gsapere 0.2.0__tar.gz

gsapere-0.2.0/.gitignore

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gsapere-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 yanzhh
+Copyright (c) 2026 ottowg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+
+The above copyright notice and this permission notice shall be included in all
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+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+SOFTWARE.

gsapere-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: gsapere
+Version: 0.2.0
+Summary: Entity and Relation Extraction on scientific text using HGERE with a span-pruning stage.
+Author: Wolfgang Otto
+License: MIT
+License-File: LICENSE
+Keywords: entity-recognition,information-extraction,nlp,relation-extraction,scientific-text
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Text Processing :: Linguistic
+Requires-Python: <3.11,>=3.9
+Requires-Dist: einops>=0.8.0
+Requires-Dist: huggingface-hub>=0.20.0
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: requests>=2.32.0
+Requires-Dist: scikit-learn>=1.6.0
+Requires-Dist: setuptools>=75.6.0
+Requires-Dist: tabulate>=0.9.0
+Requires-Dist: torch>=2.8.0
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: transformers
+Requires-Dist: wandb>=0.19.9
+Provides-Extra: dev
+Requires-Dist: lint>=1.2.1; extra == 'dev'
+Requires-Dist: pytest>=8.4.2; extra == 'dev'
+Requires-Dist: ruff>=0.15.5; extra == 'dev'
+Requires-Dist: twine>=6.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# gsapere — Entity and Relation Extraction for Scientific Text
+
+A fork of [HGERE](https://github.com/yanzhh/HGERE) adapted for scientific text, with a two-stage pipeline for **joint entity and relation extraction (ERE)**.
+
+> **Paper under review.**
+> Configs used for our experiments are in [`configs/`](configs/).
+
+The pipeline consists of:
+
+1. **Rule-based pre-filter** *(optional)* — removes deterministically non-entity spans (punctuation, function-word sequences, etc.) before the neural pruner sees training data, reducing trivial negatives and speeding up training
+2. **Span Pruner** — a binary classifier that scores remaining candidate n-grams and filters them to a manageable set (target: ≥ 98 % entity recall)
+3. **HGERE** — a Hypergraph GNN that jointly predicts entity types and relations on the pruned candidates
+
+Supported datasets: **GSAP-ERE**, **SciER**, **SciNLP**, **SciERC**
+
+---
+
+## Changes from the original
+
+- Large-scale code restructuring: Pydantic-first configs, typed signatures throughout, proper package layout under `src/`
+- All dependencies updated to current versions
+- The transformer package is **no longer hardcoded** — any compatible HuggingFace `transformers` version works
+- Added rule-based pre-filter, span pruner stage, multi-dataset joint training, and full CLI entry points
+- Tests for all major components
+
+---
+
+## Requirements
+
+- **Python 3.9** (tested; `<3.11` required by some dependencies)
+- CUDA 12.8 (adjust `pyproject.toml` for other CUDA versions)
+- A GPU with at least ~24 GB VRAM for default batch sizes (tested on A40 / 40 GB)
+
+---
+
+## Installation
+
+Install [uv](https://github.com/astral-sh/uv):
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+Clone the repository and install:
+
+```bash
+git clone <repo-url>
+cd HGERE
+uv sync
+```
+
+### Datasets
+
+Datasets are loaded from their original sources via the download command:
+
+```bash
+uv run gsapere-download-dataset --list          # list available datasets
+uv run gsapere-download-dataset gsap-ere
+uv run gsapere-download-dataset scier
+uv run gsapere-download-dataset scinlp
+uv run gsapere-download-dataset scierc
+uv run gsapere-download-dataset --all           # download everything
+```
+
+See [documentation/download-dataset.md](documentation/download-dataset.md) for split details and manual download fallbacks.
+
+#### GSAP-ERE
+
+Fine-grained entity and relation extraction focused on machine learning — 100 annotated full-text ML publications, 63K entities, 35K relations, 10 entity types, 18 relation types.
+DOI: <https://doi.org/10.60914/c4c1d-s0587>
+
+> Otto et al., "GSAP-ERE: Fine-Grained Scholarly Entity and Relation Extraction Focused on Machine Learning", AAAI 2026.
+> <https://ojs.aaai.org/index.php/AAAI/article/view/40537>
+
+#### SciER
+
+Entity and relation extraction dataset for datasets, methods, and tasks in scientific documents — 106 annotated full-text papers, 24k entities, 12k relations.
+
+> Dziadek et al., "SciER: An Entity and Relation Extraction Dataset for Datasets, Methods, and Tasks in Scientific Documents", EMNLP 2024.
+> <https://aclanthology.org/2024.emnlp-main.726/>
+
+#### SciNLP
+
+Full-text entity and relation extraction benchmark for the NLP domain — 60 annotated ACL papers, 6,409 entities, 1,648 relations.
+
+> "SciNLP: A Domain-Specific Benchmark for Full-Text Scientific Entity and Relation Extraction in NLP", EMNLP 2025.
+> <https://aclanthology.org/2025.emnlp-main.732/>
+
+#### SciERC
+
+Scientific information extraction benchmark — 500 annotated AI abstracts,
+6 entity types, 7 relation types.
+
+> Luan et al., "Multi-Task Identification of Entities, Relations, and Coreference for Scientific Knowledge Graph Construction", EMNLP 2018.
+> <https://aclanthology.org/D18-1360/>
+
+---
+
+## Training
+
+Training is a two-step process: first train the pruner, then train HGERE on the pruner's output.
+
+### Step 1 — Fit the rule-based pre-filter (optional)
+
+```bash
+uv run gsapere-fit-rulebased-pruner configs/train/gsap/fit_rulebased_pruner.yaml
+```
+
+This fits token n-gram patterns from the training data that deterministically exclude non-entity spans. The saved JSON file is referenced in the pruner training config to speed up training.
+
+### Step 2 — Train the span pruner
+
+```bash
+uv run gsapere-train-pruner configs/train/gsap/train_gsap_pruner.yaml
+```
+
+After training, run pruner inference on train/dev/test to produce the enriched input files for HGERE (see `scripts/pruner/`).
+
+### Step 3 — Train HGERE (single dataset)
+
+```bash
+uv run gsapere-train-hgere configs/train/gsap/train_gsap_hgere.yaml
+```
+
+Example config:
+
+```yaml
+schema_version: "1.0"
+label_set: gsap
+model_dir: saves/hgere/gsap
+base_model_name_or_path: pretrained_models/scibert_scivocab_uncased
+ner_prediction_dir: saves/pruner/gsap/output
+max_seq_length: 512
+n_iter: 3
+layernorm: true
+attn_self: true
+
+train_params:
+  learning_rate: 1e-5
+  num_train_epochs: 8
+  per_gpu_train_batch_size: 21
+  fp16: true
+  evaluate_during_training: true
+  eval_epochs: 1
+  loss_re_weight_alpha: 0.9
+  log_wandb: true
+```
+
+### Step 3 (alt) — Train HGERE on multiple datasets jointly
+
+Multi-dataset mode trains a shared encoder with per-dataset NER and relation heads. Each dataset must have its own pruner output directory.
+
+```bash
+uv run gsapere-train-hgere configs/multi-sciere-scinlp-gsap-ere/train/hgere/train_multi.yaml
+```
+
+Example config:
+
+```yaml
+schema_version: "1.0"
+model_dir: saves/multi/hgere/run1
+base_model_name_or_path: pretrained_models/scibert_scivocab_uncased
+max_seq_length: 512
+n_iter: 3
+layernorm: true
+attn_self: true
+sampling_temperature: 0.8   # 0 = always largest dataset, 1 = proportional to size
+seeds: [42, 43, 44]          # run once per seed; _seed<n> appended to model_dir
+
+datasets:
+  - label_set: scier
+    ner_prediction_dir: saves/pruner/scier/output
+    train_file: ent_pred_train.json
+    dev_file: ent_pred_dev.json
+    test_file: ent_pred_test.json
+  - label_set: scinlp
+    ner_prediction_dir: saves/pruner/scinlp/output
+    train_file: ent_pred_train.json
+    dev_file: ent_pred_dev.json   # omit (null) to skip dev evaluation for this dataset
+  - label_set: gsap
+    ner_prediction_dir: saves/pruner/gsap/output
+    train_file: ent_pred_train.json
+
+train_params:
+  learning_rate: 1e-5
+  num_train_epochs: 8
+  per_gpu_train_batch_size: 21
+  fp16: true
+  evaluate_during_training: true
+  log_wandb: true
+```
+
+---
+
+## Inference
+
+### Full pipeline (pruner → HGERE)
+
+```bash
+CUDA_VISIBLE_DEVICES=0 uv run gsapere-pipeline \
+    --config configs/inference/gsap-pipeline-best.yaml \
+    --input input/ \
+    --output output/
+```
+
+`--input` can be a `.jsonl` file or a directory of `.jsonl` files.
+Ready-to-use configs for all supported datasets are in [`configs/inference/`](configs/inference/).
+
+The pipeline config combines pruner and HGERE settings in a single YAML file:
+
+```yaml
+label_set: gsap
+
+pruner:
+  model_dir: saves/pruner/gsap/best
+  base_model_name_or_path: pretrained_models/scibert_scivocab_uncased
+  model_type: bertspanmarkerpruner
+  max_seq_length: 256
+  per_gpu_eval_batch_size: 32
+  final_pruning:
+    method: threshold
+    threshold: 0.0005
+
+hgere:
+  model_dir: saves/hgere/gsap/best
+  base_model_name_or_path: pretrained_models/scibert_scivocab_uncased
+  model_type: hyper
+  max_seq_length: 512
+  per_gpu_eval_batch_size: 32
+  n_iter: 3
+  layernorm: true
+  attn_self: true
+  pre_filter_params:
+    method: threshold
+    value: 0.0125
+```
+
+---
+
+## Docker API
+
+The pipeline can be served as a REST API. Build and run with Docker (requires `--gpus all`):
+
+```bash
+docker build -t gsapere-api .
+
+docker run --gpus all \
+    -v /path/to/models:/app/models \
+    -v /path/to/config.yaml:/app/config.yaml \
+    -e PIPELINE_CONFIG=/app/config.yaml \
+    -p 8000:8000 \
+    gsapere-api
+```
+
+Models and the pipeline config are mounted at runtime — the image itself contains only the code.
+
+**Endpoints:**
+
+| Method | Path | Description |
+|---|---|---|
+| `GET` | `/health` | Liveness check |
+| `POST` | `/predict` | Run the pipeline on a batch of documents |
+
+**Example request:**
+
+```bash
+curl -X POST http://localhost:8000/predict \
+    -H "Content-Type: application/json" \
+    -d '{"documents": [{"doc_key": "doc1", "sentences": [["We", "train", "BERT", "."]]}]}'
+```
+
+---
+
+## CLI reference
+
+| Command | Description |
+|---|---|
+| `gsapere-train-pruner` | Train the span pruner |
+| `gsapere-train-hgere` | Train the HGERE ERE model |
+| `gsapere-pipeline` | Run the full two-stage pipeline on new documents |
+| `gsapere-download-dataset` | Download supported datasets |
+| `gsapere-tune-pruner` | Threshold sweep and optimisation for the pruner |
+| `gsapere-fit-rulebased-pruner` | Fit a rule-based pruner baseline |
+| `infer-fixed-spans` | Run HGERE on fixed (gold) spans |
+| `infer-pruner-augmented` | Run HGERE on pruner-predicted spans |
+| `gsap-ere-benchmark-pipeline` | Benchmark pipeline throughput |
+| `gsapere-fix-gold-annos` | Add gold annotations to prediction files |
+| `gsapere-analysis-ner-length-distribution` | Analyse entity length distributions |
+| `gsapere-generate-pruner-docs` | Regenerate parameter docs in `documentation/api/` |
+
+---
+
+## Development
+
+```bash
+uv run pytest                          # run tests
+uv run ruff format src/ tests/         # format
+uv run ruff check src/ tests/          # lint
+```
+
+---
+
+## Building and publishing
+
+```bash
+uv build                               # produces dist/ wheel + sdist
+bash publish.sh                        # build + upload to PyPI (requires .pypi token file)
+```
+
+---
+
+## Citation
+
+Please cite this work and the original HGERE:
+
+```bibtex
+@article{Otto2026GSAP-ERE,
+  title   = {{GSAP-ERE}: Fine-Grained Scholarly Entity and Relation Extraction Focused on Machine Learning},
+  author  = {Otto, Wolfgang and Gan, Lu and Upadhyaya, Sharmila and Karmakar, Saurav and Dietze, Stefan},
+  journal = {Proceedings of the AAAI Conference on Artificial Intelligence},
+  volume  = {40},
+  number  = {38},
+  pages   = {32600--32609},
+  year    = {2026},
+  month   = {Mar.},
+  doi     = {10.1609/aaai.v40i38.40537},
+  url     = {https://ojs.aaai.org/index.php/AAAI/article/view/40537},
+}
+
+@misc{yan2023joint,
+  title         = {Joint Entity and Relation Extraction with Span Pruning and Hypergraph Neural Networks},
+  author        = {Zhaohui Yan and Songlin Yang and Wei Liu and Kewei Tu},
+  year          = {2023},
+  eprint        = {2310.17238},
+  archivePrefix = {arXiv},
+  primaryClass  = {cs.CL}
+}
+```
+
+---
+
+## License
+
+MIT — see [LICENSE](LICENSE).