@nahisaho/satori 0.14.0 → 0.15.0

package/src/.github/skills/scientific-deep-chemistry/SKILL.md

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+---
+name: scientific-deep-chemistry
+description: |
+  深層学習分子特性予測スキル。DeepChem による GCN/MPNN/AttentiveFP
+  分子特性予測・MoleculeNet ベンチマーク・ChemBERTa/GROVER
+  事前学習モデル・分子フィンガープリントフィーチャライザ。
+---
+
+# Scientific Deep Chemistry
+
+DeepChem を活用した深層学習ベース分子特性予測パイプラインを提供する。
+グラフニューラルネットワーク (GCN/MPNN/AttentiveFP)、MoleculeNet
+ベンチマーク、事前学習モデル (ChemBERTa/GROVER)。
+
+## When to Use
+
+- 分子の ADMET/物性を深層学習で予測するとき
+- MoleculeNet ベンチマークデータセットを使うとき
+- GCN / MPNN / AttentiveFP モデルを訓練するとき
+- ChemBERTa で分子表現学習を行うとき
+- 毒性予測 (Tox21, ToxCast) を行うとき
+- 薬理活性予測の分子特徴量を生成するとき
+
+---
+
+## Quick Start
+
+## 1. MoleculeNet データセット読込み
+
+```python
+import deepchem as dc
+import numpy as np
+import pandas as pd
+
+
+def load_moleculenet(dataset_name="delaney", featurizer="GraphConv",
+                     split="scaffold"):
+    """
+    MoleculeNet ベンチマークデータセット読込み。
+
+    Parameters:
+        dataset_name: str — データセット名
+          ("delaney", "tox21", "bbbp", "hiv", "muv", "pcba",
+           "sider", "clintox", "freesolv", "lipo")
+        featurizer: str — 特徴量化手法
+          ("GraphConv", "ECFP", "Weave", "MolGraphConv")
+        split: str — 分割方法 ("scaffold", "random", "stratified")
+
+    K-Dense: deepchem
+    """
+    loader_map = {
+        "delaney": dc.molnet.load_delaney,
+        "tox21": dc.molnet.load_tox21,
+        "bbbp": dc.molnet.load_bbbp,
+        "hiv": dc.molnet.load_hiv,
+        "muv": dc.molnet.load_muv,
+        "pcba": dc.molnet.load_pcba,
+        "sider": dc.molnet.load_sider,
+        "clintox": dc.molnet.load_clintox,
+        "freesolv": dc.molnet.load_freesolv,
+        "lipo": dc.molnet.load_lipo,
+    }
+
+    if dataset_name not in loader_map:
+        raise ValueError(f"Unknown dataset: {dataset_name}")
+
+    tasks, datasets, transformers = loader_map[dataset_name](
+        featurizer=featurizer, splitter=split
+    )
+    train, valid, test = datasets
+
+    print(f"MoleculeNet '{dataset_name}':")
+    print(f"  Tasks: {len(tasks)}")
+    print(f"  Train: {len(train)}, Valid: {len(valid)}, Test: {len(test)}")
+    print(f"  Featurizer: {featurizer}, Split: {split}")
+    return tasks, (train, valid, test), transformers
+```
+
+## 2. GCN モデル訓練
+
+```python
+def train_gcn(train_data, valid_data, tasks, n_epochs=50,
+              learning_rate=0.001, batch_size=64):
+    """
+    Graph Convolutional Network (GCN) モデル訓練。
+
+    Parameters:
+        train_data: dc.data.Dataset — 訓練データ
+        valid_data: dc.data.Dataset — 検証データ
+        tasks: list — タスク名リスト
+        n_epochs: int — エポック数
+    """
+    model = dc.models.GraphConvModel(
+        n_tasks=len(tasks),
+        mode="classification" if len(tasks) > 1 else "regression",
+        batch_size=batch_size,
+        learning_rate=learning_rate,
+    )
+
+    for epoch in range(n_epochs):
+        loss = model.fit(train_data, nb_epoch=1)
+        if (epoch + 1) % 10 == 0:
+            metric = dc.metrics.Metric(
+                dc.metrics.roc_auc_score if len(tasks) > 1
+                else dc.metrics.pearson_r2_score
+            )
+            train_score = model.evaluate(train_data, [metric])
+            valid_score = model.evaluate(valid_data, [metric])
+            print(f"  Epoch {epoch+1}: "
+                  f"train={list(train_score.values())[0]:.4f}, "
+                  f"valid={list(valid_score.values())[0]:.4f}")
+
+    return model
+```
+
+## 3. MPNN モデル訓練
+
+```python
+def train_mpnn(train_data, valid_data, tasks, n_epochs=50,
+               learning_rate=0.001):
+    """
+    Message Passing Neural Network (MPNN) 訓練。
+
+    Parameters:
+        train_data: dc.data.Dataset — GraphConv 特徴量訓練データ
+        valid_data: dc.data.Dataset — 検証データ
+        tasks: list — タスク名リスト
+    """
+    model = dc.models.MPNNModel(
+        n_tasks=len(tasks),
+        mode="classification" if len(tasks) > 1 else "regression",
+        learning_rate=learning_rate,
+        node_out_feats=64,
+        edge_hidden_feats=128,
+        num_step_message_passing=3,
+    )
+
+    model.fit(train_data, nb_epoch=n_epochs)
+
+    metric = dc.metrics.Metric(
+        dc.metrics.roc_auc_score if len(tasks) > 1
+        else dc.metrics.pearson_r2_score
+    )
+    valid_score = model.evaluate(valid_data, [metric])
+    print(f"MPNN: valid score = {list(valid_score.values())[0]:.4f}")
+    return model
+```
+
+## 4. AttentiveFP モデル訓練
+
+```python
+def train_attentivefp(train_data, valid_data, tasks, n_epochs=50,
+                      learning_rate=0.001, num_layers=2):
+    """
+    AttentiveFP (Attention-based Fingerprint) 訓練。
+
+    Parameters:
+        train_data: dc.data.Dataset — 訓練データ
+        valid_data: dc.data.Dataset — 検証データ
+        tasks: list — タスク名
+        num_layers: int — GATレイヤー数
+    """
+    model = dc.models.AttentiveFPModel(
+        n_tasks=len(tasks),
+        mode="classification" if len(tasks) > 1 else "regression",
+        learning_rate=learning_rate,
+        num_layers=num_layers,
+        graph_feat_size=200,
+        num_timesteps=2,
+    )
+
+    model.fit(train_data, nb_epoch=n_epochs)
+
+    metric = dc.metrics.Metric(
+        dc.metrics.roc_auc_score if len(tasks) > 1
+        else dc.metrics.pearson_r2_score
+    )
+    valid_score = model.evaluate(valid_data, [metric])
+    print(f"AttentiveFP: valid score = {list(valid_score.values())[0]:.4f}")
+    return model
+```
+
+## 5. ChemBERTa 分子表現学習
+
+```python
+def chemberta_embeddings(smiles_list, model_name="seyonec/ChemBERTa-zinc-base-v1"):
+    """
+    ChemBERTa で SMILES → 分子埋込みベクトル。
+
+    Parameters:
+        smiles_list: list — SMILES 文字列リスト
+        model_name: str — HuggingFace モデル名
+    """
+    from transformers import AutoTokenizer, AutoModel
+    import torch
+
+    tokenizer = AutoTokenizer.from_pretrained(model_name)
+    model = AutoModel.from_pretrained(model_name)
+    model.eval()
+
+    embeddings = []
+    batch_size = 32
+
+    for i in range(0, len(smiles_list), batch_size):
+        batch = smiles_list[i:i+batch_size]
+        inputs = tokenizer(batch, padding=True, truncation=True,
+                          max_length=512, return_tensors="pt")
+
+        with torch.no_grad():
+            outputs = model(**inputs)
+            # CLS トークン埋込み
+            cls_emb = outputs.last_hidden_state[:, 0, :].numpy()
+            embeddings.append(cls_emb)
+
+    embeddings = np.vstack(embeddings)
+    print(f"ChemBERTa: {len(smiles_list)} molecules → "
+          f"{embeddings.shape[1]}D embeddings")
+    return embeddings
+```
+
+## 6. モデル比較ベンチマーク
+
+```python
+def benchmark_models(dataset_name="tox21", models_to_test=None,
+                     n_epochs=30):
+    """
+    複数モデルのベンチマーク比較。
+
+    Parameters:
+        dataset_name: str — MoleculeNet データセット
+        models_to_test: list — テストモデル名
+        n_epochs: int — エポック数
+    """
+    if models_to_test is None:
+        models_to_test = ["GCN", "MPNN", "AttentiveFP"]
+
+    results = {}
+
+    for model_name in models_to_test:
+        featurizer = "GraphConv" if model_name != "ECFP_RF" else "ECFP"
+        tasks, (train, valid, test), transformers = load_moleculenet(
+            dataset_name, featurizer=featurizer
+        )
+
+        is_classification = len(tasks) > 1 or dataset_name in [
+            "tox21", "bbbp", "hiv", "sider", "clintox"
+        ]
+
+        if model_name == "GCN":
+            model = train_gcn(train, valid, tasks, n_epochs=n_epochs)
+        elif model_name == "MPNN":
+            model = train_mpnn(train, valid, tasks, n_epochs=n_epochs)
+        elif model_name == "AttentiveFP":
+            model = train_attentivefp(train, valid, tasks, n_epochs=n_epochs)
+        else:
+            continue
+
+        metric = dc.metrics.Metric(
+            dc.metrics.roc_auc_score if is_classification
+            else dc.metrics.pearson_r2_score
+        )
+        test_score = model.evaluate(test, [metric])
+        results[model_name] = list(test_score.values())[0]
+
+    print(f"\nBenchmark on '{dataset_name}':")
+    for name, score in sorted(results.items(), key=lambda x: -x[1]):
+        print(f"  {name}: {score:.4f}")
+    return results
+```
+
+## 7. 分子特性予測パイプライン
+
+```python
+def molecular_prediction_pipeline(smiles_list, property_name="solubility",
+                                   model_type="AttentiveFP"):
+    """
+    SMILES → 分子特性予測 統合パイプライン。
+
+    Parameters:
+        smiles_list: list — SMILES リスト
+        property_name: str — 予測対象物性
+        model_type: str — 使用モデル
+    """
+    # データセットマッピング
+    property_dataset = {
+        "solubility": "delaney",
+        "toxicity": "tox21",
+        "bbb_penetration": "bbbp",
+        "hiv_activity": "hiv",
+        "lipophilicity": "lipo",
+        "solvation_energy": "freesolv",
+    }
+
+    dataset_name = property_dataset.get(property_name, "delaney")
+
+    # 1) ベンチマークデータで訓練
+    tasks, (train, valid, test), transformers = load_moleculenet(
+        dataset_name, featurizer="GraphConv"
+    )
+
+    if model_type == "GCN":
+        model = train_gcn(train, valid, tasks)
+    elif model_type == "AttentiveFP":
+        model = train_attentivefp(train, valid, tasks)
+    else:
+        model = train_mpnn(train, valid, tasks)
+
+    # 2) 新規分子を予測
+    featurizer = dc.feat.MolGraphConvFeaturizer()
+    features = featurizer.featurize(smiles_list)
+    pred_dataset = dc.data.NumpyDataset(X=features)
+    predictions = model.predict(pred_dataset)
+
+    results = []
+    for smi, pred in zip(smiles_list, predictions):
+        results.append({
+            "smiles": smi,
+            "prediction": float(pred[0]) if pred.ndim > 1 else float(pred),
+            "property": property_name,
+            "model": model_type,
+        })
+
+    df = pd.DataFrame(results)
+    print(f"Predictions: {len(df)} molecules, property='{property_name}'")
+    return df
+```
+
+---
+
+## パイプライン統合
+
+```
+cheminformatics → deep-chemistry → drug-target-profiling
+  (RDKit/SMILES)   (GCN/MPNN/FP)   (ChEMBL/標的)
+       │                  │                ↓
+molecular-docking ───────┘         admet-pharmacokinetics
+  (AutoDock/Vina)      │            (ADMET予測)
+                       ↓
+                  md-simulation
+                  (分子動力学検証)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/predictions.csv` | 分子特性予測値 | → drug-target-profiling |
+| `results/benchmark.json` | モデルベンチマーク結果 | — |
+| `results/embeddings.npy` | ChemBERTa 埋込み | → cheminformatics |
+| `results/model/` | 訓練済みモデル | → admet-pharmacokinetics |