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Browse files- README.md +43 -20
- app.py +446 -0
- paper_classifier.py +73 -0
- requirements.txt +7 -3
- train_distilbert.py +229 -0
README.md
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Реализация задания из ноутбука через `streamlit` и `finetune` модели
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`distilbert/distilbert-base-cased` для классификации научный статей
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## Что за файлики
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- `train_distilbert.py` - на датасете архива `arxivData.json` из кагле.
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- `app.py` - веб-интерфейс на streamlit, который загружает уже обученный чекпонинт
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- `paper_classifier.py` - общие константы, примеры
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Используются поля:
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- `title`
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- `summary`
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- `tag`
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## Обучение
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```bash
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conda activate main
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pip install -r requirements.txt
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python train_distilbert.py
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```
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По умолчанию checkpoint будет сохранён в `artifacts/distilbert-arxiv`.
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## Запуск streamlit
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После обучения:
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```bash
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conda activate main
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streamlit run app.py --server.port 8080
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```
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После запуска откройте `http://localhost:8080`.
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## Как работает инференс
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- модель читает `title` и `abstract`
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- если `abstract` пустой, используется только название статьи
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- сервис показывает только те классы, которые суммарно набирают `95%` вероятности по категориям, иначе гг.
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app.py
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from __future__ import annotations
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import os
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from pathlib import Path
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import streamlit as st
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import torch
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from transformers import AutoModelForSequenceClassification, AutoTokenizer
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from paper_classifier import (
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BASE_MODEL_NAME,
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DEFAULT_MODEL_DIR,
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EXAMPLES,
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EXPECTED_ARXIV_CATEGORIES,
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MAX_LENGTH,
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TOP_P_THRESHOLD,
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format_input_text,
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take_top_p,
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)
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MODEL_DIR = Path(os.environ.get("ARXIV_MODEL_DIR", DEFAULT_MODEL_DIR))
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@st.cache_resource(show_spinner=False)
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def load_model_bundle() -> tuple[AutoTokenizer, AutoModelForSequenceClassification]:
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config_path = MODEL_DIR / "config.json"
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if not config_path.exists():
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raise FileNotFoundError(
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f"Не найден fine-tuned checkpoint в {MODEL_DIR}. Сначала обучите модель через train_distilbert.py."
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)
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tokenizer = AutoTokenizer.from_pretrained(MODEL_DIR.as_posix())
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model = AutoModelForSequenceClassification.from_pretrained(MODEL_DIR.as_posix())
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model.eval()
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return tokenizer, model
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def predict_topics(title: str, abstract: str) -> list[dict[str, float]]:
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article_text = format_input_text(title, abstract)
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if not article_text:
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raise ValueError("Введите хотя бы название статьи или abstract.")
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tokenizer, model = load_model_bundle()
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inputs = tokenizer(
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article_text,
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return_tensors="pt",
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truncation=True,
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max_length=MAX_LENGTH,
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)
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device = next(model.parameters()).device
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inputs = {name: tensor.to(device) for name, tensor in inputs.items()}
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with torch.inference_mode():
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logits = model(**inputs).logits[0]
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probabilities = torch.softmax(logits, dim=-1).cpu().tolist()
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id2label = getattr(model.config, "id2label", None) or {
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index: f"Label {index}" for index in range(len(probabilities))
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}
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records = [
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{
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"label": str(id2label.get(index, f"Label {index}")),
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"score": float(score),
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}
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for index, score in enumerate(probabilities)
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]
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records.sort(key=lambda record: record["score"], reverse=True)
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return take_top_p(records, TOP_P_THRESHOLD)
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| 69 |
+
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+
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def apply_styles() -> None:
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| 72 |
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st.markdown(
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| 73 |
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"""
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<style>
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| 75 |
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@import url('https://fonts.googleapis.com/css2?family=Manrope:wght@400;600;700;800&family=IBM+Plex+Mono:wght@400;500&display=swap');
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| 76 |
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| 77 |
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:root {
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| 78 |
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--paper: rgba(22, 27, 34, 0.92);
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| 79 |
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--card: rgba(30, 36, 46, 0.88);
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| 80 |
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--ink: #e6edf3;
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| 81 |
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--muted: #8b9cb3;
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| 82 |
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--accent: #2dd4bf;
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| 83 |
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--accent-dim: rgba(45, 212, 191, 0.14);
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| 84 |
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--accent-2: #fb923c;
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| 85 |
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--border: rgba(230, 237, 243, 0.09);
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| 86 |
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--shadow: 0 24px 80px rgba(0, 0, 0, 0.45);
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| 87 |
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--surface-0: #0d1117;
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| 88 |
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--surface-1: #161b22;
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| 89 |
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--surface-input: #21262d;
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| 90 |
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}
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| 91 |
+
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.stApp {
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| 93 |
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background:
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| 94 |
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radial-gradient(circle at 12% 8%, rgba(45, 212, 191, 0.09), transparent 32%),
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| 95 |
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radial-gradient(circle at 88% 4%, rgba(251, 146, 60, 0.07), transparent 28%),
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| 96 |
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linear-gradient(180deg, #0d1117 0%, #0a0e14 100%);
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| 97 |
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color: var(--ink);
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| 98 |
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font-family: "Manrope", sans-serif;
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| 99 |
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}
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| 100 |
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| 101 |
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[data-testid="stAppViewContainer"],
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| 102 |
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[data-testid="stHeader"] {
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| 103 |
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background: transparent;
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| 104 |
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}
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| 105 |
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| 106 |
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[data-testid="stSidebar"] {
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| 107 |
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background: linear-gradient(180deg, var(--surface-1) 0%, #121820 100%);
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| 108 |
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border-right: 1px solid var(--border);
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| 109 |
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}
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| 110 |
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| 111 |
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[data-testid="stSidebar"] .stMarkdown,
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| 112 |
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[data-testid="stSidebar"] label,
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| 113 |
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[data-testid="stSidebar"] span {
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| 114 |
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color: var(--ink) !important;
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| 115 |
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}
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| 116 |
+
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| 117 |
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.block-container {
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| 118 |
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padding-top: 2.2rem;
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| 119 |
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padding-bottom: 2.2rem;
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| 120 |
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max-width: 1100px;
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| 121 |
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}
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| 122 |
+
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| 123 |
+
section.main [data-testid="stMarkdownContainer"] p,
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| 124 |
+
section.main [data-testid="stMarkdownContainer"] li,
|
| 125 |
+
section.main label,
|
| 126 |
+
.stSubheader {
|
| 127 |
+
color: var(--ink) !important;
|
| 128 |
+
}
|
| 129 |
+
|
| 130 |
+
.stTextInput label,
|
| 131 |
+
.stTextArea label {
|
| 132 |
+
color: var(--muted) !important;
|
| 133 |
+
}
|
| 134 |
+
|
| 135 |
+
.stTextInput input,
|
| 136 |
+
.stTextArea textarea {
|
| 137 |
+
background-color: var(--surface-input) !important;
|
| 138 |
+
color: var(--ink) !important;
|
| 139 |
+
border: 1px solid var(--border) !important;
|
| 140 |
+
border-radius: 12px !important;
|
| 141 |
+
}
|
| 142 |
+
|
| 143 |
+
.stTextInput input:focus,
|
| 144 |
+
.stTextArea textarea:focus {
|
| 145 |
+
border-color: rgba(45, 212, 191, 0.45) !important;
|
| 146 |
+
box-shadow: 0 0 0 1px rgba(45, 212, 191, 0.25);
|
| 147 |
+
}
|
| 148 |
+
|
| 149 |
+
div[data-baseweb="select"] > div {
|
| 150 |
+
background-color: var(--surface-input) !important;
|
| 151 |
+
border-color: var(--border) !important;
|
| 152 |
+
color: var(--ink) !important;
|
| 153 |
+
}
|
| 154 |
+
|
| 155 |
+
.stButton > button {
|
| 156 |
+
background: linear-gradient(135deg, #0d9488 0%, #0f766e 100%) !important;
|
| 157 |
+
color: #f0fdfa !important;
|
| 158 |
+
border: none !important;
|
| 159 |
+
font-weight: 700 !important;
|
| 160 |
+
border-radius: 12px !important;
|
| 161 |
+
}
|
| 162 |
+
|
| 163 |
+
.stButton > button:hover {
|
| 164 |
+
background: linear-gradient(135deg, #14b8a6 0%, #0d9488 100%) !important;
|
| 165 |
+
color: #fff !important;
|
| 166 |
+
}
|
| 167 |
+
|
| 168 |
+
[data-testid="stExpander"] {
|
| 169 |
+
background: var(--paper);
|
| 170 |
+
border: 1px solid var(--border);
|
| 171 |
+
border-radius: 14px;
|
| 172 |
+
}
|
| 173 |
+
|
| 174 |
+
[data-testid="stExpander"] summary {
|
| 175 |
+
color: var(--ink) !important;
|
| 176 |
+
}
|
| 177 |
+
|
| 178 |
+
.stProgress > div > div {
|
| 179 |
+
background-color: rgba(45, 212, 191, 0.35) !important;
|
| 180 |
+
}
|
| 181 |
+
|
| 182 |
+
.stProgress > div > div > div {
|
| 183 |
+
background: linear-gradient(90deg, #2dd4bf, #14b8a6) !important;
|
| 184 |
+
}
|
| 185 |
+
|
| 186 |
+
.hero {
|
| 187 |
+
padding: 2rem 2.2rem;
|
| 188 |
+
border-radius: 28px;
|
| 189 |
+
background: linear-gradient(145deg, rgba(30, 36, 46, 0.95), rgba(22, 27, 34, 0.88));
|
| 190 |
+
border: 1px solid var(--border);
|
| 191 |
+
box-shadow: var(--shadow);
|
| 192 |
+
backdrop-filter: blur(12px);
|
| 193 |
+
margin-bottom: 1.2rem;
|
| 194 |
+
}
|
| 195 |
+
|
| 196 |
+
.hero-kicker {
|
| 197 |
+
font-size: 0.82rem;
|
| 198 |
+
text-transform: uppercase;
|
| 199 |
+
letter-spacing: 0.18em;
|
| 200 |
+
color: var(--accent);
|
| 201 |
+
font-weight: 800;
|
| 202 |
+
margin-bottom: 0.65rem;
|
| 203 |
+
}
|
| 204 |
+
|
| 205 |
+
.hero h1 {
|
| 206 |
+
font-size: clamp(2rem, 3.5vw, 3.7rem);
|
| 207 |
+
line-height: 0.98;
|
| 208 |
+
margin: 0;
|
| 209 |
+
max-width: 11ch;
|
| 210 |
+
color: var(--ink);
|
| 211 |
+
}
|
| 212 |
+
|
| 213 |
+
.hero p {
|
| 214 |
+
max-width: 56rem;
|
| 215 |
+
color: var(--muted);
|
| 216 |
+
font-size: 1.02rem;
|
| 217 |
+
line-height: 1.65;
|
| 218 |
+
margin-top: 0.95rem;
|
| 219 |
+
margin-bottom: 0;
|
| 220 |
+
}
|
| 221 |
+
|
| 222 |
+
.info-strip {
|
| 223 |
+
display: grid;
|
| 224 |
+
grid-template-columns: repeat(auto-fit, minmax(190px, 1fr));
|
| 225 |
+
gap: 0.8rem;
|
| 226 |
+
margin: 1rem 0 1.25rem;
|
| 227 |
+
}
|
| 228 |
+
|
| 229 |
+
.info-card {
|
| 230 |
+
padding: 1rem 1.05rem;
|
| 231 |
+
border-radius: 20px;
|
| 232 |
+
background: var(--paper);
|
| 233 |
+
border: 1px solid var(--border);
|
| 234 |
+
}
|
| 235 |
+
|
| 236 |
+
.info-label {
|
| 237 |
+
color: var(--muted);
|
| 238 |
+
font-size: 0.84rem;
|
| 239 |
+
margin-bottom: 0.3rem;
|
| 240 |
+
}
|
| 241 |
+
|
| 242 |
+
.info-value {
|
| 243 |
+
font-weight: 700;
|
| 244 |
+
color: var(--ink);
|
| 245 |
+
word-break: break-word;
|
| 246 |
+
}
|
| 247 |
+
|
| 248 |
+
.result-card {
|
| 249 |
+
padding: 1rem 1.1rem 1.1rem;
|
| 250 |
+
border-radius: 22px;
|
| 251 |
+
background: var(--card);
|
| 252 |
+
border: 1px solid var(--border);
|
| 253 |
+
margin-bottom: 0.9rem;
|
| 254 |
+
}
|
| 255 |
+
|
| 256 |
+
.result-rank {
|
| 257 |
+
display: inline-block;
|
| 258 |
+
padding: 0.2rem 0.55rem;
|
| 259 |
+
margin-bottom: 0.65rem;
|
| 260 |
+
border-radius: 999px;
|
| 261 |
+
background: var(--accent-dim);
|
| 262 |
+
color: var(--accent);
|
| 263 |
+
font-size: 0.8rem;
|
| 264 |
+
font-weight: 800;
|
| 265 |
+
letter-spacing: 0.06em;
|
| 266 |
+
text-transform: uppercase;
|
| 267 |
+
}
|
| 268 |
+
|
| 269 |
+
.result-title {
|
| 270 |
+
font-size: 1.12rem;
|
| 271 |
+
font-weight: 800;
|
| 272 |
+
margin-bottom: 0.35rem;
|
| 273 |
+
color: var(--ink);
|
| 274 |
+
}
|
| 275 |
+
|
| 276 |
+
.result-score {
|
| 277 |
+
color: var(--accent-2);
|
| 278 |
+
font-family: "IBM Plex Mono", monospace;
|
| 279 |
+
font-size: 0.92rem;
|
| 280 |
+
margin-bottom: 0.75rem;
|
| 281 |
+
}
|
| 282 |
+
|
| 283 |
+
.caption-note {
|
| 284 |
+
color: var(--muted);
|
| 285 |
+
font-size: 0.92rem;
|
| 286 |
+
}
|
| 287 |
+
|
| 288 |
+
[data-testid="stSidebar"] pre,
|
| 289 |
+
[data-testid="stSidebar"] code {
|
| 290 |
+
background-color: var(--surface-input) !important;
|
| 291 |
+
color: #a5f3fc !important;
|
| 292 |
+
border: 1px solid var(--border) !important;
|
| 293 |
+
border-radius: 10px !important;
|
| 294 |
+
}
|
| 295 |
+
|
| 296 |
+
[data-testid="stSidebar"] [data-testid="stMarkdownContainer"] a {
|
| 297 |
+
color: var(--accent) !important;
|
| 298 |
+
}
|
| 299 |
+
</style>
|
| 300 |
+
""",
|
| 301 |
+
unsafe_allow_html=True,
|
| 302 |
+
)
|
| 303 |
+
|
| 304 |
+
|
| 305 |
+
def render_hero() -> None:
|
| 306 |
+
st.markdown(
|
| 307 |
+
"""
|
| 308 |
+
<section class="hero">
|
| 309 |
+
<div class="hero-kicker">Моисейин Андрей Денисович</div>
|
| 310 |
+
<h1>Классификатор научных статей</h1>
|
| 311 |
+
<p>
|
| 312 |
+
Вот не зря я учил веб разработку 4 года, чтобы писать на html, css и js. Эх, был бы реакт.
|
| 313 |
+
</p>
|
| 314 |
+
</section>
|
| 315 |
+
""",
|
| 316 |
+
unsafe_allow_html=True,
|
| 317 |
+
)
|
| 318 |
+
|
| 319 |
+
st.markdown(
|
| 320 |
+
f"""
|
| 321 |
+
<div class="info-strip">
|
| 322 |
+
<div class="info-card">
|
| 323 |
+
<div class="info-label">Базовая модель</div>
|
| 324 |
+
<div class="info-value">{BASE_MODEL_NAME}</div>
|
| 325 |
+
</div>
|
| 326 |
+
<div class="info-card">
|
| 327 |
+
<div class="info-label">Checkpoint</div>
|
| 328 |
+
<div class="info-value">{MODEL_DIR}</div>
|
| 329 |
+
</div>
|
| 330 |
+
<div class="info-card">
|
| 331 |
+
<div class="info-label">Макс. длина</div>
|
| 332 |
+
<div class="info-value">{MAX_LENGTH} токенов</div>
|
| 333 |
+
</div>
|
| 334 |
+
</div>
|
| 335 |
+
""",
|
| 336 |
+
unsafe_allow_html=True,
|
| 337 |
+
)
|
| 338 |
+
|
| 339 |
+
|
| 340 |
+
def render_results(records: list[dict[str, float]]) -> None:
|
| 341 |
+
st.subheader("Ответ")
|
| 342 |
+
st.caption("Классы отсортированы по убыванию вероятности. Показаны только те, которые набрали 95%.")
|
| 343 |
+
|
| 344 |
+
for index, record in enumerate(records, start=1):
|
| 345 |
+
st.markdown(
|
| 346 |
+
f"""
|
| 347 |
+
<div class="result-card">
|
| 348 |
+
<div class="result-rank">#{index}</div>
|
| 349 |
+
<div class="result-title">{record["label"]}</div>
|
| 350 |
+
<div class="result-score">p = {record["score"]:.2%}</div>
|
| 351 |
+
</div>
|
| 352 |
+
""",
|
| 353 |
+
unsafe_allow_html=True,
|
| 354 |
+
)
|
| 355 |
+
st.progress(min(max(record["score"], 0.0), 1.0))
|
| 356 |
+
|
| 357 |
+
st.caption(
|
| 358 |
+
f"Суммарная вероятность показанных тем: {sum(record['score'] for record in records):.2%}"
|
| 359 |
+
)
|
| 360 |
+
|
| 361 |
+
|
| 362 |
+
def render_sidebar() -> None:
|
| 363 |
+
if "selected_preset" not in st.session_state:
|
| 364 |
+
st.session_state.selected_preset = "Свой текст"
|
| 365 |
+
if "article_title" not in st.session_state:
|
| 366 |
+
st.session_state.article_title = ""
|
| 367 |
+
if "article_abstract" not in st.session_state:
|
| 368 |
+
st.session_state.article_abstract = ""
|
| 369 |
+
|
| 370 |
+
st.sidebar.markdown("### Быстрый старт")
|
| 371 |
+
preset_name = st.sidebar.selectbox(
|
| 372 |
+
"Пример статьи",
|
| 373 |
+
options=["Свой текст"] + list(EXAMPLES.keys()),
|
| 374 |
+
)
|
| 375 |
+
|
| 376 |
+
if preset_name != st.session_state.selected_preset:
|
| 377 |
+
if preset_name == "Свой текст":
|
| 378 |
+
st.session_state.article_title = ""
|
| 379 |
+
st.session_state.article_abstract = ""
|
| 380 |
+
else:
|
| 381 |
+
st.session_state.article_title = EXAMPLES[preset_name]["title"]
|
| 382 |
+
st.session_state.article_abstract = EXAMPLES[preset_name]["abstract"]
|
| 383 |
+
st.session_state.selected_preset = preset_name
|
| 384 |
+
|
| 385 |
+
|
| 386 |
+
|
| 387 |
+
|
| 388 |
+
def main() -> None:
|
| 389 |
+
st.set_page_config(
|
| 390 |
+
page_title="Article Topic Classifier",
|
| 391 |
+
layout="wide",
|
| 392 |
+
)
|
| 393 |
+
apply_styles()
|
| 394 |
+
render_hero()
|
| 395 |
+
render_sidebar()
|
| 396 |
+
|
| 397 |
+
left_col, right_col = st.columns([1.15, 0.85], gap="large")
|
| 398 |
+
|
| 399 |
+
with left_col:
|
| 400 |
+
with st.form("classifier-form", clear_on_submit=False):
|
| 401 |
+
title = st.text_input(
|
| 402 |
+
"Название статьи",
|
| 403 |
+
key="article_title",
|
| 404 |
+
placeholder="Например: Attention is all you need",
|
| 405 |
+
)
|
| 406 |
+
abstract = st.text_area(
|
| 407 |
+
"Абстракт",
|
| 408 |
+
key="article_abstract",
|
| 409 |
+
height=280,
|
| 410 |
+
placeholder="Вставьте абстракт статьи. Если не вставишь, ну и фиг с ним.",
|
| 411 |
+
)
|
| 412 |
+
submitted = st.form_submit_button("Крутить барабан (трансформер)", use_container_width=True)
|
| 413 |
+
|
| 414 |
+
st.markdown(
|
| 415 |
+
"""
|
| 416 |
+
<div class="caption-note">
|
| 417 |
+
Если abstract пустой, классификация идёт только по названию. ОТВЕТ СНИЗУ.
|
| 418 |
+
</div>
|
| 419 |
+
""",
|
| 420 |
+
unsafe_allow_html=True,
|
| 421 |
+
)
|
| 422 |
+
|
| 423 |
+
if not submitted:
|
| 424 |
+
return
|
| 425 |
+
|
| 426 |
+
with st.spinner("Кручу барабан (трансформер)..."):
|
| 427 |
+
results = predict_topics(title, abstract)
|
| 428 |
+
|
| 429 |
+
render_results(results)
|
| 430 |
+
|
| 431 |
+
|
| 432 |
+
if __name__ == "__main__":
|
| 433 |
+
|
| 434 |
+
# как удобно
|
| 435 |
+
from streamlit.runtime.scriptrunner_utils.script_run_context import get_script_run_ctx
|
| 436 |
+
|
| 437 |
+
if get_script_run_ctx(suppress_warning=True) is None:
|
| 438 |
+
import subprocess
|
| 439 |
+
import sys
|
| 440 |
+
|
| 441 |
+
raise SystemExit(
|
| 442 |
+
subprocess.call(
|
| 443 |
+
[sys.executable, "-m", "streamlit", "run", Path(__file__).resolve().as_posix(), *sys.argv[1:]]
|
| 444 |
+
)
|
| 445 |
+
)
|
| 446 |
+
main()
|
paper_classifier.py
ADDED
|
@@ -0,0 +1,73 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from __future__ import annotations
|
| 2 |
+
|
| 3 |
+
from typing import Iterable
|
| 4 |
+
|
| 5 |
+
BASE_MODEL_NAME = "distilbert/distilbert-base-cased"
|
| 6 |
+
DEFAULT_MODEL_DIR = "artifacts/distilbert-arxiv"
|
| 7 |
+
MAX_LENGTH = 256
|
| 8 |
+
TOP_P_THRESHOLD = 0.95
|
| 9 |
+
EXPECTED_ARXIV_CATEGORIES = [
|
| 10 |
+
"Computer Science",
|
| 11 |
+
"Physics",
|
| 12 |
+
"Mathematics",
|
| 13 |
+
"Statistics",
|
| 14 |
+
"Quantitative Biology",
|
| 15 |
+
"Quantitative Finance",
|
| 16 |
+
"Economics",
|
| 17 |
+
"Electrical Engineering and Systems Science",
|
| 18 |
+
]
|
| 19 |
+
EXAMPLES = {
|
| 20 |
+
"Graph Neural Networks": {
|
| 21 |
+
"title": "Message Passing Neural Networks for Molecular Property Prediction",
|
| 22 |
+
"abstract": (
|
| 23 |
+
"We introduce a graph-based neural architecture for supervised learning on "
|
| 24 |
+
"molecular graphs. The model propagates messages between atoms, aggregates "
|
| 25 |
+
"node states into a graph embedding, and predicts physical and chemical "
|
| 26 |
+
"properties with competitive accuracy."
|
| 27 |
+
),
|
| 28 |
+
},
|
| 29 |
+
"Physics": {
|
| 30 |
+
"title": "Topological phase transitions in two-dimensional quantum materials",
|
| 31 |
+
"abstract": (
|
| 32 |
+
"We study a lattice model with strong spin-orbit coupling and show how "
|
| 33 |
+
"interactions modify the phase diagram. Using numerical simulations we "
|
| 34 |
+
"characterize edge states, quantify transport signatures, and discuss "
|
| 35 |
+
"observable consequences for low-temperature experiments."
|
| 36 |
+
),
|
| 37 |
+
},
|
| 38 |
+
"Bioinformatics": {
|
| 39 |
+
"title": "Transformer models for protein function annotation from sequence",
|
| 40 |
+
"abstract": (
|
| 41 |
+
"We pretrain a transformer encoder on amino acid sequences and finetune it "
|
| 42 |
+
"for protein function prediction. The approach improves annotation quality "
|
| 43 |
+
"for underrepresented families and reveals biologically meaningful sequence "
|
| 44 |
+
"patterns."
|
| 45 |
+
),
|
| 46 |
+
},
|
| 47 |
+
}
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
def format_input_text(title: str, abstract: str) -> str:
|
| 51 |
+
title = title.strip()
|
| 52 |
+
abstract = abstract.strip()
|
| 53 |
+
|
| 54 |
+
parts: list[str] = []
|
| 55 |
+
if title:
|
| 56 |
+
parts.append(f"Title: {title}\nTitle summary: {title}")
|
| 57 |
+
if abstract:
|
| 58 |
+
parts.append(f"Abstract: {abstract}")
|
| 59 |
+
|
| 60 |
+
return "\n\n".join(parts)
|
| 61 |
+
|
| 62 |
+
|
| 63 |
+
def take_top_p(records: Iterable[dict[str, float]], threshold: float) -> list[dict[str, float]]:
|
| 64 |
+
selected: list[dict[str, float]] = []
|
| 65 |
+
cumulative = 0.0
|
| 66 |
+
|
| 67 |
+
for record in records:
|
| 68 |
+
selected.append(record)
|
| 69 |
+
cumulative += record["score"]
|
| 70 |
+
if cumulative >= threshold:
|
| 71 |
+
break
|
| 72 |
+
|
| 73 |
+
return selected
|
requirements.txt
CHANGED
|
@@ -1,3 +1,7 @@
|
|
| 1 |
-
|
| 2 |
-
|
| 3 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
streamlit
|
| 2 |
+
transformers
|
| 3 |
+
torch
|
| 4 |
+
safetensors
|
| 5 |
+
datasets
|
| 6 |
+
accelerate
|
| 7 |
+
scikit-learn
|
train_distilbert.py
ADDED
|
@@ -0,0 +1,229 @@
|
|
|
|
|
|
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|
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|
|
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|
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|
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|
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|
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|
|
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|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from __future__ import annotations
|
| 2 |
+
|
| 3 |
+
import ast
|
| 4 |
+
import json
|
| 5 |
+
from collections import Counter
|
| 6 |
+
from functools import partial
|
| 7 |
+
from pathlib import Path
|
| 8 |
+
|
| 9 |
+
import numpy as np
|
| 10 |
+
from datasets import Dataset, DatasetDict
|
| 11 |
+
from sklearn.metrics import accuracy_score, f1_score
|
| 12 |
+
from transformers import (
|
| 13 |
+
AutoModelForSequenceClassification,
|
| 14 |
+
AutoTokenizer,
|
| 15 |
+
DataCollatorWithPadding,
|
| 16 |
+
Trainer,
|
| 17 |
+
TrainingArguments,
|
| 18 |
+
set_seed,
|
| 19 |
+
)
|
| 20 |
+
|
| 21 |
+
from paper_classifier import BASE_MODEL_NAME, DEFAULT_MODEL_DIR, MAX_LENGTH, format_input_text
|
| 22 |
+
|
| 23 |
+
DATA_PATH = Path("arxivData.json")
|
| 24 |
+
OUTPUT_DIR = Path(DEFAULT_MODEL_DIR)
|
| 25 |
+
HF_CACHE_DIR = Path("/tmp/huggingface")
|
| 26 |
+
|
| 27 |
+
TITLE_FIELD = "title"
|
| 28 |
+
ABSTRACT_FIELD = "summary"
|
| 29 |
+
TAG_FIELD = "tag"
|
| 30 |
+
|
| 31 |
+
VALIDATION_SIZE = 0.1
|
| 32 |
+
NUM_TRAIN_EPOCHS = 4
|
| 33 |
+
LEARNING_RATE = 2e-5
|
| 34 |
+
WEIGHT_DECAY = 0.01
|
| 35 |
+
PER_DEVICE_TRAIN_BATCH_SIZE = 16
|
| 36 |
+
PER_DEVICE_EVAL_BATCH_SIZE = 32
|
| 37 |
+
LOGGING_STEPS = 50
|
| 38 |
+
SEED = 42
|
| 39 |
+
|
| 40 |
+
PREFIX_TO_LABEL = {
|
| 41 |
+
"adap-org": "Quantitative Biology",
|
| 42 |
+
"astro-ph": "Physics",
|
| 43 |
+
"cmp-lg": "Computer Science",
|
| 44 |
+
"cond-mat": "Physics",
|
| 45 |
+
"cs": "Computer Science",
|
| 46 |
+
"econ": "Economics",
|
| 47 |
+
"eess": "Electrical Engineering and Systems Science",
|
| 48 |
+
"gr-qc": "Physics",
|
| 49 |
+
"hep-ex": "Physics",
|
| 50 |
+
"hep-lat": "Physics",
|
| 51 |
+
"hep-ph": "Physics",
|
| 52 |
+
"hep-th": "Physics",
|
| 53 |
+
"math": "Mathematics",
|
| 54 |
+
"nlin": "Physics",
|
| 55 |
+
"nucl-th": "Physics",
|
| 56 |
+
"physics": "Physics",
|
| 57 |
+
"q-bio": "Quantitative Biology",
|
| 58 |
+
"q-fin": "Quantitative Finance",
|
| 59 |
+
"quant-ph": "Physics",
|
| 60 |
+
"stat": "Statistics",
|
| 61 |
+
}
|
| 62 |
+
|
| 63 |
+
|
| 64 |
+
def normalize_text(value):
|
| 65 |
+
return " ".join(str(value or "").split())
|
| 66 |
+
|
| 67 |
+
|
| 68 |
+
def parse_top_level_label(raw_tag):
|
| 69 |
+
if not raw_tag:
|
| 70 |
+
return None
|
| 71 |
+
|
| 72 |
+
try:
|
| 73 |
+
parsed_tags = ast.literal_eval(str(raw_tag))
|
| 74 |
+
except (SyntaxError, ValueError):
|
| 75 |
+
return None
|
| 76 |
+
|
| 77 |
+
if not isinstance(parsed_tags, list):
|
| 78 |
+
return None
|
| 79 |
+
|
| 80 |
+
for tag in parsed_tags:
|
| 81 |
+
if not isinstance(tag, dict):
|
| 82 |
+
continue
|
| 83 |
+
term = tag.get("term")
|
| 84 |
+
if not term:
|
| 85 |
+
continue
|
| 86 |
+
prefix = str(term).split(".")[0]
|
| 87 |
+
label = PREFIX_TO_LABEL.get(prefix)
|
| 88 |
+
if label:
|
| 89 |
+
return label
|
| 90 |
+
|
| 91 |
+
return None
|
| 92 |
+
|
| 93 |
+
|
| 94 |
+
def build_records():
|
| 95 |
+
with DATA_PATH.open("r", encoding="utf-8") as file:
|
| 96 |
+
raw_records = json.load(file)
|
| 97 |
+
|
| 98 |
+
prepared_records: list[dict[str, str]] = []
|
| 99 |
+
skipped = Counter()
|
| 100 |
+
|
| 101 |
+
for item in raw_records:
|
| 102 |
+
title = normalize_text(item.get(TITLE_FIELD))
|
| 103 |
+
abstract = normalize_text(item.get(ABSTRACT_FIELD))
|
| 104 |
+
label = parse_top_level_label(item.get(TAG_FIELD))
|
| 105 |
+
text = format_input_text(title, abstract)
|
| 106 |
+
prepared_records.append(
|
| 107 |
+
{
|
| 108 |
+
"text": text,
|
| 109 |
+
"label": label,
|
| 110 |
+
}
|
| 111 |
+
)
|
| 112 |
+
|
| 113 |
+
print(f"Loaded {len(prepared_records)}")
|
| 114 |
+
|
| 115 |
+
label_distribution = Counter(record["label"] for record in prepared_records)
|
| 116 |
+
print("Label distribution:", dict(label_distribution))
|
| 117 |
+
return prepared_records
|
| 118 |
+
|
| 119 |
+
|
| 120 |
+
def build_splits(records):
|
| 121 |
+
dataset = Dataset.from_list(records)
|
| 122 |
+
split = dataset.train_test_split(test_size=VALIDATION_SIZE, seed=SEED)
|
| 123 |
+
return DatasetDict(train=split["train"], validation=split["test"])
|
| 124 |
+
|
| 125 |
+
|
| 126 |
+
def preprocess(batch, *, tokenizer, label2id):
|
| 127 |
+
tokenized = tokenizer(batch["text"], truncation=True, max_length=MAX_LENGTH)
|
| 128 |
+
tokenized["labels"] = [label2id[label] for label in batch["label"]]
|
| 129 |
+
return tokenized
|
| 130 |
+
|
| 131 |
+
|
| 132 |
+
def compute_metrics(eval_prediction):
|
| 133 |
+
logits, labels = eval_prediction
|
| 134 |
+
predictions = np.argmax(logits, axis=-1)
|
| 135 |
+
return {
|
| 136 |
+
"accuracy": accuracy_score(labels, predictions),
|
| 137 |
+
"macro_f1": f1_score(labels, predictions, average="macro"),
|
| 138 |
+
}
|
| 139 |
+
|
| 140 |
+
|
| 141 |
+
def main() -> None:
|
| 142 |
+
if not DATA_PATH.exists():
|
| 143 |
+
raise FileNotFoundError(f"Dataset file not found: {DATA_PATH}")
|
| 144 |
+
|
| 145 |
+
set_seed(SEED)
|
| 146 |
+
OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
|
| 147 |
+
HF_CACHE_DIR.mkdir(parents=True, exist_ok=True)
|
| 148 |
+
|
| 149 |
+
records = build_records()
|
| 150 |
+
raw_splits = build_splits(records)
|
| 151 |
+
|
| 152 |
+
label_names = sorted({record["label"] for record in records})
|
| 153 |
+
label2id = {label: index for index, label in enumerate(label_names)}
|
| 154 |
+
id2label = {index: label for label, index in label2id.items()}
|
| 155 |
+
|
| 156 |
+
tokenizer = AutoTokenizer.from_pretrained(
|
| 157 |
+
BASE_MODEL_NAME,
|
| 158 |
+
cache_dir=HF_CACHE_DIR.as_posix(),
|
| 159 |
+
)
|
| 160 |
+
|
| 161 |
+
tokenized_splits = raw_splits.map(
|
| 162 |
+
partial(preprocess, tokenizer=tokenizer, label2id=label2id),
|
| 163 |
+
batched=True,
|
| 164 |
+
remove_columns=raw_splits["train"].column_names,
|
| 165 |
+
)
|
| 166 |
+
|
| 167 |
+
model = AutoModelForSequenceClassification.from_pretrained(
|
| 168 |
+
BASE_MODEL_NAME,
|
| 169 |
+
cache_dir=HF_CACHE_DIR.as_posix(),
|
| 170 |
+
num_labels=len(label_names),
|
| 171 |
+
id2label=id2label,
|
| 172 |
+
label2id=label2id,
|
| 173 |
+
)
|
| 174 |
+
data_collator = DataCollatorWithPadding(tokenizer=tokenizer)
|
| 175 |
+
|
| 176 |
+
training_args = TrainingArguments(
|
| 177 |
+
output_dir=OUTPUT_DIR.as_posix(),
|
| 178 |
+
do_train=True,
|
| 179 |
+
do_eval=True,
|
| 180 |
+
eval_strategy="epoch",
|
| 181 |
+
save_strategy="epoch",
|
| 182 |
+
logging_strategy="steps",
|
| 183 |
+
logging_steps=LOGGING_STEPS,
|
| 184 |
+
learning_rate=LEARNING_RATE,
|
| 185 |
+
weight_decay=WEIGHT_DECAY,
|
| 186 |
+
num_train_epochs=NUM_TRAIN_EPOCHS,
|
| 187 |
+
per_device_train_batch_size=PER_DEVICE_TRAIN_BATCH_SIZE,
|
| 188 |
+
per_device_eval_batch_size=PER_DEVICE_EVAL_BATCH_SIZE,
|
| 189 |
+
load_best_model_at_end=True,
|
| 190 |
+
metric_for_best_model="macro_f1",
|
| 191 |
+
greater_is_better=True,
|
| 192 |
+
save_total_limit=2,
|
| 193 |
+
report_to=[],
|
| 194 |
+
seed=SEED,
|
| 195 |
+
)
|
| 196 |
+
|
| 197 |
+
trainer = Trainer(
|
| 198 |
+
model=model,
|
| 199 |
+
args=training_args,
|
| 200 |
+
train_dataset=tokenized_splits["train"],
|
| 201 |
+
eval_dataset=tokenized_splits["validation"],
|
| 202 |
+
processing_class=tokenizer,
|
| 203 |
+
data_collator=data_collator,
|
| 204 |
+
compute_metrics=compute_metrics,
|
| 205 |
+
)
|
| 206 |
+
|
| 207 |
+
trainer.train()
|
| 208 |
+
metrics = trainer.evaluate()
|
| 209 |
+
trainer.save_model(OUTPUT_DIR.as_posix())
|
| 210 |
+
tokenizer.save_pretrained(OUTPUT_DIR.as_posix())
|
| 211 |
+
|
| 212 |
+
summary_path = OUTPUT_DIR / "training_summary.json"
|
| 213 |
+
summary = {
|
| 214 |
+
"base_model": BASE_MODEL_NAME,
|
| 215 |
+
"data_path": DATA_PATH.as_posix(),
|
| 216 |
+
"output_dir": OUTPUT_DIR.as_posix(),
|
| 217 |
+
"title_field": TITLE_FIELD,
|
| 218 |
+
"abstract_field": ABSTRACT_FIELD,
|
| 219 |
+
"tag_field": TAG_FIELD,
|
| 220 |
+
"labels": label_names,
|
| 221 |
+
"metrics": metrics,
|
| 222 |
+
}
|
| 223 |
+
summary_path.write_text(json.dumps(summary, indent=2), encoding="utf-8")
|
| 224 |
+
|
| 225 |
+
print(json.dumps(summary, indent=2))
|
| 226 |
+
|
| 227 |
+
|
| 228 |
+
if __name__ == "__main__":
|
| 229 |
+
main()
|