and Nynorsk), the corpus contains around 600,000 tokens and annotates a rich set of entity types including persons, organizations, locations, geo-political entities, products, and events, in addition to a class corresponding to nominals derived from names. We here present details on the annotation effort, guidelines, inter-annotator agreement and an experimental analysis of the corpus using a neural sequence labeling architecture.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Electronic Theses and Dissertations (ETDs) contain domain knowledge that can be used for many digital library tasks, such as analyzing citation networks and predicting research trends. Automatic metadata extraction is important to build scalable digital library search engines. Most existing methods are designed for born-digital documents, so they often fail to extract metadata from scanned documents such as for ETDs. Traditional sequence tagging methods mainly rely on text-based features. In this paper, we propose a conditional random field (CRF) model that combines text-based and visual features. To verify the robustness of our model, we extended an existing corpus and created a new ground truth corpus consisting of 500 ETD cover pages with human validated metadata. Our experiments show that CRF with visual features outperformed both a heuristic and a CRF model with only text-based features. The proposed model achieved 81.3%-96% F1 measure on seven metadata fields. The data and source code are publicly available on Google Drive (https://tinyurl.com/y8kxzwrp) and a GitHub repository (https://github.com/lamps-lab/ETDMiner/tree/master/etd_crf), respectively.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

This paper describes our submission to CoNLL 2018 UD Shared Task. We have extended an LSTM-based neural network designed for sequence tagging to additionally generate character-level sequences. The network was jointly trained to produce lemmas, part-of-speech tags and morphological features. Sentence segmentation, tokenization and dependency parsing were handled by UDPipe 1.2 baseline. The results demonstrate the viability of the proposed multitask architecture, although its performance still remains far from state-of-the-art.

Patent examiners need to solve a complex information retrieval task when they assess the novelty and inventive step of claims made in a patent application. Given a claim, they search for prior art, which comprises all relevant publicly available information. This time-consuming task requires a deep understanding of the respective technical domain and the patent-domain-specific language. For these reasons, we address the computer-assisted search for prior art by creating a training dataset for supervised machine learning called PatentMatch. It contains pairs of claims from patent applications and semantically corresponding text passages of different degrees from cited patent documents. Each pair has been labeled by technically-skilled patent examiners from the European Patent Office. Accordingly, the label indicates the degree of semantic correspondence (matching), i.e., whether the text passage is prejudicial to the novelty of the claimed invention or not. Preliminary experiments using a baseline system show that PatentMatch can indeed be used for training a binary text pair classifier on this challenging information retrieval task. The dataset is available online: https://hpi.de/naumann/s/patentmatch.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Several recent works have suggested to represent semantic relations with questions and answers, decomposing textual information into separate interrogative natural language statements. In this paper, we consider three QA-based semantic tasks - namely, QA-SRL, QANom and QADiscourse, each targeting a certain type of predication - and propose to regard them as jointly providing a comprehensive representation of textual information. To promote this goal, we investigate how to best utilize the power of sequence-to-sequence (seq2seq) pre-trained language models, within the unique setup of semi-structured outputs, consisting of an unordered set of question-answer pairs. We examine different input and output linearization strategies, and assess the effect of multitask learning and of simple data augmentation techniques in the setting of imbalanced training data. Consequently, we release the first unified QASem parsing tool, practical for downstream applications who can benefit from an explicit, QA-based account of information units in a text.

Incremental Learning (IL) has been a long-standing problem in both vision and Natural Language Processing (NLP) communities. In recent years, as Pre-trained Language Models (PLMs) have achieved remarkable progress in various NLP downstream tasks, utilizing PLMs as backbones has become a common practice in recent research of IL in NLP. Most assume that catastrophic forgetting is the biggest obstacle to achieving superior IL performance and propose various techniques to overcome this issue. However, we find that this assumption is problematic. Specifically, we revisit more than 20 methods on four classification tasks (Text Classification, Intent Classification, Relation Extraction, and Named Entity Recognition) under the two most popular IL settings (Class-Incremental and Task-Incremental) and reveal that most of them severely underestimate the inherent anti-forgetting ability of PLMs. Based on the observation, we propose a frustratingly easy method called SEQ* for IL with PLMs. The results show that SEQ* has competitive or superior performance compared to state-of-the-art (SOTA) IL methods and requires considerably less trainable parameters and training time. These findings urge us to revisit the IL with PLMs and encourage future studies to have a fundamental understanding of the catastrophic forgetting in PLMs. The data, code and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

Empirical Risk Minimization (ERM) is fragile in scenarios with insufficient labeled samples. A vanilla extension of ERM to unlabeled samples is Entropy Minimization (EntMin), which employs the soft-labels of unlabeled samples to guide their learning. However, EntMin emphasizes prediction discriminability while neglecting prediction diversity. To alleviate this issue, in this paper, we rethink the guidance information to utilize unlabeled samples. By analyzing the learning objective of ERM, we find that the guidance information for labeled samples in a specific category is the corresponding label encoding. Inspired by this finding, we propose a Label-Encoding Risk Minimization (LERM). It first estimates the label encodings through prediction means of unlabeled samples and then aligns them with their corresponding ground-truth label encodings. As a result, the LERM ensures both prediction discriminability and diversity, and it can be integrated into existing methods as a plugin. Theoretically, we analyze the relationships between LERM and ERM as well as EntMin. Empirically, we verify the superiority of the LERM under several label insufficient scenarios. The codes are available at https://github.com/zhangyl660/LERM.

We present QueryNER, a manually-annotated dataset and accompanying model for e-commerce query segmentation. Prior work in sequence labeling for e-commerce has largely addressed aspect-value extraction which focuses on extracting portions of a product title or query for narrowly defined aspects. Our work instead focuses on the goal of dividing a query into meaningful chunks with broadly applicable types. We report baseline tagging results and conduct experiments comparing token and entity dropping for null and low recall query recovery. Challenging test sets are created using automatic transformations and show how simple data augmentation techniques can make the models more robust to noise. We make the QueryNER dataset publicly available.

Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

Named entity detection and Parts-of-speech tagging are the key tasks for many NLP applications. Although the current state of the art methods achieved near perfection for long, formal, structured text there are hindrances in deploying these models on memory-constrained devices such as mobile phones. Furthermore, the performance of these models is degraded when they encounter short, informal, and casual conversations. To overcome these difficulties, we present LiteMuL - a lightweight on-device sequence tagger that can efficiently process the user conversations using a Multi-Task Learning (MTL) approach. To the best of our knowledge, the proposed model is the first on-device MTL neural model for sequence tagging. Our LiteMuL model is about 2.39 MB in size and achieved an accuracy of 0.9433 (for NER), 0.9090 (for POS) on the CoNLL 2003 dataset. The proposed LiteMuL not only outperforms the current state of the art results but also surpasses the results of our proposed on-device task-specific models, with accuracy gains of up to 11% and model-size reduction by 50%-56%. Our model is competitive with other MTL approaches for NER and POS tasks while outshines them with a low memory footprint. We also evaluated our model on custom-curated user conversations and observed impressive results.

The RNN transducer is a promising end-to-end model candidate. We compare the original training criterion with the full marginalization over all alignments, to the commonly used maximum approximation, which simplifies, improves and speeds up our training. We also generalize from the original neural network model and study more powerful models, made possible due to the maximum approximation. We further generalize the output label topology to cover RNN-T, RNA and CTC. We perform several studies among all these aspects, including a study on the effect of external alignments. We find that the transducer model generalizes much better on longer sequences than the attention model. Our final transducer model outperforms our attention model on Switchboard 300h by over 6% relative WER.

Language model based pre-trained models such as BERT have provided significant gains across different NLP tasks. In this paper, we study different types of transformer based pre-trained models such as auto-regressive models (GPT-2), auto-encoder models (BERT), and seq2seq models (BART) for conditional data augmentation. We show that prepending the class labels to text sequences provides a simple yet effective way to condition the pre-trained models for data augmentation. Additionally, on three classification benchmarks, pre-trained Seq2Seq model outperforms other data augmentation methods in a low-resource setting. Further, we explore how different pre-trained model based data augmentation differs in-terms of data diversity, and how well such methods preserve the class-label information.

Sequence-to-sequence (Seq2Seq) models with attention have excelled at tasks which involve generating natural language sentences such as machine translation, image captioning and speech recognition. Performance has further been improved by leveraging unlabeled data, often in the form of a language model. In this work, we present the Cold Fusion method, which leverages a pre-trained language model during training, and show its effectiveness on the speech recognition task. We show that Seq2Seq models with Cold Fusion are able to better utilize language information enjoying i) faster convergence and better generalization, and ii) almost complete transfer to a new domain while using less than 10% of the labeled training data.

Part of speech tagging in zero-resource settings can be an effective approach for low-resource languages when no labeled training data is available. Existing systems use two main techniques for POS tagging i.e. pretrained multilingual large language models(LLM) or project the source language labels into the zero resource target language and train a sequence labeling model on it. We explore the latter approach using the off-the-shelf alignment module and train a hidden Markov model(HMM) to predict the POS tags. We evaluate transfer learning setup with English as a source language and French, German, and Spanish as target languages for part-of-speech tagging. Our conclusion is that projected alignment data in zero-resource language can be beneficial to predict POS tags.

Recently, the usefulness of self-supervised representation learning (SSRL) methods has been confirmed in various downstream tasks. Many of these models, as exemplified by HuBERT and WavLM, use pseudo-labels generated from spectral features or the model's own representation features. From previous studies, it is known that the pseudo-labels contain semantic information. However, the masked prediction task, the learning criterion of HuBERT, focuses on local contextual information and may not make effective use of global semantic information such as speaker, theme of speech, and so on. In this paper, we propose a new approach to enrich the semantic representation of HuBERT. We apply topic model to pseudo-labels to generate a topic label for each utterance. An auxiliary topic classification task is added to HuBERT by using topic labels as teachers. This allows additional global semantic information to be incorporated in an unsupervised manner. Experimental results demonstrate that our method achieves comparable or better performance than the baseline in most tasks, including automatic speech recognition and five out of the eight SUPERB tasks. Moreover, we find that topic labels include various information about utterance, such as gender, speaker, and its theme. This highlights the effectiveness of our approach in capturing multifaceted semantic nuances.

Code embeddings capture the semantic representations of code and are crucial for various code-related large language model (LLM) applications, such as code search. Previous training primarily relies on optimizing the InfoNCE loss by comparing positive natural language (NL)-code pairs with in-batch negatives. However, due to the sparse nature of code contexts, training solely by comparing the major differences between positive and negative pairs may fail to capture deeper semantic nuances. To address this issue, we propose a novel order-augmented strategy for improved code search (OASIS). It leverages order-based similarity labels to train models to capture subtle differences in similarity among negative pairs. Extensive benchmark evaluations demonstrate that our OASIS model significantly outperforms previous state-of-the-art models focusing solely on major positive-negative differences. It underscores the value of exploiting subtle differences among negative pairs with order labels for effective code embedding training.

Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural language processing (NLP) techniques, there are still challenges including limited availability of data due to privacy constraints and the high variability of clinical notes caused by different writing habits of medical professionals and various pathological features of patients. In this work, we investigate the semi-structured nature of clinical notes and propose an automatic algorithm to segment them into sections. To address the variability issues in existing ICD coding models with limited data, we introduce a contrastive pre-training approach on sections using a soft multi-label similarity metric based on tree edit distance. Additionally, we design a masked section training strategy to enable ICD coding models to locate sections related to ICD codes. Extensive experimental results demonstrate that our proposed training strategies effectively enhance the performance of existing ICD coding methods.

Slot Filling (SF) is one of the sub-tasks of Spoken Language Understanding (SLU) which aims to extract semantic constituents from a given natural language utterance. It is formulated as a sequence labeling task. Recently, it has been shown that contextual information is vital for this task. However, existing models employ contextual information in a restricted manner, e.g., using self-attention. Such methods fail to distinguish the effects of the context on the word representation and the word label. To address this issue, in this paper, we propose a novel method to incorporate the contextual information in two different levels, i.e., representation level and task-specific (i.e., label) level. Our extensive experiments on three benchmark datasets on SF show the effectiveness of our model leading to new state-of-the-art results on all three benchmark datasets for the task of SF.

We present a novel approach to feature labeling using gradient descent in token-space. While existing methods typically use language models to generate hypotheses about feature meanings, our method directly optimizes label representations by using a language model as a discriminator to predict feature activations. We formulate this as a multi-objective optimization problem in token-space, balancing prediction accuracy, entropy minimization, and linguistic naturalness. Our proof-of-concept experiments demonstrate successful convergence to interpretable single-token labels across diverse domains, including features for detecting animals, mammals, Chinese text, and numbers. Although our current implementation is constrained to single-token labels and relatively simple features, the results suggest that token-space gradient descent could become a valuable addition to the interpretability researcher's toolkit.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Named entity recognition (NER) suffers from the scarcity of annotated training data, especially for low-resource languages without labeled data. Cross-lingual NER has been proposed to alleviate this issue by transferring knowledge from high-resource languages to low-resource languages via aligned cross-lingual representations or machine translation results. However, the performance of cross-lingual NER methods is severely affected by the unsatisfactory quality of translation or label projection. To address these problems, we propose a Cross-lingual Entity Projection framework (CROP) to enable zero-shot cross-lingual NER with the help of a multilingual labeled sequence translation model. Specifically, the target sequence is first translated into the source language and then tagged by a source NER model. We further adopt a labeled sequence translation model to project the tagged sequence back to the target language and label the target raw sentence. Ultimately, the whole pipeline is integrated into an end-to-end model by the way of self-training. Experimental results on two benchmarks demonstrate that our method substantially outperforms the previous strong baseline by a large margin of +3~7 F1 scores and achieves state-of-the-art performance.

Do state-of-the-art natural language understanding models care about word order - one of the most important characteristics of a sequence? Not always! We found 75% to 90% of the correct predictions of BERT-based classifiers, trained on many GLUE tasks, remain constant after input words are randomly shuffled. Despite BERT embeddings are famously contextual, the contribution of each individual word to downstream tasks is almost unchanged even after the word's context is shuffled. BERT-based models are able to exploit superficial cues (e.g. the sentiment of keywords in sentiment analysis; or the word-wise similarity between sequence-pair inputs in natural language inference) to make correct decisions when tokens are arranged in random orders. Encouraging classifiers to capture word order information improves the performance on most GLUE tasks, SQuAD 2.0 and out-of-samples. Our work suggests that many GLUE tasks are not challenging machines to understand the meaning of a sentence.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Multi-label classification problems with thousands of classes are hard to solve with in-context learning alone, as language models (LMs) might lack prior knowledge about the precise classes or how to assign them, and it is generally infeasible to demonstrate every class in a prompt. We propose a general program, Infer--Retrieve--Rank, that defines multi-step interactions between LMs and retrievers to efficiently tackle such problems. We implement this program using the DSPy programming model, which specifies in-context systems in a declarative manner, and use DSPy optimizers to tune it towards specific datasets by bootstrapping only tens of few-shot examples. Our primary extreme classification program, optimized separately for each task, attains state-of-the-art results across three benchmarks (HOUSE, TECH, TECHWOLF). We apply the same program to a benchmark with vastly different characteristics and attain competitive performance as well (BioDEX). Unlike prior work, our proposed solution requires no finetuning, is easily applicable to new tasks, alleviates prompt engineering, and requires only tens of labeled examples. Our code is public at https://github.com/KarelDO/xmc.dspy.

We present a self-supervised learning framework, COCO-LM, that pretrains Language Models by COrrecting and COntrasting corrupted text sequences. Following ELECTRA-style pretraining, COCO-LM employs an auxiliary language model to corrupt text sequences, upon which it constructs two new tasks for pretraining the main model. The first token-level task, Corrective Language Modeling, is to detect and correct tokens replaced by the auxiliary model, in order to better capture token-level semantics. The second sequence-level task, Sequence Contrastive Learning, is to align text sequences originated from the same source input while ensuring uniformity in the representation space. Experiments on GLUE and SQuAD demonstrate that COCO-LM not only outperforms recent state-of-the-art pretrained models in accuracy, but also improves pretraining efficiency. It achieves the MNLI accuracy of ELECTRA with 50% of its pretraining GPU hours. With the same pretraining steps of standard base/large-sized models, COCO-LM outperforms the previous best models by 1+ GLUE average points.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

In this paper, we introduce a multi-label lazy learning approach to deal with automatic semantic indexing in large document collections in the presence of complex and structured label vocabularies with high inter-label correlation. The proposed method is an evolution of the traditional k-Nearest Neighbors algorithm which uses a large autoencoder trained to map the large label space to a reduced size latent space and to regenerate the predicted labels from this latent space. We have evaluated our proposal in a large portion of the MEDLINE biomedical document collection which uses the Medical Subject Headings (MeSH) thesaurus as a controlled vocabulary. In our experiments we propose and evaluate several document representation approaches and different label autoencoder configurations.

Learning specific hands-on skills such as cooking, car maintenance, and home repairs increasingly happens via instructional videos. The user experience with such videos is known to be improved by meta-information such as time-stamped annotations for the main steps involved. Generating such annotations automatically is challenging, and we describe here two relevant contributions. First, we construct and release a new dense video captioning dataset, Video Timeline Tags (ViTT), featuring a variety of instructional videos together with time-stamped annotations. Second, we explore several multimodal sequence-to-sequence pretraining strategies that leverage large unsupervised datasets of videos and caption-like texts. We pretrain and subsequently finetune dense video captioning models using both YouCook2 and ViTT. We show that such models generalize well and are robust over a wide variety of instructional videos.

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single pre-training tasks. Although adding data modalities or supervised objectives can improve the performance of PLMs, pre-training often remains focused on denoising corrupted sequences. To push the boundaries of PLMs, our research investigated a multi-task pre-training strategy. We developed Ankh3, a model jointly optimized on two objectives: masked language modeling with multiple masking probabilities and protein sequence completion relying only on protein sequences as input. This multi-task pre-training demonstrated that PLMs can learn richer and more generalizable representations solely from protein sequences. The results demonstrated improved performance in downstream tasks, such as secondary structure prediction, fluorescence, GB1 fitness, and contact prediction. The integration of multiple tasks gave the model a more comprehensive understanding of protein properties, leading to more robust and accurate predictions.

Large Language Models (LLMs), including GPT-x and LLaMA2, have achieved remarkable performance in multiple Natural Language Processing (NLP) tasks. Under the premise that protein sequences constitute the protein language, Protein Large Language Models (ProLLMs) trained on protein corpora excel at de novo protein sequence generation. However, as of now, unlike LLMs in NLP, no ProLLM is capable of multiple tasks in the Protein Language Processing (PLP) field. This prompts us to delineate the inherent limitations in current ProLLMs: (i) the lack of natural language capabilities, (ii) insufficient instruction understanding, and (iii) high training resource demands. To address these challenges, we introduce a training framework to transform any general LLM into a ProLLM capable of handling multiple PLP tasks. Specifically, our framework utilizes low-rank adaptation and employs a two-stage training approach, and it is distinguished by its universality, low overhead, and scalability. Through training under this framework, we propose the ProLLaMA model, the first known ProLLM to handle multiple PLP tasks simultaneously. Experiments show that ProLLaMA achieves state-of-the-art results in the unconditional protein sequence generation task. In the controllable protein sequence generation task, ProLLaMA can design novel proteins with desired functionalities. In the protein property prediction task, ProLLaMA achieves nearly 100\% accuracy across many categories. The latter two tasks are beyond the reach of other ProLLMs. Code is available at https://github.com/Lyu6PosHao/ProLLaMA.

Memorization in language models is typically treated as a homogenous phenomenon, neglecting the specifics of the memorized data. We instead model memorization as the effect of a set of complex factors that describe each sample and relate it to the model and corpus. To build intuition around these factors, we break memorization down into a taxonomy: recitation of highly duplicated sequences, reconstruction of inherently predictable sequences, and recollection of sequences that are neither. We demonstrate the usefulness of our taxonomy by using it to construct a predictive model for memorization. By analyzing dependencies and inspecting the weights of the predictive model, we find that different factors influence the likelihood of memorization differently depending on the taxonomic category.

Dense retrieval methods have demonstrated promising performance in multilingual information retrieval, where queries and documents can be in different languages. However, dense retrievers typically require a substantial amount of paired data, which poses even greater challenges in multilingual scenarios. This paper introduces UMR, an Unsupervised Multilingual dense Retriever trained without any paired data. Our approach leverages the sequence likelihood estimation capabilities of multilingual language models to acquire pseudo labels for training dense retrievers. We propose a two-stage framework which iteratively improves the performance of multilingual dense retrievers. Experimental results on two benchmark datasets show that UMR outperforms supervised baselines, showcasing the potential of training multilingual retrievers without paired data, thereby enhancing their practicality. Our source code, data, and models are publicly available at https://github.com/MiuLab/UMR

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

Due to the difficulty of collecting exhaustive multi-label annotations, multi-label datasets often contain partial labels. We consider an extreme of this weakly supervised learning problem, called single positive multi-label learning (SPML), where each multi-label training image has only one positive label. Traditionally, all unannotated labels are assumed as negative labels in SPML, which introduces false negative labels and causes model training to be dominated by assumed negative labels. In this work, we choose to treat all unannotated labels from an alternative perspective, i.e. acknowledging they are unknown. Hence, we propose entropy-maximization (EM) loss to attain a special gradient regime for providing proper supervision signals. Moreover, we propose asymmetric pseudo-labeling (APL), which adopts asymmetric-tolerance strategies and a self-paced procedure, to cooperate with EM loss and then provide more precise supervision. Experiments show that our method significantly improves performance and achieves state-of-the-art results on all four benchmarks. Code is available at https://github.com/Correr-Zhou/SPML-AckTheUnknown.

Named Entity Recognition (NER) models capable of Continual Learning (CL) are realistically valuable in areas where entity types continuously increase (e.g., personal assistants). Meanwhile the learning paradigm of NER advances to new patterns such as the span-based methods. However, its potential to CL has not been fully explored. In this paper, we propose SpanKL, a simple yet effective Span-based model with Knowledge distillation (KD) to preserve memories and multi-Label prediction to prevent conflicts in CL-NER. Unlike prior sequence labeling approaches, the inherently independent modeling in span and entity level with the designed coherent optimization on SpanKL promotes its learning at each incremental step and mitigates the forgetting. Experiments on synthetic CL datasets derived from OntoNotes and Few-NERD show that SpanKL significantly outperforms previous SoTA in many aspects, and obtains the smallest gap from CL to the upper bound revealing its high practiced value. The code is available at https://github.com/Qznan/SpanKL.

Neural models that do not rely on pre-training have excelled in the keyphrase generation task with large annotated datasets. Meanwhile, new approaches have incorporated pre-trained language models (PLMs) for their data efficiency. However, there lacks a systematic study of how the two types of approaches compare and how different design choices can affect the performance of PLM-based models. To fill in this knowledge gap and facilitate a more informed use of PLMs for keyphrase extraction and keyphrase generation, we present an in-depth empirical study. Formulating keyphrase extraction as sequence labeling and keyphrase generation as sequence-to-sequence generation, we perform extensive experiments in three domains. After showing that PLMs have competitive high-resource performance and state-of-the-art low-resource performance, we investigate important design choices including in-domain PLMs, PLMs with different pre-training objectives, using PLMs with a parameter budget, and different formulations for present keyphrases. Further results show that (1) in-domain BERT-like PLMs can be used to build strong and data-efficient keyphrase generation models; (2) with a fixed parameter budget, prioritizing model depth over width and allocating more layers in the encoder leads to better encoder-decoder models; and (3) introducing four in-domain PLMs, we achieve a competitive performance in the news domain and the state-of-the-art performance in the scientific domain.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

In multi-label classification, each example in a dataset may be annotated as belonging to one or more classes (or none of the classes). Example applications include image (or document) tagging where each possible tag either applies to a particular image (or document) or not. With many possible classes to consider, data annotators are likely to make errors when labeling such data in practice. Here we consider algorithms for finding mislabeled examples in multi-label classification datasets. We propose an extension of the Confident Learning framework to this setting, as well as a label quality score that ranks examples with label errors much higher than those which are correctly labeled. Both approaches can utilize any trained classifier. After demonstrating that our methodology empirically outperforms other algorithms for label error detection, we apply our approach to discover many label errors in the CelebA image tagging dataset.

Prompt Tuning is emerging as a scalable and cost-effective method to fine-tune Pretrained Language Models (PLMs), which are often referred to as Large Language Models (LLMs). This study benchmarks the performance and computational efficiency of Prompt Tuning and baselines for multi-label text classification. This is applied to the challenging task of classifying companies into an investment firm's proprietary industry taxonomy, supporting their thematic investment strategy. Text-to-text classification is frequently reported to outperform task-specific classification heads, but has several limitations when applied to a multi-label classification problem where each label consists of multiple tokens: (a) Generated labels may not match any label in the label taxonomy; (b) The fine-tuning process lacks permutation invariance and is sensitive to the order of the provided labels; (c) The model provides binary decisions rather than appropriate confidence scores. Limitation (a) is addressed by applying constrained decoding using Trie Search, which slightly improves classification performance. All limitations (a), (b), and (c) are addressed by replacing the PLM's language head with a classification head, which is referred to as Prompt Tuned Embedding Classification (PTEC). This improves performance significantly, while also reducing computational costs during inference. In our industrial application, the training data is skewed towards well-known companies. We confirm that the model's performance is consistent across both well-known and less-known companies. Our overall results indicate the continuing need to adapt state-of-the-art methods to domain-specific tasks, even in the era of PLMs with strong generalization abilities. We release our codebase and a benchmarking dataset at https://github.com/EQTPartners/PTEC.

We present bgGLUE(Bulgarian General Language Understanding Evaluation), a benchmark for evaluating language models on Natural Language Understanding (NLU) tasks in Bulgarian. Our benchmark includes NLU tasks targeting a variety of NLP problems (e.g., natural language inference, fact-checking, named entity recognition, sentiment analysis, question answering, etc.) and machine learning tasks (sequence labeling, document-level classification, and regression). We run the first systematic evaluation of pre-trained language models for Bulgarian, comparing and contrasting results across the nine tasks in the benchmark. The evaluation results show strong performance on sequence labeling tasks, but there is a lot of room for improvement for tasks that require more complex reasoning. We make bgGLUE publicly available together with the fine-tuning and the evaluation code, as well as a public leaderboard at https://bgglue.github.io/, and we hope that it will enable further advancements in developing NLU models for Bulgarian.

Quotation extraction and attribution are challenging tasks, aiming at determining the spans containing quotations and attributing each quotation to the original speaker. Applying this task to news data is highly related to fact-checking, media monitoring and news tracking. Direct quotations are more traceable and informative, and therefore of great significance among different types of quotations. Therefore, this paper introduces DirectQuote, a corpus containing 19,760 paragraphs and 10,279 direct quotations manually annotated from online news media. To the best of our knowledge, this is the largest and most complete corpus that focuses on direct quotations in news texts. We ensure that each speaker in the annotation can be linked to a specific named entity on Wikidata, benefiting various downstream tasks. In addition, for the first time, we propose several sequence labeling models as baseline methods to extract and attribute quotations simultaneously in an end-to-end manner.

A major challenge in structured prediction is to represent the interdependencies within output structures. When outputs are structured as sequences, linear-chain conditional random fields (CRFs) are a widely used model class which can learn local dependencies in the output. However, the CRF's Markov assumption makes it impossible for CRFs to represent distributions with nonlocal dependencies, and standard CRFs are unable to respect nonlocal constraints of the data (such as global arity constraints on output labels). We present a generalization of CRFs that can enforce a broad class of constraints, including nonlocal ones, by specifying the space of possible output structures as a regular language L. The resulting regular-constrained CRF (RegCCRF) has the same formal properties as a standard CRF, but assigns zero probability to all label sequences not in L. Notably, RegCCRFs can incorporate their constraints during training, while related models only enforce constraints during decoding. We prove that constrained training is never worse than constrained decoding, and show empirically that it can be substantially better in practice. Additionally, we demonstrate a practical benefit on downstream tasks by incorporating a RegCCRF into a deep neural model for semantic role labeling, exceeding state-of-the-art results on a standard dataset.

Recent development in Large Language Models (LLMs) and Multi-modal Large Language Models (MLLMs) have leverage Attention-based Transformer architectures and achieved superior performance and generalization capabilities. They have since covered extensive areas of traditional learning tasks. For instance, text-based tasks such as text-classification and sequence-labeling, as well as multi-modal tasks like Visual Question Answering (VQA) and Optical Character Recognition (OCR), which were previously addressed using different models, can now be tackled based on one foundation model. Consequently, the training and lightweight fine-tuning of LLMs and MLLMs, especially those based on Transformer architecture, has become particularly important. In recognition of these overwhelming needs, we develop SWIFT, a customizable one-stop infrastructure for large models. With support of over 300+ LLMs and 50+ MLLMs, SWIFT stands as the open-source framework that provide the most comprehensive support for fine-tuning large models. In particular, it is the first training framework that provides systematic support for MLLMs. In addition to the core functionalities of fine-tuning, SWIFT also integrates post-training processes such as inference, evaluation, and model quantization, to facilitate fast adoptions of large models in various application scenarios. With a systematic integration of various training techniques, SWIFT offers helpful utilities such as benchmark comparisons among different training techniques for large models. For fine-tuning models specialized in agent framework, we show that notable improvements on the ToolBench leader-board can be achieved by training with customized dataset on SWIFT, with an increase of 5.2%-21.8% in the Act.EM metric over various baseline models, a reduction in hallucination by 1.6%-14.1%, and an average performance improvement of 8%-17%.

In this work, we present the first dataset, MailEx, for performing event extraction from conversational email threads. To this end, we first proposed a new taxonomy covering 10 event types and 76 arguments in the email domain. Our final dataset includes 1.5K email threads and ~4K emails, which are annotated with totally ~8K event instances. To understand the task challenges, we conducted a series of experiments comparing three types of approaches, i.e., fine-tuned sequence labeling, fine-tuned generative extraction, and few-shot in-context learning. Our results showed that the task of email event extraction is far from being addressed, due to challenges lying in, e.g., extracting non-continuous, shared trigger spans, extracting non-named entity arguments, and modeling the email conversational history. Our work thus suggests more future investigations in this domain-specific event extraction task.

The increasing number of benchmarks for Natural Language Processing (NLP) tasks in the computational job market domain highlights the demand for methods that can handle job-related tasks such as skill extraction, skill classification, job title classification, and de-identification. While some approaches have been developed that are specific to the job market domain, there is a lack of generalized, multilingual models and benchmarks for these tasks. In this study, we introduce a language model called ESCOXLM-R, based on XLM-R, which uses domain-adaptive pre-training on the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy, covering 27 languages. The pre-training objectives for ESCOXLM-R include dynamic masked language modeling and a novel additional objective for inducing multilingual taxonomical ESCO relations. We comprehensively evaluate the performance of ESCOXLM-R on 6 sequence labeling and 3 classification tasks in 4 languages and find that it achieves state-of-the-art results on 6 out of 9 datasets. Our analysis reveals that ESCOXLM-R performs better on short spans and outperforms XLM-R on entity-level and surface-level span-F1, likely due to ESCO containing short skill and occupation titles, and encoding information on the entity-level.

This paper presents a monolingual BERT model for Galician. We follow the recent trend that shows that it is feasible to build robust monolingual BERT models even for relatively low-resource languages, while performing better than the well-known official multilingual BERT (mBERT). More particularly, we release two monolingual Galician BERT models, built using 6 and 12 transformer layers, respectively; trained with limited resources (~45 million tokens on a single GPU of 24GB). We then provide an exhaustive evaluation on a number of tasks such as POS-tagging, dependency parsing and named entity recognition. For this purpose, all these tasks are cast in a pure sequence labeling setup in order to run BERT without the need to include any additional layers on top of it (we only use an output classification layer to map the contextualized representations into the predicted label). The experiments show that our models, especially the 12-layer one, outperform the results of mBERT in most tasks.

In industry deep learning application, our manually labeled data has a certain number of noisy data. To solve this problem and achieve more than 90 score in dev dataset, we present a simple method to find the noisy data and re-label the noisy data by human, given the model predictions as references in human labeling. In this paper, we illustrate our idea for a broad set of deep learning tasks, includes classification, sequence tagging, object detection, sequence generation, click-through rate prediction. The dev dataset evaluation results and human evaluation results verify our idea.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks.

Traditional approaches to Named Entity Recognition (NER) frame the task into a BIO sequence labeling problem. Although these systems often excel in the downstream task at hand, they require extensive annotated data and struggle to generalize to out-of-distribution input domains and unseen entity types. On the contrary, Large Language Models (LLMs) have demonstrated strong zero-shot capabilities. While several works address Zero-Shot NER in English, little has been done in other languages. In this paper, we define an evaluation framework for Zero-Shot NER, applying it to the Italian language. Furthermore, we introduce SLIMER-IT, the Italian version of SLIMER, an instruction-tuning approach for zero-shot NER leveraging prompts enriched with definition and guidelines. Comparisons with other state-of-the-art models, demonstrate the superiority of SLIMER-IT on never-seen-before entity tags.

Retrieval-augmented generation improves various aspects of large language models (LLMs) generation, but suffers from computational overhead caused by long contexts as well as the propagation of irrelevant retrieved information into generated responses. Context pruning deals with both aspects, by removing irrelevant parts of retrieved contexts before LLM generation. Existing context pruning approaches are however limited, and do not provide a universal model that would be both efficient and robust in a wide range of scenarios, e.g., when contexts contain a variable amount of relevant information or vary in length, or when evaluated on various domains. In this work, we close this gap and introduce Provence (Pruning and Reranking Of retrieVEd relevaNt ContExts), an efficient and robust context pruner for Question Answering, which dynamically detects the needed amount of pruning for a given context and can be used out-of-the-box for various domains. The three key ingredients of Provence are formulating the context pruning task as sequence labeling, unifying context pruning capabilities with context reranking, and training on diverse data. Our experimental results show that Provence enables context pruning with negligible to no drop in performance, in various domains and settings, at almost no cost in a standard RAG pipeline. We also conduct a deeper analysis alongside various ablations to provide insights into training context pruners for future work.

Aspect-based sentiment analysis (ABSA), a sequence labeling task, has attracted increasing attention in multilingual contexts. While previous research has focused largely on fine-tuning or training models specifically for ABSA, we evaluate large language models (LLMs) under zero-shot conditions to explore their potential to tackle this challenge with minimal task-specific adaptation. We conduct a comprehensive empirical evaluation of a series of LLMs on multilingual ABSA tasks, investigating various prompting strategies, including vanilla zero-shot, chain-of-thought (CoT), self-improvement, self-debate, and self-consistency, across nine different models. Results indicate that while LLMs show promise in handling multilingual ABSA, they generally fall short of fine-tuned, task-specific models. Notably, simpler zero-shot prompts often outperform more complex strategies, especially in high-resource languages like English. These findings underscore the need for further refinement of LLM-based approaches to effectively address ABSA task across diverse languages.

This work presents a new resource for borrowing identification and analyzes the performance and errors of several models on this task. We introduce a new annotated corpus of Spanish newswire rich in unassimilated lexical borrowings -- words from one language that are introduced into another without orthographic adaptation -- and use it to evaluate how several sequence labeling models (CRF, BiLSTM-CRF, and Transformer-based models) perform. The corpus contains 370,000 tokens and is larger, more borrowing-dense, OOV-rich, and topic-varied than previous corpora available for this task. Our results show that a BiLSTM-CRF model fed with subword embeddings along with either Transformer-based embeddings pretrained on codeswitched data or a combination of contextualized word embeddings outperforms results obtained by a multilingual BERT-based model.

Prompt tuning, which only tunes continuous prompts with a frozen language model, substantially reduces per-task storage and memory usage at training. However, in the context of NLU, prior work reveals that prompt tuning does not perform well for normal-sized pretrained models. We also find that existing methods of prompt tuning cannot handle hard sequence labeling tasks, indicating a lack of universality. We present a novel empirical finding that properly optimized prompt tuning can be universally effective across a wide range of model scales and NLU tasks. It matches the performance of finetuning while having only 0.1%-3% tuned parameters. Our method P-Tuning v2 is an implementation of Deep Prompt Tuning li2021prefix,qin2021learning optimized and adapted for NLU. Given the universality and simplicity of P-Tuning v2, we believe it can serve as an alternative to finetuning and a strong baseline for future research.Our code and data are released at https://github.com/THUDM/P-tuning-v2.

Most pre-trained language models (PLMs) construct word representations at subword level with Byte-Pair Encoding (BPE) or its variations, by which OOV (out-of-vocab) words are almost avoidable. However, those methods split a word into subword units and make the representation incomplete and fragile. In this paper, we propose a character-aware pre-trained language model named CharBERT improving on the previous methods (such as BERT, RoBERTa) to tackle these problems. We first construct the contextual word embedding for each token from the sequential character representations, then fuse the representations of characters and the subword representations by a novel heterogeneous interaction module. We also propose a new pre-training task named NLM (Noisy LM) for unsupervised character representation learning. We evaluate our method on question answering, sequence labeling, and text classification tasks, both on the original datasets and adversarial misspelling test sets. The experimental results show that our method can significantly improve the performance and robustness of PLMs simultaneously. Pretrained models, evaluation sets, and code are available at https://github.com/wtma/CharBERT

Recent work in Dialogue Act classification has treated the task as a sequence labeling problem using hierarchical deep neural networks. We build on this prior work by leveraging the effectiveness of a context-aware self-attention mechanism coupled with a hierarchical recurrent neural network. We conduct extensive evaluations on standard Dialogue Act classification datasets and show significant improvement over state-of-the-art results on the Switchboard Dialogue Act (SwDA) Corpus. We also investigate the impact of different utterance-level representation learning methods and show that our method is effective at capturing utterance-level semantic text representations while maintaining high accuracy.

Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target labels is unknown. Residual network is a new structure of convolutional neural network and works well in various computer vision tasks. In this paper, we take advantage of the architectures mentioned above to create a new network for handwritten digit string recognition. First we design a residual network to extract features from input images, then we employ a RNN to model the contextual information within feature sequences and predict recognition results. At the top of this network, a standard CTC is applied to calculate the loss and yield the final results. These three parts compose an end-to-end trainable network. The proposed new architecture achieves the highest performances on ORAND-CAR-A and ORAND-CAR-B with recognition rates 89.75% and 91.14%, respectively. In addition, the experiments on a generated captcha dataset which has much longer string length show the potential of the proposed network to handle long strings.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

We present the first approach to automated audio captioning. We employ an encoder-decoder scheme with an alignment model in between. The input to the encoder is a sequence of log mel-band energies calculated from an audio file, while the output is a sequence of words, i.e. a caption. The encoder is a multi-layered, bi-directional gated recurrent unit (GRU) and the decoder a multi-layered GRU with a classification layer connected to the last GRU of the decoder. The classification layer and the alignment model are fully connected layers with shared weights between timesteps. The proposed method is evaluated using data drawn from a commercial sound effects library, ProSound Effects. The resulting captions were rated through metrics utilized in machine translation and image captioning fields. Results from metrics show that the proposed method can predict words appearing in the original caption, but not always correctly ordered.

Despite the predominance of English in their training data, English-centric Large Language Models (LLMs) like GPT-3 and LLaMA display a remarkable ability to perform multilingual tasks, raising questions about the depth and nature of their cross-lingual capabilities. This paper introduces the decomposed prompting approach to probe the linguistic structure understanding of these LLMs in sequence labeling tasks. Diverging from the single text-to-text prompt, our method generates for each token of the input sentence an individual prompt which asks for its linguistic label. We assess our method on the Universal Dependencies part-of-speech tagging dataset for 38 languages, utilizing both English-centric and multilingual LLMs. Our findings show that decomposed prompting surpasses the iterative prompting baseline in efficacy and efficiency under zero- and few-shot settings. Further analysis reveals the influence of evaluation methods and the use of instructions in prompts. Our multilingual investigation shows that English-centric language models perform better on average than multilingual models. Our study offers insights into the multilingual transferability of English-centric LLMs, contributing to the understanding of their multilingual linguistic knowledge.

Most pretrained language models rely on subword tokenization, which processes text as a sequence of subword tokens. However, different granularities of text, such as characters, subwords, and words, can contain different kinds of information. Previous studies have shown that incorporating multiple input granularities improves model generalization, yet very few of them outputs useful representations for each granularity. In this paper, we introduce the entanglement model, aiming to combine character and subword language models. Inspired by vision-language models, our model treats characters and subwords as separate modalities, and it generates mutually informed representations for both granularities as output. We evaluate our model on text classification, named entity recognition, and POS-tagging tasks. Notably, the entanglement model outperforms its backbone language models, particularly in the presence of noisy texts and low-resource languages. Furthermore, the entanglement model even outperforms larger pre-trained models on all English sequence labeling tasks and classification tasks. Our anonymized code is available at https://anonymous.4open.science/r/noisy-IE-A673

Research on definition extraction has been conducted for well over a decade, largely with significant constraints on the type of definitions considered. In this work, we present DeftEval, a SemEval shared task in which participants must extract definitions from free text using a term-definition pair corpus that reflects the complex reality of definitions in natural language. Definitions and glosses in free text often appear without explicit indicators, across sentences boundaries, or in an otherwise complex linguistic manner. DeftEval involved 3 distinct subtasks: 1)Sentence classification, 2) sequence labeling, and 3) relation extraction.

Multimodal language models can exhibit hallucinations in their outputs, which limits their reliability. The ability to automatically detect these errors is important for mitigating them, but has been less explored and existing efforts do not localize hallucinations, instead framing this as a classification task. In this work, we first pose multimodal hallucination detection as a sequence labeling task where models must localize hallucinated text spans and present a strong baseline model. Given the high cost of human annotations for this task, we propose an approach to improve the sample efficiency of these models by creating corrupted grounding data, which we use for pre-training. Leveraging phrase grounding data, we generate hallucinations to replace grounded spans and create hallucinated text. Experiments show that pre-training on this data improves sample efficiency when fine-tuning, and that the learning signal from the grounding data plays an important role in these improvements.

In the contemporary era of widespread online recruitment, resume understanding has been widely acknowledged as a fundamental and crucial task, which aims to extract structured information from resume documents automatically. Compared to the traditional rule-based approaches, the utilization of recently proposed pre-trained document understanding models can greatly enhance the effectiveness of resume understanding. The present approaches have, however, disregarded the hierarchical relations within the structured information presented in resumes, and have difficulty parsing resumes in an efficient manner. To this end, in this paper, we propose a novel model, namely ERU, to achieve efficient resume understanding. Specifically, we first introduce a layout-aware multi-modal fusion transformer for encoding the segments in the resume with integrated textual, visual, and layout information. Then, we design three self-supervised tasks to pre-train this module via a large number of unlabeled resumes. Next, we fine-tune the model with a multi-granularity sequence labeling task to extract structured information from resumes. Finally, extensive experiments on a real-world dataset clearly demonstrate the effectiveness of ERU.

Recently, prompt-based methods have achieved significant performance in few-shot learning scenarios by bridging the gap between language model pre-training and fine-tuning for downstream tasks. However, existing prompt templates are mostly designed for sentence-level tasks and are inappropriate for sequence labeling objectives. To address the above issue, we propose a multi-task instruction-based generative framework, named InstructionNER, for low-resource named entity recognition. Specifically, we reformulate the NER task as a generation problem, which enriches source sentences with task-specific instructions and answer options, then inferences the entities and types in natural language. We further propose two auxiliary tasks, including entity extraction and entity typing, which enable the model to capture more boundary information of entities and deepen the understanding of entity type semantics, respectively. Experimental results show that our method consistently outperforms other baselines on five datasets in few-shot settings.

Although Indonesian is known to be the fourth most frequently used language over the internet, the research progress on this language in the natural language processing (NLP) is slow-moving due to a lack of available resources. In response, we introduce the first-ever vast resource for the training, evaluating, and benchmarking on Indonesian natural language understanding (IndoNLU) tasks. IndoNLU includes twelve tasks, ranging from single sentence classification to pair-sentences sequence labeling with different levels of complexity. The datasets for the tasks lie in different domains and styles to ensure task diversity. We also provide a set of Indonesian pre-trained models (IndoBERT) trained from a large and clean Indonesian dataset Indo4B collected from publicly available sources such as social media texts, blogs, news, and websites. We release baseline models for all twelve tasks, as well as the framework for benchmark evaluation, and thus it enables everyone to benchmark their system performances.

In this paper, we introduce the NER dataset from CLUE organization (CLUENER2020), a well-defined fine-grained dataset for named entity recognition in Chinese. CLUENER2020 contains 10 categories. Apart from common labels like person, organization, and location, it contains more diverse categories. It is more challenging than current other Chinese NER datasets and could better reflect real-world applications. For comparison, we implement several state-of-the-art baselines as sequence labeling tasks and report human performance, as well as its analysis. To facilitate future work on fine-grained NER for Chinese, we release our dataset, baselines, and leader-board.

Joint extraction of entities and relations aims to detect entity pairs along with their relations using a single model. Prior work typically solves this task in the extract-then-classify or unified labeling manner. However, these methods either suffer from the redundant entity pairs, or ignore the important inner structure in the process of extracting entities and relations. To address these limitations, in this paper, we first decompose the joint extraction task into two interrelated subtasks, namely HE extraction and TER extraction. The former subtask is to distinguish all head-entities that may be involved with target relations, and the latter is to identify corresponding tail-entities and relations for each extracted head-entity. Next, these two subtasks are further deconstructed into several sequence labeling problems based on our proposed span-based tagging scheme, which are conveniently solved by a hierarchical boundary tagger and a multi-span decoding algorithm. Owing to the reasonable decomposition strategy, our model can fully capture the semantic interdependency between different steps, as well as reduce noise from irrelevant entity pairs. Experimental results show that our method outperforms previous work by 5.2%, 5.9% and 21.5% (F1 score), achieving a new state-of-the-art on three public datasets

Transforming unstructured text into structured and meaningful forms, organized by useful category labels, is a fundamental step in text mining for downstream analysis and application. However, most existing methods for producing label taxonomies and building text-based label classifiers still rely heavily on domain expertise and manual curation, making the process expensive and time-consuming. This is particularly challenging when the label space is under-specified and large-scale data annotations are unavailable. In this paper, we address these challenges with Large Language Models (LLMs), whose prompt-based interface facilitates the induction and use of large-scale pseudo labels. We propose TnT-LLM, a two-phase framework that employs LLMs to automate the process of end-to-end label generation and assignment with minimal human effort for any given use-case. In the first phase, we introduce a zero-shot, multi-stage reasoning approach which enables LLMs to produce and refine a label taxonomy iteratively. In the second phase, LLMs are used as data labelers that yield training samples so that lightweight supervised classifiers can be reliably built, deployed, and served at scale. We apply TnT-LLM to the analysis of user intent and conversational domain for Bing Copilot (formerly Bing Chat), an open-domain chat-based search engine. Extensive experiments using both human and automatic evaluation metrics demonstrate that TnT-LLM generates more accurate and relevant label taxonomies when compared against state-of-the-art baselines, and achieves a favorable balance between accuracy and efficiency for classification at scale. We also share our practical experiences and insights on the challenges and opportunities of using LLMs for large-scale text mining in real-world applications.

Name tagging is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a name tagging model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments we observed that such a model is prone to mis-labeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, however, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mis-labeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We carry out our extensive experiments across three source and three target datasets, and demonstrate that our method outperforms the baselines, in some scenarios by 5\% absolute value.

Recently, substantial progress has been made in text ranking based on pretrained language models such as BERT. However, there are limited studies on how to leverage more powerful sequence-to-sequence models such as T5. Existing attempts usually formulate text ranking as classification and rely on postprocessing to obtain a ranked list. In this paper, we propose RankT5 and study two T5-based ranking model structures, an encoder-decoder and an encoder-only one, so that they not only can directly output ranking scores for each query-document pair, but also can be fine-tuned with "pairwise" or "listwise" ranking losses to optimize ranking performances. Our experiments show that the proposed models with ranking losses can achieve substantial ranking performance gains on different public text ranking data sets. Moreover, when fine-tuned with listwise ranking losses, the ranking model appears to have better zero-shot ranking performance on out-of-domain data sets compared to the model fine-tuned with classification losses.

Large-scale pretraining followed by task-specific finetuning has achieved great success in various NLP tasks. Since finetuning all parameters of large pretrained models poses substantial computational and memory challenges, several efficient finetuning methods have been developed. Among them, low-rank adaptation (LoRA), which finetunes low-rank incremental update matrices on top of frozen pretrained weights, has proven particularly effective. Nonetheless, LoRA's uniform rank assignment across all layers, along with its reliance on an exhaustive search to find the best rank, leads to high computation costs and suboptimal finetuning performance. To address these limitations, we introduce AutoLoRA, a meta learning based framework for automatically identifying the optimal rank of each LoRA layer. AutoLoRA associates each rank-1 matrix in a low-rank update matrix with a selection variable, which determines whether the rank-1 matrix should be discarded. A meta learning based method is developed to learn these selection variables. The optimal rank is determined by thresholding the values of these variables. Our comprehensive experiments on natural language understanding, generation, and sequence labeling demonstrate the effectiveness of AutoLoRA.

Automatically and accurately identifying user intents and filling the associated slots from their spoken language are critical to the success of dialogue systems. Traditional methods require manually defining the DOMAIN-INTENT-SLOT schema and asking many domain experts to annotate the corresponding utterances, upon which neural models are trained. This procedure brings the challenges of information sharing hindering, out-of-schema, or data sparsity in open-domain dialogue systems. To tackle these challenges, we explore a new task of {\em automatic intent-slot induction} and propose a novel domain-independent tool. That is, we design a coarse-to-fine three-step procedure including Role-labeling, Concept-mining, And Pattern-mining (RCAP): (1) role-labeling: extracting keyphrases from users' utterances and classifying them into a quadruple of coarsely-defined intent-roles via sequence labeling; (2) concept-mining: clustering the extracted intent-role mentions and naming them into abstract fine-grained concepts; (3) pattern-mining: applying the Apriori algorithm to mine intent-role patterns and automatically inferring the intent-slot using these coarse-grained intent-role labels and fine-grained concepts. Empirical evaluations on both real-world in-domain and out-of-domain datasets show that: (1) our RCAP can generate satisfactory SLU schema and outperforms the state-of-the-art supervised learning method; (2) our RCAP can be directly applied to out-of-domain datasets and gain at least 76\% improvement of F1-score on intent detection and 41\% improvement of F1-score on slot filling; (3) our RCAP exhibits its power in generic intent-slot extractions with less manual effort, which opens pathways for schema induction on new domains and unseen intent-slot discovery for generalizable dialogue systems.

Large language models (LLMs) are advancing at an unprecedented pace globally, with regions increasingly adopting these models for applications in their primary language. Evaluation of these models in diverse linguistic environments, especially in low-resource languages, has become a major challenge for academia and industry. Existing evaluation frameworks are disproportionately focused on English and a handful of high-resource languages, thereby overlooking the realistic performance of LLMs in multilingual and lower-resource scenarios. To address this gap, we introduce GlotEval, a lightweight framework designed for massively multilingual evaluation. Supporting seven key tasks (machine translation, text classification, summarization, open-ended generation, reading comprehension, sequence labeling, and intrinsic evaluation), spanning over dozens to hundreds of languages, GlotEval highlights consistent multilingual benchmarking, language-specific prompt templates, and non-English-centric machine translation. This enables a precise diagnosis of model strengths and weaknesses in diverse linguistic contexts. A multilingual translation case study demonstrates GlotEval's applicability for multilingual and language-specific evaluations.

Pre-trained multilingual language models show significant performance gains for zero-shot cross-lingual model transfer on a wide range of natural language understanding (NLU) tasks. Previously, for zero-shot cross-lingual evaluation, pre-trained models are only fine-tuned on English data and tested on a variety of target languages. In this paper, we do cross-lingual evaluation on various NLU tasks (sentence classification, sequence labeling, question answering) using prompt-tuning and compare it with fine-tuning. The results show that prompt tuning achieves much better cross-lingual transfer than fine-tuning across datasets, with only 0.1% to 0.3% tuned parameters. Additionally, we demonstrate through the analysis that prompt tuning can have better cross-lingual transferability of representations on downstream tasks with better aligned decision boundaries.

Historical and linguistic connections within the Sinosphere have led researchers to use Classical Chinese resources for cross-lingual transfer when processing historical documents from Korea and Japan. In this paper, we question the assumption of cross-lingual transferability from Classical Chinese to Hanja and Kanbun, the ancient written languages of Korea and Japan, respectively. Our experiments across machine translation, named entity recognition, and punctuation restoration tasks show minimal impact of Classical Chinese datasets on language model performance for ancient Korean documents written in Hanja, with performance differences within 0.0068 F1-score for sequence labeling tasks and up to +0.84 BLEU score for translation. These limitations persist consistently across various model sizes, architectures, and domain-specific datasets. Our analysis reveals that the benefits of Classical Chinese resources diminish rapidly as local language data increases for Hanja, while showing substantial improvements only in extremely low-resource scenarios for both Korean and Japanese historical documents. These mixed results emphasize the need for careful empirical validation rather than assuming benefits from indiscriminate cross-lingual transfer.

This paper addresses the privacy and security concerns associated with deep neural language models, which serve as crucial components in various modern AI-based applications. These models are often used after being pre-trained and fine-tuned for specific tasks, with deployment on servers accessed through the internet. However, this introduces two fundamental risks: (a) the transmission of user inputs to the server via the network gives rise to interception vulnerabilities, and (b) privacy concerns emerge as organizations that deploy such models store user data with restricted context. To address this, we propose a novel method to adapt and fine-tune transformer-based language models on passkey-encrypted user-specific text. The original pre-trained language model first undergoes a quick adaptation (without any further pre-training) with a series of irreversible transformations applied to the tokenizer and token embeddings. This enables the model to perform inference on encrypted inputs while preventing reverse engineering of text from model parameters and intermediate outputs. After adaptation, models are fine-tuned on encrypted versions of existing training datasets. Experimental evaluation employing adapted versions of renowned models (e.g., BERT, RoBERTa) across established benchmark English and multilingual datasets for text classification and sequence labeling shows that encrypted models achieve performance parity with their original counterparts. This serves to safeguard performance, privacy, and security cohesively.

Zero-shot entity linking (EL) aims at aligning entity mentions to unseen entities to challenge the generalization ability. Previous methods largely focus on the candidate retrieval stage and ignore the essential candidate ranking stage, which disambiguates among entities and makes the final linking prediction. In this paper, we propose a read-and-select (ReS) framework by modeling the main components of entity disambiguation, i.e., mention-entity matching and cross-entity comparison. First, for each candidate, the reading module leverages mention context to output mention-aware entity representations, enabling mention-entity matching. Then, in the selecting module, we frame the choice of candidates as a sequence labeling problem, and all candidate representations are fused together to enable cross-entity comparison. Our method achieves the state-of-the-art performance on the established zero-shot EL dataset ZESHEL with a 2.55% micro-average accuracy gain, with no need for laborious multi-phase pre-training used in most of the previous work, showing the effectiveness of both mention-entity and cross-entity interaction.

Recent studies report that autoregressive language models can successfully solve many NLP tasks via zero- and few-shot learning paradigms, which opens up new possibilities for using the pre-trained language models. This paper introduces two autoregressive GPT-like models with 1.3 billion and 13 billion parameters trained on 60 languages from 25 language families using Wikipedia and Colossal Clean Crawled Corpus. We reproduce the GPT-3 architecture using GPT-2 sources and the sparse attention mechanism; Deepspeed and Megatron frameworks allow us to parallelize the training and inference steps effectively. The resulting models show performance on par with the recently released XGLM models by Facebook, covering more languages and enhancing NLP possibilities for low resource languages of CIS countries and Russian small nations. We detail the motivation for the choices of the architecture design, thoroughly describe the data preparation pipeline, and train five small versions of the model to choose the most optimal multilingual tokenization strategy. We measure the model perplexity in all covered languages and evaluate it on the wide spectre of multilingual tasks, including classification, generative, sequence labeling and knowledge probing. The models were evaluated with the zero-shot and few-shot methods. Furthermore, we compared the classification tasks with the state-of-the-art multilingual model XGLM. source code and the mGPT XL model are publicly released.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

In this work, we introduce BanglaBERT, a BERT-based Natural Language Understanding (NLU) model pretrained in Bangla, a widely spoken yet low-resource language in the NLP literature. To pretrain BanglaBERT, we collect 27.5 GB of Bangla pretraining data (dubbed `Bangla2B+') by crawling 110 popular Bangla sites. We introduce two downstream task datasets on natural language inference and question answering and benchmark on four diverse NLU tasks covering text classification, sequence labeling, and span prediction. In the process, we bring them under the first-ever Bangla Language Understanding Benchmark (BLUB). BanglaBERT achieves state-of-the-art results outperforming multilingual and monolingual models. We are making the models, datasets, and a leaderboard publicly available at https://github.com/csebuetnlp/banglabert to advance Bangla NLP.

Estimating probability distribution is one of the core issues in the NLP field. However, in both deep learning (DL) and pre-DL eras, unlike the vast applications of linear-chain CRF in sequence labeling tasks, very few works have applied tree-structure CRF to constituency parsing, mainly due to the complexity and inefficiency of the inside-outside algorithm. This work presents a fast and accurate neural CRF constituency parser. The key idea is to batchify the inside algorithm for loss computation by direct large tensor operations on GPU, and meanwhile avoid the outside algorithm for gradient computation via efficient back-propagation. We also propose a simple two-stage bracketing-then-labeling parsing approach to improve efficiency further. To improve the parsing performance, inspired by recent progress in dependency parsing, we introduce a new scoring architecture based on boundary representation and biaffine attention, and a beneficial dropout strategy. Experiments on PTB, CTB5.1, and CTB7 show that our two-stage CRF parser achieves new state-of-the-art performance on both settings of w/o and w/ BERT, and can parse over 1,000 sentences per second. We release our code at https://github.com/yzhangcs/crfpar.

Transformer-based language models are now widely used in Natural Language Processing (NLP). This statement is especially true for English language, in which many pre-trained models utilizing transformer-based architecture have been published in recent years. This has driven forward the state of the art for a variety of standard NLP tasks such as classification, regression, and sequence labeling, as well as text-to-text tasks, such as machine translation, question answering, or summarization. The situation have been different for low-resource languages, such as Polish, however. Although some transformer-based language models for Polish are available, none of them have come close to the scale, in terms of corpus size and the number of parameters, of the largest English-language models. In this study, we present two language models for Polish based on the popular BERT architecture. The larger model was trained on a dataset consisting of over 1 billion polish sentences, or 135GB of raw text. We describe our methodology for collecting the data, preparing the corpus, and pre-training the model. We then evaluate our models on thirteen Polish linguistic tasks, and demonstrate improvements over previous approaches in eleven of them.

Arabic word segmentation is essential for a variety of NLP applications such as machine translation and information retrieval. Segmentation entails breaking words into their constituent stems, affixes and clitics. In this paper, we compare two approaches for segmenting four major Arabic dialects using only several thousand training examples for each dialect. The two approaches involve posing the problem as a ranking problem, where an SVM ranker picks the best segmentation, and as a sequence labeling problem, where a bi-LSTM RNN coupled with CRF determines where best to segment words. We are able to achieve solid segmentation results for all dialects using rather limited training data. We also show that employing Modern Standard Arabic data for domain adaptation and assuming context independence improve overall results.

Semi-supervised learning through pseudo-labeling has become a staple of state-of-the-art monolingual speech recognition systems. In this work, we extend pseudo-labeling to massively multilingual speech recognition with 60 languages. We propose a simple pseudo-labeling recipe that works well even with low-resource languages: train a supervised multilingual model, fine-tune it with semi-supervised learning on a target language, generate pseudo-labels for that language, and train a final model using pseudo-labels for all languages, either from scratch or by fine-tuning. Experiments on the labeled Common Voice and unlabeled VoxPopuli datasets show that our recipe can yield a model with better performance for many languages that also transfers well to LibriSpeech.

Annotating training data for sequence tagging of texts is usually very time-consuming. Recent advances in transfer learning for natural language processing in conjunction with active learning open the possibility to significantly reduce the necessary annotation budget. We are the first to thoroughly investigate this powerful combination for the sequence tagging task. We conduct an extensive empirical study of various Bayesian uncertainty estimation methods and Monte Carlo dropout options for deep pre-trained models in the active learning framework and find the best combinations for different types of models. Besides, we also demonstrate that to acquire instances during active learning, a full-size Transformer can be substituted with a distilled version, which yields better computational performance and reduces obstacles for applying deep active learning in practice.

We present a character-based model for joint segmentation and POS tagging for Chinese. The bidirectional RNN-CRF architecture for general sequence tagging is adapted and applied with novel vector representations of Chinese characters that capture rich contextual information and lower-than-character level features. The proposed model is extensively evaluated and compared with a state-of-the-art tagger respectively on CTB5, CTB9 and UD Chinese. The experimental results indicate that our model is accurate and robust across datasets in different sizes, genres and annotation schemes. We obtain state-of-the-art performance on CTB5, achieving 94.38 F1-score for joint segmentation and POS tagging.

Open vocabulary models (e.g. CLIP) have shown strong performance on zero-shot classification through their ability generate embeddings for each class based on their (natural language) names. Prior work has focused on improving the accuracy of these models through prompt engineering or by incorporating a small amount of labeled downstream data (via finetuning). However, there has been little focus on improving the richness of the class names themselves, which can pose issues when class labels are coarsely-defined and are uninformative. We propose Classification with Hierarchical Label Sets (or CHiLS), an alternative strategy for zero-shot classification specifically designed for datasets with implicit semantic hierarchies. CHiLS proceeds in three steps: (i) for each class, produce a set of subclasses, using either existing label hierarchies or by querying GPT-3; (ii) perform the standard zero-shot CLIP procedure as though these subclasses were the labels of interest; (iii) map the predicted subclass back to its parent to produce the final prediction. Across numerous datasets with underlying hierarchical structure, CHiLS leads to improved accuracy in situations both with and without ground-truth hierarchical information. CHiLS is simple to implement within existing zero-shot pipelines and requires no additional training cost. Code is available at: https://github.com/acmi-lab/CHILS.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Predicting high-dimensional or extreme multilabels, such as in medical coding, requires both accuracy and interpretability. Existing works often rely on local interpretability methods, failing to provide comprehensive explanations of the overall mechanism behind each label prediction within a multilabel set. We propose a mechanistic interpretability module called DIctionary Label Attention (\method) that disentangles uninterpretable dense embeddings into a sparse embedding space, where each nonzero element (a dictionary feature) represents a globally learned medical concept. Through human evaluations, we show that our sparse embeddings are more human understandable than its dense counterparts by at least 50 percent. Our automated dictionary feature identification pipeline, leveraging large language models (LLMs), uncovers thousands of learned medical concepts by examining and summarizing the highest activating tokens for each dictionary feature. We represent the relationships between dictionary features and medical codes through a sparse interpretable matrix, enhancing the mechanistic and global understanding of the model's predictions while maintaining competitive performance and scalability without extensive human annotation.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Large language models (LLMs) have achieved impressive success in text-formatted learning problems, and most popular LLMs have been deployed in a black-box fashion. Meanwhile, fine-tuning is usually necessary for a specific downstream task to obtain better performance, and this functionality is provided by the owners of the black-box LLMs. To fine-tune a black-box LLM, labeled data are always required to adjust the model parameters. However, in many real-world applications, LLMs can label textual datasets with even better quality than skilled human annotators, motivating us to explore the possibility of fine-tuning black-box LLMs with unlabeled data. In this paper, we propose unsupervised prompt learning for classification with black-box LLMs, where the learning parameters are the prompt itself and the pseudo labels of unlabeled data. Specifically, the prompt is modeled as a sequence of discrete tokens, and every token has its own to-be-learned categorical distribution. On the other hand, for learning the pseudo labels, we are the first to consider the in-context learning (ICL) capabilities of LLMs: we first identify reliable pseudo-labeled data using the LLM, and then assign pseudo labels to other unlabeled data based on the prompt, allowing the pseudo-labeled data to serve as in-context demonstrations alongside the prompt. Those in-context demonstrations matter: previously, they are involved when the prompt is used for prediction while they are not involved when the prompt is trained; thus, taking them into account during training makes the prompt-learning and prompt-using stages more consistent. Experiments on benchmark datasets show the effectiveness of our proposed algorithm. After unsupervised prompt learning, we can use the pseudo-labeled dataset for further fine-tuning by the owners of the black-box LLMs.

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

State-of-the-art language models are autoregressive and operate on subword units known as tokens. Specifically, one must encode the conditioning string into a list of tokens before passing to the language models for next-token prediction. We show that popular encoding schemes, such as maximum prefix encoding (MPE) and byte-pair-encoding (BPE), induce a sampling bias that cannot be mitigated with more training or data. To counter this universal problem, for each encoding scheme above, we propose a novel algorithm to obtain unbiased estimates from any language model trained on tokenized data. Our methods do not require finetuning the model, and the complexity, defined as the number of model runs, scales linearly with the sequence length in the case of MPE. As a result, we show that one can simulate token-free behavior from a tokenized language model. We empirically verify the correctness of our method through a Markov-chain setup, where it accurately recovers the transition probabilities, as opposed to the conventional method of directly prompting tokens into the language model.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Pre-trained Programming Language Models (PPLMs) achieved many recent states of the art results for many code-related software engineering tasks. Though some studies use data flow or propose tree-based models that utilize Abstract Syntax Tree (AST), most PPLMs do not fully utilize the rich syntactical information in source code. Still, the input is considered a sequence of tokens. There are two issues; the first is computational inefficiency due to the quadratic relationship between input length and attention complexity. Second, any syntactical information, when needed as an extra input to the current PPLMs, requires the model to be pre-trained from scratch, wasting all the computational resources already used for pre-training the current models. In this work, we propose Named Entity Recognition (NER) adapters, lightweight modules that can be inserted into Transformer blocks to learn type information extracted from the AST. These adapters can be used with current PPLMs such as CodeBERT, GraphCodeBERT, and CodeT5. We train the NER adapters using a novel Token Type Classification objective function (TTC). We insert our proposed work in CodeBERT, building CodeBERTER, and evaluate the performance on two tasks of code refinement and code summarization. CodeBERTER improves the accuracy of code refinement from 16.4 to 17.8 while using 20% of training parameter budget compared to the fully fine-tuning approach, and the BLEU score of code summarization from 14.75 to 15.90 while reducing 77% of training parameters compared to the fully fine-tuning approach.

For multilingual sequence-to-sequence pretrained language models (multilingual Seq2Seq PLMs), e.g. mBART, the self-supervised pretraining task is trained on a wide range of monolingual languages, e.g. 25 languages from CommonCrawl, while the downstream cross-lingual tasks generally progress on a bilingual language subset, e.g. English-German, making there exists the data discrepancy, namely domain discrepancy, and cross-lingual learning objective discrepancy, namely task discrepancy, between the pretraining and finetuning stages. To bridge the above cross-lingual domain and task gaps, we extend the vanilla pretrain-finetune pipeline with extra code-switching restore task. Specifically, the first stage employs the self-supervised code-switching restore task as a pretext task, allowing the multilingual Seq2Seq PLMs to acquire some in-domain alignment information. And for the second stage, we fine-tune the model on downstream data normally. Experiments on both NLG evaluation (12 bilingual translation tasks, 30 zero-shot translation tasks, and 2 cross-lingual summarization tasks) and NLU evaluation (7 cross-lingual natural language inference tasks) show our model outperforms the strong baseline mBART with standard finetuning strategy, consistently. Analyses indicate our approach could narrow the Euclidean distance of cross-lingual sentence representations, and improve the model generalization with trivial computational cost. We release the code at: https://github.com/zanchangtong/CSR4mBART.

Few-shot named entity recognition (NER) detects named entities within text using only a few annotated examples. One promising line of research is to leverage natural language descriptions of each entity type: the common label PER might, for example, be verbalized as ''person entity.'' In an initial label interpretation learning phase, the model learns to interpret such verbalized descriptions of entity types. In a subsequent few-shot tagset extension phase, this model is then given a description of a previously unseen entity type (such as ''music album'') and optionally a few training examples to perform few-shot NER for this type. In this paper, we systematically explore the impact of a strong semantic prior to interpret verbalizations of new entity types by massively scaling up the number and granularity of entity types used for label interpretation learning. To this end, we leverage an entity linking benchmark to create a dataset with orders of magnitude of more distinct entity types and descriptions as currently used datasets. We find that this increased signal yields strong results in zero- and few-shot NER in in-domain, cross-domain, and even cross-lingual settings. Our findings indicate significant potential for improving few-shot NER through heuristical data-based optimization.

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Large language models (LLMs) have shown impressive ability for open-domain NLP tasks. However, LLMs are sometimes too footloose for natural language understanding (NLU) tasks which always have restricted output and input format. Their performances on NLU tasks are highly related to prompts or demonstrations and are shown to be poor at performing several representative NLU tasks, such as event extraction and entity typing. To this end, we present SeqGPT, a bilingual (i.e., English and Chinese) open-source autoregressive model specially enhanced for open-domain natural language understanding. We express all NLU tasks with two atomic tasks, which define fixed instructions to restrict the input and output format but still ``open'' for arbitrarily varied label sets. The model is first instruction-tuned with extremely fine-grained labeled data synthesized by ChatGPT and then further fine-tuned by 233 different atomic tasks from 152 datasets across various domains. The experimental results show that SeqGPT has decent classification and extraction ability, and is capable of performing language understanding tasks on unseen domains. We also conduct empirical studies on the scaling of data and model size as well as on the transfer across tasks. Our model is accessible at https://github.com/Alibaba-NLP/SeqGPT.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

We explore different ways to utilize position-based cross-attention in seq2seq networks to enable length generalization in algorithmic tasks. We show that a simple approach of interpolating the original and reversed encoded representations combined with relative attention allows near-perfect length generalization for both forward and reverse lookup tasks or copy tasks that had been generally hard to tackle. We also devise harder diagnostic tasks where the relative distance of the ideal attention position varies with timestep. In such settings, the simple interpolation trick with relative attention is not sufficient. We introduce novel variants of location attention building on top of Dubois et al. (2020) to address the new diagnostic tasks. We also show the benefits of our approaches for length generalization in SCAN (Lake & Baroni, 2018) and CFQ (Keysers et al., 2020). Our code is available on GitHub.

We present the first dataset targeted at end-to-end NLG in Czech in the restaurant domain, along with several strong baseline models using the sequence-to-sequence approach. While non-English NLG is under-explored in general, Czech, as a morphologically rich language, makes the task even harder: Since Czech requires inflecting named entities, delexicalization or copy mechanisms do not work out-of-the-box and lexicalizing the generated outputs is non-trivial. In our experiments, we present two different approaches to this this problem: (1) using a neural language model to select the correct inflected form while lexicalizing, (2) a two-step generation setup: our sequence-to-sequence model generates an interleaved sequence of lemmas and morphological tags, which are then inflected by a morphological generator.

We present the Charles University system for the MRL~2023 Shared Task on Multi-lingual Multi-task Information Retrieval. The goal of the shared task was to develop systems for named entity recognition and question answering in several under-represented languages. Our solutions to both subtasks rely on the translate-test approach. We first translate the unlabeled examples into English using a multilingual machine translation model. Then, we run inference on the translated data using a strong task-specific model. Finally, we project the labeled data back into the original language. To keep the inferred tags on the correct positions in the original language, we propose a method based on scoring the candidate positions using a label-sensitive translation model. In both settings, we experiment with finetuning the classification models on the translated data. However, due to a domain mismatch between the development data and the shared task validation and test sets, the finetuned models could not outperform our baselines.

Integer sequences are of central importance to the modeling of concepts admitting complete finitary descriptions. We introduce a novel view on the learning of such concepts and lay down a set of benchmarking tasks aimed at conceptual understanding by machine learning models. These tasks indirectly assess model ability to abstract, and challenge them to reason both interpolatively and extrapolatively from the knowledge gained by observing representative examples. To further aid research in knowledge representation and reasoning, we present FACT, the Finitary Abstraction Comprehension Toolkit. The toolkit surrounds a large dataset of integer sequences comprising both organic and synthetic entries, a library for data pre-processing and generation, a set of model performance evaluation tools, and a collection of baseline model implementations, enabling the making of the future advancements with ease.

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions, generalizing both autoregressive models (e.g., GPT) and conventional diffusion models (e.g., SEDD, MDLM) as special cases. Second, we propose two hybrid token-wise noising processes that interpolate between absorbing and uniform processes, enabling the model to fix past mistakes, and we introduce a novel inference algorithm that leverages this new feature in a simplified context inspired from MDLM. To support efficient training and inference, we design attention masks compatible with KV-caching. Our methods achieve state-of-the-art perplexity and generate diverse, high-quality sequences across standard benchmarks, suggesting a promising path for autoregressive diffusion-based sequence generation.

Recent work attributes progress in NLP to large language models (LMs) with increased model size and large quantities of pretraining data. Despite this, current state-of-the-art LMs for Hebrew are both under-parameterized and under-trained compared to LMs in other languages. Additionally, previous work on pretrained Hebrew LMs focused on encoder-only models. While the encoder-only architecture is beneficial for classification tasks, it does not cater well for sub-word prediction tasks, such as Named Entity Recognition, when considering the morphologically rich nature of Hebrew. In this paper we argue that sequence-to-sequence generative architectures are more suitable for LLMs in the case of morphologically rich languages (MRLs) such as Hebrew. We demonstrate that by casting tasks in the Hebrew NLP pipeline as text-to-text tasks, we can leverage powerful multilingual, pretrained sequence-to-sequence models as mT5, eliminating the need for a specialized, morpheme-based, separately fine-tuned decoder. Using this approach, our experiments show substantial improvements over previously published results on existing Hebrew NLP benchmarks. These results suggest that multilingual sequence-to-sequence models present a promising building block for NLP for MRLs.

Breakthroughs in deep learning and memory networks have made major advances in natural language understanding. Language is sequential and information carried through the sequence can be captured through memory networks. Learning the sequence is one of the key aspects in learning the language. However, memory networks are not capable of holding infinitely long sequences in their memories and are limited by various constraints such as the vanishing or exploding gradient problem. Therefore, natural language understanding models are affected when presented with long sequential text. We introduce Long Term Memory network (LTM) to learn from infinitely long sequences. LTM gives priority to the current inputs to allow it to have a high impact. Language modeling is an important factor in natural language understanding. LTM was tested in language modeling, which requires long term memory. LTM is tested on Penn Tree bank dataset, Google Billion Word dataset and WikiText-2 dataset. We compare LTM with other language models which require long term memory.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Recently, binary representation has been proposed as a novel representation that lies between continuous and discrete representations. It exhibits considerable information-preserving capability when being used to replace continuous input vectors. In this paper, we investigate the feasibility of further introducing it to the output side, aiming to allow models to output binary labels instead. To preserve the structural information on the output side along with label information, we extend the previous contrastive hashing method as structured contrastive hashing. More specifically, we upgrade CKY from label-level to bit-level, define a new similarity function with span marginal probabilities, and introduce a novel contrastive loss function with a carefully designed instance selection strategy. Our model achieves competitive performance on various structured prediction tasks, and demonstrates that binary representation can be considered a novel representation that further bridges the gap between the continuous nature of deep learning and the discrete intrinsic property of natural languages.

Sequential recommendation aims to model dynamic user behavior from historical interactions. Existing methods rely on either explicit item IDs or general textual features for sequence modeling to understand user preferences. While promising, these approaches still struggle to model cold-start items or transfer knowledge to new datasets. In this paper, we propose to model user preferences and item features as language representations that can be generalized to new items and datasets. To this end, we present a novel framework, named Recformer, which effectively learns language representations for sequential recommendation. Specifically, we propose to formulate an item as a "sentence" (word sequence) by flattening item key-value attributes described by text so that an item sequence for a user becomes a sequence of sentences. For recommendation, Recformer is trained to understand the "sentence" sequence and retrieve the next "sentence". To encode item sequences, we design a bi-directional Transformer similar to the model Longformer but with different embedding layers for sequential recommendation. For effective representation learning, we propose novel pretraining and finetuning methods which combine language understanding and recommendation tasks. Therefore, Recformer can effectively recommend the next item based on language representations. Extensive experiments conducted on six datasets demonstrate the effectiveness of Recformer for sequential recommendation, especially in low-resource and cold-start settings.

Set-of-Mark (SoM) Prompting unleashes the visual grounding capability of GPT-4V, by enabling the model to associate visual objects with tags inserted on the image. These tags, marked with alphanumerics, can be indexed via text tokens for easy reference. Despite the extraordinary performance from GPT-4V, we observe that other Multimodal Large Language Models (MLLMs) struggle to understand these visual tags. To promote the learning of SoM prompting for open-source models, we propose a new learning paradigm: "list items one by one," which asks the model to enumerate and describe all visual tags placed on the image following the alphanumeric orders of tags. By integrating our curated dataset with other visual instruction tuning datasets, we are able to equip existing MLLMs with the SoM prompting ability. Furthermore, we evaluate our finetuned SoM models on five MLLM benchmarks. We find that this new dataset, even in a relatively small size (10k-30k images with tags), significantly enhances visual reasoning capabilities and reduces hallucinations for MLLMs. Perhaps surprisingly, these improvements persist even when the visual tags are omitted from input images during inference. This suggests the potential of "list items one by one" as a new paradigm for training MLLMs, which strengthens the object-text alignment through the use of visual tags in the training stage. Finally, we conduct analyses by probing trained models to understand the working mechanism of SoM. Our code and data are available at https://github.com/zzxslp/SoM-LLaVA.

Sequence modeling has demonstrated state-of-the-art performance on natural language and document understanding tasks. However, it is challenging to correctly serialize tokens in form-like documents in practice due to their variety of layout patterns. We propose FormNet, a structure-aware sequence model to mitigate the suboptimal serialization of forms. First, we design Rich Attention that leverages the spatial relationship between tokens in a form for more precise attention score calculation. Second, we construct Super-Tokens for each word by embedding representations from their neighboring tokens through graph convolutions. FormNet therefore explicitly recovers local syntactic information that may have been lost during serialization. In experiments, FormNet outperforms existing methods with a more compact model size and less pre-training data, establishing new state-of-the-art performance on CORD, FUNSD and Payment benchmarks.

A naive application of state-of-the-art bidirectional encoders for streaming sequence tagging would require encoding each token from scratch for each new token in an incremental streaming input (like transcribed speech). The lack of re-usability of previous computation leads to a higher number of Floating Point Operations (or FLOPs) and higher number of unnecessary label flips. Increased FLOPs consequently lead to higher wall-clock time and increased label flipping leads to poorer streaming performance. In this work, we present a Hybrid Encoder with Adaptive Restart (HEAR) that addresses these issues while maintaining the performance of bidirectional encoders over the offline (or complete) inputs while improving performance on streaming (or incomplete) inputs. HEAR has a Hybrid unidirectional-bidirectional encoder architecture to perform sequence tagging, along with an Adaptive Restart Module (ARM) to selectively guide the restart of bidirectional portion of the encoder. Across four sequence tagging tasks, HEAR offers FLOP savings in streaming settings upto 71.1% and also outperforms bidirectional encoders for streaming predictions by upto +10% streaming exact match.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

This paper describes our submission to the shared task on word/phrase level Quality Estimation (QE) in the First Conference on Statistical Machine Translation (WMT16). The objective of the shared task was to predict if the given word/phrase is a correct/incorrect (OK/BAD) translation in the given sentence. In this paper, we propose a novel approach for word level Quality Estimation using Recurrent Neural Network Language Model (RNN-LM) architecture. RNN-LMs have been found very effective in different Natural Language Processing (NLP) applications. RNN-LM is mainly used for vector space language modeling for different NLP problems. For this task, we modify the architecture of RNN-LM. The modified system predicts a label (OK/BAD) in the slot rather than predicting the word. The input to the system is a word sequence, similar to the standard RNN-LM. The approach is language independent and requires only the translated text for QE. To estimate the phrase level quality, we use the output of the word level QE system.

Labeling training data has become one of the major roadblocks to using machine learning. Among various weak supervision paradigms, programmatic weak supervision (PWS) has achieved remarkable success in easing the manual labeling bottleneck by programmatically synthesizing training labels from multiple potentially noisy supervision sources. This paper presents a comprehensive survey of recent advances in PWS. In particular, we give a brief introduction of the PWS learning paradigm, and review representative approaches for each component within PWS's learning workflow. In addition, we discuss complementary learning paradigms for tackling limited labeled data scenarios and how these related approaches can be used in conjunction with PWS. Finally, we identify several critical challenges that remain under-explored in the area to hopefully inspire future research directions in the field.

We present our submission to the Task 5 of SemEval-2025 that aims to aid librarians in assigning subject tags to the library records by producing a list of likely relevant tags for a given document. We frame the task as an information retrieval problem, where the document content is used to retrieve subject tags from a large subject taxonomy. We leverage two types of encoder models to build a two-stage information retrieval system -- a bi-encoder for coarse-grained candidate extraction at the first stage, and a cross-encoder for fine-grained re-ranking at the second stage. This approach proved effective, demonstrating significant improvements in recall compared to single-stage methods and showing competitive results according to qualitative evaluation.

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence embedding, which maps Levenshtein distance to a conventional distance between embedding vectors, has emerged as a promising solution. In this paper, a novel neural network-based sequence embedding technique using Poisson regression is proposed. We first provide a theoretical analysis of the impact of embedding dimension on model performance and present a criterion for selecting an appropriate embedding dimension. Under this embedding dimension, the Poisson regression is introduced by assuming the Levenshtein distance between sequences of fixed length following a Poisson distribution, which naturally aligns with the definition of Levenshtein distance. Moreover, from the perspective of the distribution of embedding distances, Poisson regression approximates the negative log likelihood of the chi-squared distribution and offers advancements in removing the skewness. Through comprehensive experiments on real DNA storage data, we demonstrate the superior performance of the proposed method compared to state-of-the-art approaches.

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been difficult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades first yielded and then made practical these powerful learning models. When appropriate, we reconcile conflicting notation and nomenclature. Our goal is to provide a self-contained explication of the state of the art together with a historical perspective and references to primary research.

Research on question answering with knowledge base has recently seen an increasing use of deep architectures. In this extended abstract, we study the application of the neural machine translation paradigm for question parsing. We employ a sequence-to-sequence model to learn graph patterns in the SPARQL graph query language and their compositions. Instead of inducing the programs through question-answer pairs, we expect a semi-supervised approach, where alignments between questions and queries are built through templates. We argue that the coverage of language utterances can be expanded using late notable works in natural language generation.

This article introduces byteSteady -- a fast model for classification using byte-level n-gram embeddings. byteSteady assumes that each input comes as a sequence of bytes. A representation vector is produced using the averaged embedding vectors of byte-level n-grams, with a pre-defined set of n. The hashing trick is used to reduce the number of embedding vectors. This input representation vector is then fed into a linear classifier. A straightforward application of byteSteady is text classification. We also apply byteSteady to one type of non-language data -- DNA sequences for gene classification. For both problems we achieved competitive classification results against strong baselines, suggesting that byteSteady can be applied to both language and non-language data. Furthermore, we find that simple compression using Huffman coding does not significantly impact the results, which offers an accuracy-speed trade-off previously unexplored in machine learning.

Many large language models (LLMs) for medicine have largely been evaluated on short texts, and their ability to handle longer sequences such as a complete electronic health record (EHR) has not been systematically explored. Assessing these models on long sequences is crucial since prior work in the general domain has demonstrated performance degradation of LLMs on longer texts. Motivated by this, we introduce LongBoX, a collection of seven medical datasets in text-to-text format, designed to investigate model performance on long sequences. Preliminary experiments reveal that both medical LLMs (e.g., BioGPT) and strong general domain LLMs (e.g., FLAN-T5) struggle on this benchmark. We further evaluate two techniques designed for long-sequence handling: (i) local-global attention, and (ii) Fusion-in-Decoder (FiD). Our results demonstrate mixed results with long-sequence handling - while scores on some datasets increase, there is substantial room for improvement. We hope that LongBoX facilitates the development of more effective long-sequence techniques for the medical domain. Data and source code are available at https://github.com/Mihir3009/LongBoX.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.