code

Dependencies and Library Versions

For specific lib versions, see requirements.txt and install them with

pip install -r requirements.txt

Hardware Requirements

The code runs on:

CPU Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz
GPU NVIDIA Tesla V100-PCIE-16GB
RAM 16GB
HDD 16GB

General Description

Each directory bert, bilstm and linear_models contains a baseline model.

Generally, a model should produce output directory (e.g. bert/out) with result jsonl files named after the task name (e.g. RuMedTop3.jsonl).

Each file contains same samples as in test parts enhanced with the prediction field.
Examples,
for RuMedTop3.jsonl

{
    "idx": "qaf1454f",
    "code": "I11",
    "prediction": ["I11", "I20", "I10"]
}

or RuMedSymptomRec.jsonl

{
    "idx": "q45f6321",
    "code": "боль в шее",
    "prediction": ["тошнота", "боль в шее", "частые головные боли"]
}

or RuMedDaNet.jsonl

{
    "pairID": "f5309eadb4eacf0f144b24e260643ea2",
    "answer": "да",
    "prediction": "нет"
}

or RuMedNLI.jsonl

{
    "pairID": "1f2a8146-66c7-11e7-b4f2-f45c89b91419",
    "gold_label": "entailment",
    "prediction": "neutral"
}

or RuMedNER.jsonl

{
    "idx": "769708.tsv_5",
    "ner_tags": ["B-Drugname", "O", "B-Drugclass", "O", "O"],
    "prediction": ["B-Drugclass", "O", "O", "O", "O"]
}

tasks_builder.py

It is the script used to prepare data for the benchmark tasks from raw data files.

python tasks_builder.py

eval.py

It is the script to evaluate the test results.

Run it like

python eval.py --out_dir bert/out

or

python eval.py --out_dir human