README.md

---
language:
  - en
library_name: transformers
pipeline_tag: summarization
license: apache-2.0
tags:
  - chemistry
  - scientific-summarization
  - distilbart
  - abstractive
  - tldr
  - knowledge-graphs
datasets:
  - Bocklitz-Lab/lit2vec-tldr-bart-dataset
model-index:
- name: lit2vec-tldr-bart
  results:
  - task:
      name: Summarization
      type: summarization
    dataset:
      name: Lit2Vec TL;DR Chemistry Dataset
      type: Bocklitz-Lab/lit2vec-tldr-bart-dataset
      split: test
      size: 1001
    metrics:
      - type: rouge1
        value: 56.11
      - type: rouge2
        value: 30.78
      - type: rougeLsum
        value: 45.43
---

# lit2vec-tldr-bart (DistilBART fine-tuned for chemistry TL;DRs)

**lit2vec-tldr-bart** is a DistilBART model fine-tuned on **19,992** CC-BY licensed chemistry abstracts to produce **concise TL;DR-style summaries** aligned with methods → results → significance. It’s designed for scientific **abstractive summarization**, **semantic indexing**, and **knowledge-graph population** in chemistry and related fields.

- **Base model:** `sshleifer/distilbart-cnn-12-6`
- **Training data:** [`Bocklitz-Lab/lit2vec-tldr-bart-dataset`](https://huggingface.co/datasets/Bocklitz-Lab/lit2vec-tldr-bart-dataset)
- **Max input length:** 1024 tokens  
- **Target length:** ~128 tokens

---

## 🧪 Evaluation (held-out test)

| Split | ROUGE-1 | ROUGE-2 | ROUGE-Lsum |
|------:|--------:|--------:|-----------:|
| Test  | **56.11** | **30.78** | **45.43** |

> Validation RLsum: 46.05  
> Metrics computed with `evaluate`'s `rouge` (NLTK sentence segmentation, `use_stemmer=True`).

---

## 🚀 Quickstart

```python
from transformers import AutoTokenizer, AutoModelForSeq2SeqLM, GenerationConfig

repo = "Bocklitz-Lab/lit2vec-tldr-bart"

tok = AutoTokenizer.from_pretrained(repo)
model = AutoModelForSeq2SeqLM.from_pretrained(repo)
gen = GenerationConfig.from_pretrained(repo)  # loads default decoding params

text = "Proton exchange membrane fuel cells convert chemical energy into electricity..."
inputs = tok(text, return_tensors="pt", truncation=True, max_length=1024)

summary_ids = model.generate(**inputs, **gen.to_dict())
print(tok.decode(summary_ids[0], skip_special_tokens=True))
````

### Batch inference (PyTorch)

```python
texts = [
  "Abstract 1 ...",
  "Abstract 2 ...",
]
batch = tok(texts, return_tensors="pt", padding=True, truncation=True, max_length=1024)
out = model.generate(**batch, **gen.to_dict())
summaries = tok.batch_decode(out, skip_special_tokens=True)
```

---

## 🔧 Default decoding (saved in `generation_config.json`)

These are the defaults saved with the model (you can override at `generate()` time):

```json
{
  "max_length": 142,
  "min_length": 56,
  "early_stopping": true,
  "num_beams": 4,
  "length_penalty": 2.0,
  "no_repeat_ngram_size": 3,
  "forced_bos_token_id": 0,
  "forced_eos_token_id": 2
}
```

---

## 📊 Training details

* **Base:** `sshleifer/distilbart-cnn-12-6` (Distilled BART)
* **Data:** 19,992 CC-BY chemistry abstracts with TL;DR summaries
* **Splits:** train=17,992 / val=999 / test=1,001
* **Max lengths:** input 1024, target 128
* **Optimizer:** AdamW, **lr=2e-5**
* **Batching:** per-device train/eval batch size 4, **gradient\_accumulation\_steps=4**
* **Epochs:** 5
* **Precision:** fp16 (when CUDA available)
* **Hardware:** single NVIDIA RTX 3090
* **Seed:** 42
* **Libraries:** 🤗 Transformers + Datasets, `evaluate` for ROUGE, NLTK for sentence splitting

---

## ✅ Intended use

* TL;DR abstractive summaries for **chemistry** and adjacent domains (materials science, chemical engineering, environmental science).
* **Semantic indexing**, **IR reranking**, and **knowledge graph** ingestion where concise method/result statements are helpful.

### Limitations & risks

* May **hallucinate** details not present in the abstract (typical for abstractive models).
* Not a substitute for expert judgment; avoid using summaries as sole evidence for scientific claims.
* Trained on CC-BY English abstracts; performance may degrade on other domains/languages.

---

## 📦 Files

This repo should include:

* `config.json`, `pytorch_model.bin` or `model.safetensors`
* `tokenizer.json`, `tokenizer_config.json`, `special_tokens_map.json`, merges/vocab as applicable
* `generation_config.json` (decoding defaults)

---

## 🔁 Reproducibility

* Dataset: [`Bocklitz-Lab/lit2vec-tldr-bart-dataset`](https://huggingface.co/datasets/Bocklitz-Lab/lit2vec-tldr-bart-dataset)
* Recommended preprocessing: truncate inputs at 1024 tokens; targets at 128.
* ROUGE evaluation: `evaluate.load("rouge")`, NLTK sentence tokenization, `use_stemmer=True`.

---

## 📚 Citation

If you use this model or dataset, please cite:

```bibtex
@software{lit2vec_tldr_bart_2025,
  title   = {lit2vec-tldr-bart: DistilBART fine-tuned for chemistry TL;DR summarization},
  author  = {Bocklitz Lab},
  year    = {2025},
  url     = {https://huggingface.co/Bocklitz-Lab/lit2vec-tldr-bart},
  note    = {Model trained on CC-BY chemistry abstracts; dataset at Bocklitz-Lab/lit2vec-tldr-bart-dataset}
}
```

Dataset:

```bibtex
@dataset{lit2vec_tldr_dataset_2025,
  title   = {Lit2Vec TL;DR Chemistry Dataset},
  author  = {Bocklitz Lab},
  year    = {2025},
  url     = {https://huggingface.co/datasets/Bocklitz-Lab/lit2vec-tldr-bart-dataset}
}
```

---

## 📝 License

* **Model weights & code:** Apache-2.0
* **Dataset:** CC BY 4.0 (attribution in per-record metadata)

---

## 🙌 Acknowledgements

* Base model: DistilBART (`sshleifer/distilbart-cnn-12-6`)
* Licensing and OA links curated from publisher/aggregator sources; dataset restricted to **CC-BY** content.