s2and 0.31.0
S2AND
License: MIT
Requires Python: <3.12,>=3.11

# S2AND
This repository provides access to the S2AND dataset and S2AND reference model described in the paper [S2AND: A Benchmark and Evaluation System for Author Name Disambiguation](https://api.semanticscholar.org/CorpusID:232233421) by Shivashankar Subramanian, Daniel King, Doug Downey, Sergey Feldman.

The reference model is live on semanticscholar.org, and the trained model is available now as part of the data download (see below).

## Installation Prereqs (one-time)
Clone the repo. 

If `uv` is not installed yet, install it:

```bash
# (any OS) install uv into the Python you use to bootstrap environments
python -m pip install --user --upgrade uv
# Alternatively (if you use pipx): pipx install uv
```

---

## Installation

1. From repo root:

```bash
# create the project venv (uv defaults to .venv if you don't give a name)
# use Python 3.11.x (fasttext doesn't support 3.12+ here)
uv venv --python 3.11.13
```

2. Activate the venv (choose one):

```bash
# macOS / Linux (bash / zsh)
source .venv/bin/activate

# Windows PowerShell
. .venv\Scripts\Activate.ps1

# Windows CMD
.venv\Scripts\activate.bat
```

3. Install project dependencies (dev extras):

```bash
# prefer uv --active so uv uses your activated environment
uv sync --active --extra dev
```

4. (Recommended) Build/install the Rust extension into the active venv:

```bash
# requires Rust toolchain on PATH (rustc/cargo)
uv run --active --no-project maturin develop -m s2and_rust/Cargo.toml
```

Notes:
- This installs the native module into site-packages so imports use the compiled extension.
- If you don't want an editable install, you can `uv pip install .` instead of `uv sync`, then run the
  `maturin develop` step above.
- Once wheels are published, you can install the native extension via extras:
  `uv pip install "s2and[rust]"`.

## Running Tests

To run the tests, use the following command:

```bash
uv run --no-project pytest tests/
```

To run the entire CI suite mimicking the GH Actions, use the following command:
```bash
python scripts\run_ci_locally.py
```

## Version bumping
Versioning is centralized in the `VERSION` file (single source of truth). When you update it, we sync the Python/Rust
manifests and regenerate lockfiles.

One-time setup for hooks (recommended):
```bash
git config core.hooksPath .githooks
```

Workflow:
```bash
# 1) edit VERSION
echo 0.31.0 > VERSION

# 2) sync manifests
uv run python scripts/sync_version.py

# 3) regenerate lockfiles
uv sync --extra dev
uv run --active --no-project cargo generate-lockfile --manifest-path s2and_rust/Cargo.toml
```

Notes:
- The pre-commit hook only runs when `VERSION` is staged and will auto-sync + regenerate lockfiles if needed.
- `uv.lock` and `s2and_rust/Cargo.lock` are generated files and will contain the version after syncing.

## Running scripts
When running scripts from the repo, prefer `uv run --no-project` so the installed packages (including the Rust extension)
resolve from site-packages. Avoid setting `PYTHONPATH` to the repo root, which can shadow the compiled module.

```bash
uv run --no-project python scripts/tutorial_for_predicting_with_the_prod_model.py --use-rust 1
```

Profiling (Rust, prod-mode):

```bash
S2AND_RUST_PROD_MODE=1 S2AND_USE_RUST_FEATURIZER=1 S2AND_USE_RUST_CONSTRAINT=1 \
  uv run --no-project python scripts/profile_kisti_rust_prod.py
```

## Rust featurizer (optional, enabled by default)
S2AND can use a Rust-backed featurizer for faster pairwise feature generation. This is **enabled by default** and falls back
to Python if the native extension is not available.

Install the Rust extension from wheels (when available):
```bash
uv pip install "s2and[rust]"
```

Environment toggles:
- `S2AND_USE_RUST_FEATURIZER=0` to force the Python path.
- `S2AND_USE_RUST_CONSTRAINT=0` to force Python `get_constraint`.
- `S2AND_RUST_BATCH=0` to disable Rust batch mode in `many_pairs_featurize`.
- `S2AND_RUST_BATCH_THRESHOLD` to fall back to Python for tiny batches (default: disabled).
- `RAYON_NUM_THREADS` controls Rust parallelism (when batch mode is used).
- `S2AND_RUST_FEATURIZER_DISK_CACHE=0` to disable on-disk Rust featurizer caching.
- `S2AND_RUST_FEATURIZER_DISK_CACHE_WRITE=1` to force saving Rust featurizer snapshots even when feature caching is off.
- `S2AND_RUST_PROD_MODE=1` to disable Rust snapshot load/save entirely (best for one-shot inference).
- `S2AND_RUST_FEATURIZER_CACHE_DIR` to override the cache directory.

Notes:
- Rust batch mode is used for all `n_jobs` by default and uses Rayon internally for parallelism.
- Rust featurizer snapshots are saved only when feature caching is enabled unless overridden via `S2AND_RUST_FEATURIZER_DISK_CACHE_WRITE=1`.
- The Rust featurizer is built with `maturin develop -m s2and_rust/Cargo.toml`.

## Prod mode (low-latency, one-shot inference)
If your service handles single or batched blocks that are **only seen once**, enabling prod mode avoids costly
snapshot I/O. This keeps everything in memory and relies on the per-process Rust featurizer cache.

Default behavior:
- If `S2AND_RUST_PROD_MODE` is **unset**, `dataset.mode == "inference"` implies prod mode.
- If `S2AND_RUST_PROD_MODE` is set, it overrides the dataset mode.

Recommended settings:
- `S2AND_RUST_PROD_MODE=1`
- `S2AND_RUST_FEATURIZER_DISK_CACHE=0` (optional; prod mode already disables read/write)
- keep `S2AND_USE_RUST_FEATURIZER=1` and `S2AND_USE_RUST_CONSTRAINT=1`

Pre-warm once at server start so requests are hot:

```python
from s2and.feature_port import warm_rust_featurizer

# after you build/load your ANDData dataset:
warm_rust_featurizer(dataset)
```

## Data 
To obtain the S2AND dataset, run the following command after the package is installed (from inside the `S2AND` directory):  
```[Expected download size is: 50.4 GiB]```

`aws s3 sync --no-sign-request s3://ai2-s2-research-public/s2and-release data/`

Note that this software package comes with tools specifically designed to access and model the dataset.

## Configuration
Modify the config file at `data/path_config.json`. This file should look like this
```
{
    "main_data_dir": "absolute path to wherever you downloaded the data to",
    "internal_data_dir": "ignore this one unless you work at AI2"
}
```
As the dummy file says, `main_data_dir` should be set to the location of wherever you downloaded the data to, and
`internal_data_dir` can be ignored, as it is used for some scripts that rely on unreleased data, internal to Semantic Scholar.

## How to use S2AND for loading data and training a model
Once you have downloaded the datasets, you can go ahead and load up one of them:

```python
from os.path import join
from s2and.data import ANDData

dataset_name = "pubmed"
parent_dir = f"data/{dataset_name}"
dataset = ANDData(
    signatures=join(parent_dir, f"{dataset_name}_signatures.json"),
    papers=join(parent_dir, f"{dataset_name}_papers.json"),
    mode="train",
    specter_embeddings=join(parent_dir, f"{dataset_name}_specter.pickle"),
    clusters=join(parent_dir, f"{dataset_name}_clusters.json"),
    block_type="s2",
    train_pairs_size=100000,
    val_pairs_size=10000,
    test_pairs_size=10000,
    name=dataset_name,
    n_jobs=8,
)
```

This may take a few minutes - there is a lot of text pre-processing to do.

The first step in the S2AND pipeline is to specify a featurizer and then train a binary classifier
that tries to guess whether two signatures are referring to the same person. 

We'll do hyperparameter selection with the validation set and then get the test area under ROC curve.

Here's how to do all that:

```python
from s2and.model import PairwiseModeler
from s2and.featurizer import FeaturizationInfo
from s2and.eval import pairwise_eval

featurization_info = FeaturizationInfo()
# the cache will make it faster to train multiple times - it stores the features on disk for you
train, val, test = featurize(dataset, featurization_info, n_jobs=8, use_cache=True)
X_train, y_train = train
X_val, y_val = val
X_test, y_test = test

# calibration fits isotonic regression after the binary classifier is fit
# monotone constraints help the LightGBM classifier behave sensibly
pairwise_model = PairwiseModeler(
    n_iter=25, calibrate=True, monotone_constraints=featurization_info.lightgbm_monotone_constraints
)
# this does hyperparameter selection, which is why we need to pass in the validation set.
pairwise_model.fit(X_train, y_train, X_val, y_val)

# this will also dump a lot of useful plots (ROC, PR, SHAP) to the figs_path
pairwise_metrics = pairwise_eval(X_test, y_test, pairwise_model.classifier, figs_path='figs/', title='example')
print(pairwise_metrics)
```

The second stage in the S2AND pipeline is to tune hyperparameters for the clusterer on the validation data
and then evaluate the full clustering pipeline on the test blocks.

We use agglomerative clustering as implemented in `fastcluster` with average linkage.
There is only one hyperparameter to tune.

```python
from s2and.model import Clusterer, FastCluster
from hyperopt import hp

clusterer = Clusterer(
    featurization_info,
    pairwise_model,
    cluster_model=FastCluster(linkage="average"),
    search_space={"eps": hp.uniform("eps", 0, 1)},
    n_iter=25,
    n_jobs=8,
)
clusterer.fit(dataset)

# the metrics_per_signature are there so we can break out the facets if needed
metrics, metrics_per_signature = cluster_eval(dataset, clusterer)
print(metrics)
```

For a fuller example, please see the transfer script: `scripts/transfer_experiment.py`.

## How to use S2AND for predicting with a saved model
Assuming you have a clusterer already fit, you can dump the model to disk like so
```python
import pickle

with open("saved_model.pkl", "wb") as _pkl_file:
    pickle.dump(clusterer, _pkl_file)
```

You can then reload it, load a new dataset, and run prediction
```python
import pickle

with open("saved_model.pkl", "rb") as _pkl_file:
    clusterer = pickle.load(_pkl_file)

anddata = ANDData(
    signatures=signatures,
    papers=papers,
    specter_embeddings=paper_embeddings,
    name="your_name_here",
    mode="inference",
    block_type="s2",
)
pred_clusters, pred_distance_matrices = clusterer.predict(anddata.get_blocks(), anddata)
```
## How to use the released production model
We provide a trained production model (the one that is used in the Semantic Scholar website and API) in the S3 bucket along with the datasets, in the file `production_model_v1.1.pickle`. To see an example of using it, please see the script `scripts/tutorial_for_predicting_with_the_prod_model.py`. You can also use it on your own data, as long as it is formatted the same way as the S2AND data. The older "v1.0" model is also available, but it's worse.

Please note that the production models still use SPECTER1, and these embeddings are still available via the S2 API.

### Incremental prediction
There is a also a `predict_incremental` function on the `Clusterer`, that allows prediction for just a small set of *new* signatures. When instantiating `ANDData`, you can pass in `cluster_seeds`, which will be used instead of model predictions for those signatures. If you call `predict_incremental`, the full distance matrix will not be created, and the new signatures will simply be assigned to the cluster they have the lowest average distance to, as long as it is below the model's `eps`, or separately reclustered with the other unassigned signatures, if not within `eps` of any existing cluster.

## Reproducibility
The experiments in the paper were run with the python (3.7.9) package versions in `paper_experiments_env.txt`, in the branch `s2and_paper`. 

To install, run:
```bash
git checkout s2and_paper
pip install pip==21.0.0
pip install -r paper_experiments_env.txt --use-feature=fast-deps --use-deprecated=legacy-resolver
``` 

Then, Rerunning `scripts/paper_experiments.sh` on the branch `s2and_paper` should produce the same numbers as in the paper (we will udpate here if this becomes not true). 

Our trained, released models are in the `s3` folder referenced above, and are called `production_model.pickle` (very close to what is running on the Semantic Scholar website, except the production model doesn't compute the reference features) and `full_union_seed_*.pickle` (models trained during benchmark experiments). They can be loaded the same way as in the section above called "How to use S2AND for predicting with a saved model", except that the pickled object is a *dictionary*, with a `clusterer` key. *Important*: these pickles will only run on the branch `s2and_paper` and not on main.

Note that by default we are using the `--use_cache` flag, which will cache all the features so future reruns are faster. There are two things to be aware of: (a) the cache is stored in RAM and can be huge (100gb+) and (b) if you intend to change the features and rerun, you'll have to turn off the cache or the new features won't be used.

## Licensing
The code in this repo is released under the Apache 2.0 license. The dataset is released under ODC-BY (included in S3 bucket with the data). We would also like to acknowledge that some of the affiliations data comes directly from the Microsoft Academic Graph (https://aka.ms/msracad).

## Citation

If you use S2AND in your research, please cite [S2AND: A Benchmark and Evaluation System for Author Name Disambiguation](https://api.semanticscholar.org/CorpusID:232233421).

```
@inproceedings{subramanian2021s2and,
      title={{S}2{AND}: {A} {B}enchmark and {E}valuation {S}ystem for {A}uthor {N}ame {D}isambiguation}, 
      author={Subramanian, Shivashankar and King, Daniel and Downey, Doug and Feldman, Sergey},
      year={2021},
      publisher = {Association for Computing Machinery},
      address = {New York, NY, USA},
      booktitle = {{JCDL} '21: Proceedings of the {ACM/IEEE} Joint Conference on Digital Libraries in 2021},
      series = {JCDL '21}
}
```

S2AND is an open-source project developed by [the Allen Institute for Artificial Intelligence (AI2)](http://www.allenai.org).
AI2 is a non-profit institute with the mission to contribute to humanity through high-impact AI research and engineering.