Upload cafa_5_finetune_v2.ipynb

cafa_5_finetune_v2.ipynb

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+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Finetuneing ESM-2 Models for CAFA-5"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Finetune an ESM-2 Model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "from torch.utils.data import DataLoader, Dataset\n",
+    "from transformers import AutoTokenizer, EsmForSequenceClassification\n",
+    "from accelerate import Accelerator\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "from torchmetrics.classification import MultilabelF1Score\n",
+    "from sklearn.metrics import accuracy_score, precision_score, recall_score, average_precision_score\n",
+    "import datetime\n",
+    "import pandas as pd\n",
+    "\n",
+    "# Load the data\n",
+    "data = pd.read_csv(\"C:/Users/OWO/Desktop/amelie_vscode/cafa5/data/merged_protein_data.tsv\", sep=\"\\t\")\n",
+    "# Use only the first 100 entries\n",
+    "# data = data.head(100)\n",
+    "\n",
+    "# Initialize the accelerator\n",
+    "accelerator = Accelerator()\n",
+    "device = accelerator.device\n",
+    "\n",
+    "# Data Preprocessing\n",
+    "tokenizer = AutoTokenizer.from_pretrained(\"facebook/esm2_t6_8M_UR50D\")\n",
+    "MAX_LENGTH = tokenizer.model_max_length\n",
+    "NUM_EPOCHS = 3\n",
+    "LR = 5e-4\n",
+    "BATCH_SIZE = 2\n",
+    "\n",
+    "class ProteinDataset(Dataset):\n",
+    "    def __init__(self, sequences, labels):\n",
+    "        self.sequences = sequences\n",
+    "        self.labels = labels\n",
+    "\n",
+    "    def __len__(self):\n",
+    "        return len(self.sequences)\n",
+    "\n",
+    "    def __getitem__(self, idx):\n",
+    "        sequence = self.sequences[idx]\n",
+    "        label = self.labels[idx]\n",
+    "        encoding = tokenizer(sequence, return_tensors=\"pt\", padding='max_length', truncation=True, max_length=MAX_LENGTH)\n",
+    "        return {\n",
+    "            'input_ids': encoding['input_ids'].flatten(),\n",
+    "            'attention_mask': encoding['attention_mask'].flatten(),\n",
+    "            'labels': torch.tensor(label, dtype=torch.float)\n",
+    "        }\n",
+    "\n",
+    "def encode_labels(go_terms, unique_terms):\n",
+    "    encoded = []\n",
+    "    for terms in go_terms:\n",
+    "        encoding = [1 if term in terms else 0 for term in unique_terms]\n",
+    "        encoded.append(encoding)\n",
+    "    return encoded\n",
+    "\n",
+    "train_sequences, val_sequences, train_labels, val_labels = train_test_split(data['sequence'], data['term'], test_size=0.1)\n",
+    "\n",
+    "# Reset the indices\n",
+    "train_sequences = train_sequences.reset_index(drop=True)\n",
+    "val_sequences = val_sequences.reset_index(drop=True)\n",
+    "train_labels = train_labels.reset_index(drop=True)\n",
+    "val_labels = val_labels.reset_index(drop=True)\n",
+    "\n",
+    "unique_terms = list(set(term for sublist in data['term'] for term in sublist))\n",
+    "train_labels_encoded = encode_labels(train_labels, unique_terms)\n",
+    "val_labels_encoded = encode_labels(val_labels, unique_terms)\n",
+    "\n",
+    "train_dataset = ProteinDataset(train_sequences, train_labels_encoded)\n",
+    "val_dataset = ProteinDataset(val_sequences, val_labels_encoded)\n",
+    "\n",
+    "train_loader = DataLoader(train_dataset, batch_size=BATCH_SIZE, shuffle=True)\n",
+    "val_loader = DataLoader(val_dataset, batch_size=BATCH_SIZE)\n",
+    "\n",
+    "# Model Training\n",
+    "model = EsmForSequenceClassification.from_pretrained(\"facebook/esm2_t6_8M_UR50D\", num_labels=len(unique_terms), problem_type=\"multi_label_classification\")\n",
+    "model = model.to(device)\n",
+    "model.train()\n",
+    "\n",
+    "optimizer = torch.optim.AdamW(model.parameters(), lr=LR)\n",
+    "optimizer, model = accelerator.prepare(optimizer, model)\n",
+    "\n",
+    "# Initialize metrics\n",
+    "f1_metric = MultilabelF1Score(num_labels=len(unique_terms), threshold=0.5)\n",
+    "f1_metric = f1_metric.to(device)\n",
+    "\n",
+    "num_epochs = NUM_EPOCHS\n",
+    "\n",
+    "for epoch in range(num_epochs):\n",
+    "    total_loss = 0\n",
+    "    for batch in train_loader:\n",
+    "        optimizer.zero_grad()\n",
+    "        input_ids = batch['input_ids'].to(device)\n",
+    "        attention_mask = batch['attention_mask'].to(device)\n",
+    "        labels = batch['labels'].to(device)\n",
+    "\n",
+    "        outputs = model(input_ids=input_ids, attention_mask=attention_mask, labels=labels)\n",
+    "        loss = outputs.loss\n",
+    "        accelerator.backward(loss)\n",
+    "        optimizer.step()\n",
+    "\n",
+    "        total_loss += loss.item()\n",
+    "\n",
+    "    print(f'Epoch {epoch + 1}/{num_epochs}, Training loss: {total_loss/len(train_loader)}')\n",
+    "\n",
+    "    model.eval()\n",
+    "    predictions = []\n",
+    "    true_labels_list = []\n",
+    "    with torch.no_grad():\n",
+    "        for batch in val_loader:\n",
+    "            input_ids = batch['input_ids'].to(device)\n",
+    "            attention_mask = batch['attention_mask'].to(device)\n",
+    "            labels = batch['labels'].to(device)\n",
+    "\n",
+    "            outputs = model(input_ids=input_ids, attention_mask=attention_mask)\n",
+    "            logits = outputs.logits\n",
+    "            predictions.append(torch.sigmoid(logits))\n",
+    "            true_labels_list.append(labels)\n",
+    "\n",
+    "    predictions_tensor = torch.cat(predictions, dim=0).cpu().numpy()\n",
+    "    true_labels_tensor = torch.cat(true_labels_list, dim=0).cpu().numpy()\n",
+    "\n",
+    "    threshold = 0.5\n",
+    "    predictions_bin = (predictions_tensor > threshold).astype(int)\n",
+    "\n",
+    "    # Compute metrics\n",
+    "    val_f1 = f1_metric(torch.tensor(predictions_tensor).to(device), torch.tensor(true_labels_tensor).to(device))\n",
+    "    val_accuracy = accuracy_score(true_labels_tensor.flatten(), predictions_bin.flatten())\n",
+    "    val_precision = precision_score(true_labels_tensor.flatten(), predictions_bin.flatten(), average='micro')\n",
+    "    val_recall = recall_score(true_labels_tensor.flatten(), predictions_bin.flatten(), average='micro')\n",
+    "    val_auc = average_precision_score(true_labels_tensor, predictions_tensor, average='micro')\n",
+    "\n",
+    "    # Print metrics\n",
+    "    print(f'Validation F1 Score: {val_f1}')\n",
+    "    print(f'Validation Accuracy: {val_accuracy}')\n",
+    "    print(f'Validation Precision: {val_precision}')\n",
+    "    print(f'Validation Recall: {val_recall}')\n",
+    "    print(f'Validation AUC: {val_auc}')\n",
+    "\n",
+    "    timestamp = datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')\n",
+    "    model_path = f'./esm2_t6_8M_finetuned_cafa5_{timestamp}'\n",
+    "    model.save_pretrained(model_path)\n",
+    "    tokenizer.save_pretrained(model_path)\n",
+    "\n",
+    "    print(f'Model checkpoint saved to {model_path}')\n"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Save the Train/Validation Split Data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pickle\n",
+    "\n",
+    "# After you've created the train and validation splits:\n",
+    "data_splits = {\n",
+    "    \"train_sequences\": train_sequences,\n",
+    "    \"val_sequences\": val_sequences,\n",
+    "    \"train_labels\": train_labels,\n",
+    "    \"val_labels\": val_labels\n",
+    "}\n",
+    "\n",
+    "with open('data_splits.pkl', 'wb') as file:\n",
+    "    pickle.dump(data_splits, file)\n"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Reload the Data Later"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pickle\n",
+    "\n",
+    "# Load the data splits\n",
+    "with open('data_splits.pkl', 'rb') as file:\n",
+    "    data_splits = pickle.load(file)\n",
+    "\n",
+    "train_sequences = data_splits[\"train_sequences\"]\n",
+    "val_sequences = data_splits[\"val_sequences\"]\n",
+    "train_labels = data_splits[\"train_labels\"]\n",
+    "val_labels = data_splits[\"val_labels\"]\n",
+    "\n",
+    "# Now, the rest of your code can proceed as it is, \n",
+    "# with the train and validation sets loaded from the pickle file."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Data Preprocessing"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "from torch.utils.data import DataLoader, Dataset\n",
+    "from transformers import AutoTokenizer, EsmForSequenceClassification\n",
+    "from accelerate import Accelerator\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "from torchmetrics.classification import MultilabelF1Score\n",
+    "from sklearn.metrics import accuracy_score, precision_score, recall_score, average_precision_score\n",
+    "import datetime\n",
+    "import pandas as pd\n",
+    "\n",
+    "# Load the data\n",
+    "data = pd.read_csv(\"C:/Users/OWO/Desktop/amelie_vscode/cafa5/data/merged_protein_data.tsv\", sep=\"\\t\")\n",
+    "# Use only the first 100 entries\n",
+    "data = data.head(100)\n",
+    "\n",
+    "# Initialize the accelerator\n",
+    "accelerator = Accelerator()\n",
+    "device = accelerator.device\n",
+    "\n",
+    "# Data Preprocessing\n",
+    "tokenizer = AutoTokenizer.from_pretrained(\"facebook/esm2_t6_8M_UR50D\")\n",
+    "MAX_LENGTH = tokenizer.model_max_length\n",
+    "\n",
+    "class ProteinDataset(Dataset):\n",
+    "    def __init__(self, sequences, labels):\n",
+    "        self.sequences = sequences\n",
+    "        self.labels = labels\n",
+    "\n",
+    "    def __len__(self):\n",
+    "        return len(self.sequences)\n",
+    "\n",
+    "    def __getitem__(self, idx):\n",
+    "        sequence = self.sequences[idx]\n",
+    "        label = self.labels[idx]\n",
+    "        encoding = tokenizer(sequence, return_tensors=\"pt\", padding='max_length', truncation=True, max_length=MAX_LENGTH)\n",
+    "        return {\n",
+    "            'input_ids': encoding['input_ids'].flatten(),\n",
+    "            'attention_mask': encoding['attention_mask'].flatten(),\n",
+    "            'labels': torch.tensor(label, dtype=torch.float)\n",
+    "        }\n",
+    "\n",
+    "def encode_labels(go_terms, unique_terms):\n",
+    "    encoded = []\n",
+    "    for terms in go_terms:\n",
+    "        encoding = [1 if term in terms else 0 for term in unique_terms]\n",
+    "        encoded.append(encoding)\n",
+    "    return encoded\n",
+    "\n",
+    "# train_sequences, val_sequences, train_labels, val_labels = train_test_split(data['sequence'], data['term'], test_size=0.1)\n",
+    "\n",
+    "# Reset the indices\n",
+    "# train_sequences = train_sequences.reset_index(drop=True)\n",
+    "# val_sequences = val_sequences.reset_index(drop=True)\n",
+    "# train_labels = train_labels.reset_index(drop=True)\n",
+    "# val_labels = val_labels.reset_index(drop=True)\n",
+    "\n",
+    "unique_terms = list(set(term for sublist in data['term'] for term in sublist))\n",
+    "train_labels_encoded = encode_labels(train_labels, unique_terms)\n",
+    "val_labels_encoded = encode_labels(val_labels, unique_terms)\n",
+    "\n",
+    "train_dataset = ProteinDataset(train_sequences, train_labels_encoded)\n",
+    "val_dataset = ProteinDataset(val_sequences, val_labels_encoded)\n",
+    "\n",
+    "train_loader = DataLoader(train_dataset, batch_size=2, shuffle=True)\n",
+    "val_loader = DataLoader(val_dataset, batch_size=2)"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Fine-tune with LoRA"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from collections import Counter\n",
+    "from peft import get_peft_config, get_peft_model, LoraConfig\n",
+    "import datetime\n",
+    "from sklearn.metrics import accuracy_score, precision_score, recall_score, hamming_loss, average_precision_score\n",
+    "from torchmetrics.classification import MultilabelF1Score\n",
+    "\n",
+    "# Constants\n",
+    "MODEL_NAME = \"facebook/esm2_t6_8M_UR50D\" # Replace with your trained model above\n",
+    "BATCH_SIZE = 4\n",
+    "NUM_EPOCHS = 7\n",
+    "LR = 3e-5\n",
+    "\n",
+    "# Initialize model with LoRA\n",
+    "peft_config = LoraConfig(\n",
+    "    task_type=\"SEQ_CLS\", \n",
+    "    inference_mode=False, \n",
+    "    r=16, \n",
+    "    bias=\"none\",\n",
+    "    lora_alpha=16, \n",
+    "    lora_dropout=0.1, \n",
+    "    target_modules=[\"query\", \"key\", \"value\"]\n",
+    ")\n",
+    "\n",
+    "base_model = EsmForSequenceClassification.from_pretrained(MODEL_NAME, num_labels=len(unique_terms), problem_type=\"multi_label_classification\")\n",
+    "model = get_peft_model(base_model, peft_config)\n",
+    "model = model.to(accelerator.device)\n",
+    "\n",
+    "optimizer = torch.optim.AdamW(model.parameters(), lr=LR)\n",
+    "optimizer, model = accelerator.prepare(optimizer, model)\n",
+    "\n",
+    "f1_metric = MultilabelF1Score(num_labels=len(unique_terms), threshold=0.5)\n",
+    "f1_metric = f1_metric.to(device)\n",
+    "\n",
+    "# Compute Class Weights\n",
+    "def compute_class_weights(terms, term_to_id):\n",
+    "    all_terms = [term for terms_list in terms for term in terms_list]\n",
+    "    term_counts = Counter(all_terms)\n",
+    "    total_terms = sum(term_counts.values())\n",
+    "    class_weights = {term: total_terms / count for term, count in term_counts.items()}\n",
+    "    weights = torch.tensor([class_weights[term] for term in term_to_id.keys()], dtype=torch.float)\n",
+    "    normalized_weights = weights / weights.sum()\n",
+    "    return normalized_weights\n",
+    "\n",
+    "term_to_id = {term: idx for idx, term in enumerate(unique_terms)}\n",
+    "all_terms_combined = train_labels.tolist() + val_labels.tolist()\n",
+    "weights = compute_class_weights(all_terms_combined, term_to_id)\n",
+    "weights = weights.to(accelerator.device)\n",
+    "loss_criterion = torch.nn.BCEWithLogitsLoss(pos_weight=weights)\n",
+    "\n",
+    "# Training loop\n",
+    "for epoch in range(NUM_EPOCHS):\n",
+    "    # Training Phase\n",
+    "    model.train()\n",
+    "    total_train_loss = 0\n",
+    "    for batch in train_loader:\n",
+    "        optimizer.zero_grad()\n",
+    "        input_ids = batch['input_ids'].to(accelerator.device)\n",
+    "        attention_mask = batch['attention_mask'].to(accelerator.device)\n",
+    "        labels = batch['labels'].to(accelerator.device)\n",
+    "\n",
+    "        outputs = model(input_ids=input_ids, attention_mask=attention_mask, labels=labels)\n",
+    "        logits = outputs.logits\n",
+    "        loss = loss_criterion(logits, labels)\n",
+    "        accelerator.backward(loss)\n",
+    "        optimizer.step()\n",
+    "\n",
+    "        total_train_loss += loss.item()\n",
+    "\n",
+    "    avg_train_loss = total_train_loss / len(train_loader)\n",
+    "\n",
+    "    # Validation Phase\n",
+    "    model.eval()\n",
+    "    total_val_loss = 0\n",
+    "    predictions = []\n",
+    "    true_labels = []\n",
+    "    with torch.no_grad():\n",
+    "        for batch in val_loader:\n",
+    "            input_ids = batch['input_ids'].to(accelerator.device)\n",
+    "            attention_mask = batch['attention_mask'].to(accelerator.device)\n",
+    "            labels = batch['labels'].to(accelerator.device)\n",
+    "\n",
+    "            outputs = model(input_ids=input_ids, attention_mask=attention_mask, labels=labels)\n",
+    "            logits = outputs.logits\n",
+    "            loss = loss_criterion(logits, labels)\n",
+    "\n",
+    "            total_val_loss += loss.item()\n",
+    "            predictions.append(torch.sigmoid(logits).detach())\n",
+    "            true_labels.append(labels.detach())\n",
+    "\n",
+    "\n",
+    "    avg_val_loss = total_val_loss / len(val_loader)\n",
+    "    \n",
+    "    predictions_tensor = torch.cat(predictions, dim=0).cpu().numpy()\n",
+    "    true_labels_tensor = torch.cat(true_labels, dim=0).cpu().numpy()\n",
+    "\n",
+    "    threshold = 0.5\n",
+    "    predictions_bin = (predictions_tensor > threshold).astype(int)\n",
+    "\n",
+    "    val_f1 = f1_metric(torch.tensor(predictions_tensor).to(device), torch.tensor(true_labels_tensor).to(device))\n",
+    "    val_accuracy = accuracy_score(true_labels_tensor.flatten(), predictions_bin.flatten())\n",
+    "    val_precision = precision_score(true_labels_tensor.flatten(), predictions_bin.flatten(), average='micro')\n",
+    "    val_recall = recall_score(true_labels_tensor.flatten(), predictions_bin.flatten(), average='micro')\n",
+    "    val_auc = average_precision_score(true_labels_tensor, predictions_tensor, average='micro')\n",
+    "\n",
+    "    print(f\"Epoch {epoch + 1}/{NUM_EPOCHS} - Training Loss: {avg_train_loss:.4f} - Validation Loss: {avg_val_loss:.4f}\")\n",
+    "    print(f\"Validation Metrics - Accuracy: {val_accuracy:.4f} - Precision (Micro): {val_precision:.4f} - Recall (Micro): {val_recall:.4f} - AUC: {val_auc:.4f} - F1 Score: {val_f1:.4f}\")\n",
+    "\n",
+    "    timestamp = datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')\n",
+    "    # Save model and tokenizer. Note that Accelerator has a save method for models.\n",
+    "    model_path = f'./esm2_t6_8M_cafa5_lora_{timestamp}'\n",
+    "    model.save_pretrained(model_path)\n",
+    "    tokenizer.save_pretrained(model_path)\n",
+    "    model.base_model.save_pretrained(model_path)\n",
+    "    print(f'Model checkpoint saved to {model_path}')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "cafa_5",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.17"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}