smftools 0.1.7__py3-none-any.whl → 0.2.3__py3-none-any.whl

smftools/tools/models/sklearn_models.py

@@ -1,40 +0,0 @@
-from sklearn.ensemble import RandomForestClassifier
-from sklearn.naive_bayes import GaussianNB
-from sklearn.metrics import (
-    roc_curve, precision_recall_curve, auc, f1_score, confusion_matrix
-)
-from sklearn.utils.class_weight import compute_class_weight
-
-import numpy as np
-
-class SklearnModelWrapper:
-    def __init__(self, model):
-        self.model = model
-
-    def fit(self, X_train, y_train):
-        self.model.fit(X_train, y_train)
-
-    def predict(self, X):
-        return self.model.predict(X)
-
-    def predict_proba(self, X):
-        return self.model.predict_proba(X)
-
-    def evaluate(self, X_test, y_test):
-        probs = self.predict_proba(X_test)[:, 1]
-        preds = self.predict(X_test)
-
-        fpr, tpr, _ = roc_curve(y_test, probs)
-        precision, recall, _ = precision_recall_curve(y_test, probs)
-        f1 = f1_score(y_test, preds)
-        auc_score = auc(fpr, tpr)
-        pr_auc = auc(recall, precision)
-        cm = confusion_matrix(y_test, preds)
-        pos_freq = np.mean(y_test == 1)
-        pr_auc_norm = pr_auc / pos_freq
-
-        return {
-            "fpr": fpr, "tpr": tpr, "precision": precision, "recall": recall,
-            "f1": f1, "auc": auc_score, "pr_auc": pr_auc,
-            "pr_auc_norm": pr_auc_norm, "confusion_matrix": cm
-        }

smftools/tools/models/transformer.py

@@ -1,133 +0,0 @@
-import torch
-import torch.nn as nn
-from .base import BaseTorchModel
-from .positional import PositionalEncoding 
-from ..utils.grl import grad_reverse
-
-    
-class BaseTransformer(BaseTorchModel):
-    def __init__(self, input_dim, model_dim, num_heads=4, num_layers=2, seq_len=None, use_learnable_pos=False, **kwargs):
-        super().__init__(**kwargs)
-        # Input FC layer to map D_input to D_model
-        self.input_fc = nn.Linear(input_dim, model_dim)
-
-        if use_learnable_pos:
-            assert seq_len is not None, "Must provide seq_len if use_learnable_pos=True"
-            self.pos_embed = nn.Parameter(torch.randn(seq_len, model_dim))  # (S, D)
-            self.pos_encoder = None
-        else:
-            self.pos_encoder = PositionalEncoding(model_dim)
-            self.pos_embed = None
-
-        # Specify the transformer encoder structure
-        encoder_layer = nn.TransformerEncoderLayer(d_model=model_dim, nhead=num_heads, batch_first=False)
-        # Stack the transformer encoder layers
-        self.transformer = nn.TransformerEncoder(encoder_layer, num_layers=num_layers)
-
-    def encode(self, x, mask=None):
-        """
-        x: (B, S, D_input)
-        mask: (B, S) optional
-        """
-        x = self.input_fc(x)  # (B, S, D_model)
-        if self.pos_embed is not None:
-            x = x + self.pos_embed.unsqueeze(0).to(x.device)  # (B, S, D_model)
-        elif self.pos_encoder is not None:
-            x = self.pos_encoder(x)  # (B, S, D_model)
-        if mask is not None:
-            x = x * mask.unsqueeze(-1)  # (B, S, D_model)
-        x = x.permute(1, 0, 2)  # (S, B, D_model)
-        encoded = self.transformer(x)  # (S, B, D_model)
-        return encoded.permute(1, 0, 2)  # (B, S, D_model)
-    
-class TransformerClassifier(BaseTransformer):
-    def __init__(self, input_dim, model_dim, num_classes, num_heads=4, num_layers=2, **kwargs):
-        super().__init__(input_dim, model_dim, num_heads, num_layers, **kwargs)
-        # Classification head
-        self.cls_head = nn.Linear(model_dim, num_classes)
-
-    def forward(self, x):
-        """
-        x: (batch, seq_len, input_dim)
-        """
-        encoded = self.encode(x) # -> (B, S, D_model)
-        pooled = encoded.mean(dim=1) # -> (B, D_model)
-        return self.cls_head(pooled) # -> (B, C)
-    
-class DANNTransformerClassifier(TransformerClassifier):
-    def __init__(self, input_dim, model_dim, num_classes, n_domains, **kwargs):
-        super().__init__(input_dim, model_dim, num_classes, **kwargs)
-        self.domain_classifier = nn.Sequential(
-            nn.Linear(model_dim, 128),
-            nn.ReLU(),
-            nn.Linear(128, n_domains)
-        )
-
-    def forward(self, x, alpha=1.0):
-        encoded = self.encode(x)  # (B, S, D_model)
-        pooled = encoded.mean(dim=1)  # (B, D_model)
-
-        class_logits = self.cls_head(pooled)
-        domain_logits = self.domain_classifier(grad_reverse(pooled, alpha))
-
-        return class_logits, domain_logits
-
-class MaskedTransformerPretrainer(BaseTransformer):
-    def __init__(self, input_dim, model_dim, num_heads=4, num_layers=2, **kwargs):
-        super().__init__(input_dim, model_dim, num_heads, num_layers, **kwargs)
-        self.decoder = nn.Linear(model_dim, input_dim)
-
-    def forward(self, x, mask):
-        """
-        x: (batch, seq_len, input_dim)
-        mask: (batch, seq_len) optional
-        """
-        if x.dim() == 2:
-            x = x.unsqueeze(-1)
-        encoded = self.encode(x, mask=mask) # -> (B, S, D_model)
-        return self.decoder(encoded) # -> (B, D_input)
-    
-class DANNTransformer(BaseTransformer):
-    """
-    """
-    def __init__(self, seq_len, model_dim, n_heads, n_layers, n_domains):
-        super().__init__(
-            input_dim=1,  # 1D scalar input per token
-            model_dim=model_dim,
-            num_heads=n_heads,
-            num_layers=n_layers,
-            seq_len=seq_len,
-            use_learnable_pos=True  # enables learnable pos_embed in base
-        )
-
-        # Reconstruction head
-        self.recon_head = nn.Linear(model_dim, 1)
-
-        # Domain classification head
-        self.domain_classifier = nn.Sequential(
-            nn.Linear(model_dim, 128),
-            nn.ReLU(),
-            nn.Linear(128, n_domains)
-        )
-
-    def forward(self, x, alpha=1.0):
-        """
-        x: Tensor of shape (B, S) or (B, S, 1)
-        alpha: GRL coefficient (float)
-        """
-        if x.dim() == 2:
-            x = x.unsqueeze(-1)  # (B, S, 1)
-
-        # Encode sequence
-        h = self.encode(x)  # (B, S, D_model)
-
-        # Head 1: Reconstruction
-        recon = self.recon_head(h).squeeze(-1)  # (B, S)
-
-        # Head 2: Domain classification via GRL
-        pooled = h.mean(dim=1)  # (B, D_model)
-        rev = grad_reverse(pooled, alpha)
-        domain_logits = self.domain_classifier(rev)  # (B, n_batches)
-
-        return recon, domain_logits
-    

smftools/tools/training/__init__.py

@@ -1 +0,0 @@
-from .train_lightning_model import train_lightning_model

smftools/tools/training/train_lightning_model.py

@@ -1,47 +0,0 @@
-import torch
-from pytorch_lightning import Trainer
-from pytorch_lightning.callbacks import EarlyStopping, ModelCheckpoint
-
-def train_lightning_model(
-    model,
-    datamodule,
-    max_epochs=20,
-    patience=5,
-    monitor_metric="val_loss",
-    checkpoint_path=None,
-):
-    # Device logic
-    if torch.cuda.is_available():
-        accelerator = "gpu"
-        devices = 1
-    elif torch.backends.mps.is_available():
-        accelerator = "mps"
-        devices = 1
-    else:
-        accelerator = "cpu"
-        devices = 1
-
-    # Callbacks
-    callbacks = [
-        EarlyStopping(monitor=monitor_metric, patience=patience, mode="min"),
-    ]
-    if checkpoint_path:
-        callbacks.append(ModelCheckpoint(
-            dirpath=checkpoint_path,
-            filename="{epoch}-{val_loss:.4f}",
-            monitor=monitor_metric,
-            save_top_k=1,
-            mode="min",
-        ))
-
-    # Trainer setup
-    trainer = Trainer(
-        max_epochs=max_epochs,
-        callbacks=callbacks,
-        accelerator=accelerator,
-        devices=devices,
-        log_every_n_steps=10,
-    )
-    trainer.fit(model, datamodule=datamodule)
-    
-    return trainer

smftools-0.1.7.dist-info/RECORD

@@ -1,136 +0,0 @@
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-smftools/datasets/__init__.py,sha256=xkSTlPuakVYVCuRurif9BceNBDt6bsngJvvjI8757QI,142
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