Merge branch 'main' of github.com:BojarLab/GIFFLAR

configs/lgi/test.yaml

@@ -0,0 +1,18 @@
+seed: 42
+root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/data
+logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/logs
+origin: path/to/dataset
+model:
+  glycan_encoder:
+    name: gifflar
+    feat_dim: 128
+    hidden_dim: 1024
+    batch_size: 256
+    num_layers: 8
+    pooling: global_pool
+  lectin_encoder:
+    name: esm
+    layer_num: 11
+  epochs: 100
+  learning_rate: 0.001
+  optimizer: Adam

experiments/aquire_lgi_dataset.py

@@ -1,13 +1,27 @@
-from glycowork.glycan_data.loader import glycan_binding as lgi
+import pickle
 
-import pandas as pd
 import numpy as np
+from glycowork.glycan_data.loader import glycan_binding as lgi
 
 
 # Use stack to convert to a Series with a MultiIndex
+lgi.index = lgi["target"]
+lgi.drop(columns=["target", "protein"], inplace=True)
 s = lgi.stack()
 
+glycans = {f"Gly{i:04d}": iupac for i, iupac in enumerate(lgi.columns[:-2])}
+glycans.update({iupac: f"Gly{i:04d}" for i, iupac in enumerate(lgi.columns[:-2])})
+
+lectins = {f"Lec{i:04d}": aa_seq for i, aa_seq in enumerate(lgi.index)}
+lectins.update({aa_seq: f"Lec{i:04d}" for i, aa_seq in enumerate(lgi.index)})
+
 # Convert the Series to a list of triplets (row, col, val)
-triplets = [(i, j, val) for (i, j), val in s.items()]
+data = []
+splits = np.random.choice(s.index, len(s))
+for i, ((aa_seq, iupac), val) in enumerate(s.items()):
+    data.append((lectins[aa_seq], glycans[iupac], val, splits[i]))
+    if i == 1000:
+        break
 
-print(len(triplets))
+with open("lgi_data.pkl", "wb") as f:
+    pickle.dump((data, lectins, glycans), f)

experiments/lgi_model.py

@@ -0,0 +1,140 @@
+from pathlib import Path
+from typing import Any, Literal
+
+import torch
+from pytorch_lightning import LightningModule
+from torch_geometric.data import HeteroData
+
+from experiments.protein_encoding import ENCODER_MAP, EMBED_SIZES
+from gifflar.data.utils import GlycanStorage
+from gifflar.model.base import GlycanGIN
+from gifflar.model.baselines.sweetnet import SweetNetLightning
+from gifflar.model.utils import GIFFLARPooling, get_prediction_head
+
+
+class LectinStorage(GlycanStorage):
+    def __init__(self, lectin_encoder: str, le_layer_num: int, path: str | None = None):
+        """
+        Initialize the wrapper around a dict.
+
+        Args:
+            path: Path to the directory. If there's a lectin_storage.pkl, it will be used to fill this object,
+                otherwise, such file will be created.
+        """
+        self.path = Path(path or "data") / f"{lectin_encoder}_{le_layer_num}.pkl"
+        self.encoder = ENCODER_MAP[lectin_encoder](le_layer_num)
+        self.data = self._load()
+
+    def query(self, aa_seq: str) -> torch.Tensor:
+        if aa_seq not in self.data:
+            try:
+                self.data[aa_seq] = self.encoder(aa_seq)
+            except:
+                self.data[aa_seq] = None
+        return self.data[aa_seq]
+
+
+class LGI_Model(LightningModule):
+    def __init__(
+            self,
+            glycan_encoder: GlycanGIN | SweetNetLightning,
+            lectin_encoder: str,
+            le_layer_num: int,
+            **kwargs: Any,
+    ):
+        """
+        Initialize the LGI model, a model for predicting lectin-glycan interactions.
+
+        Args:
+            glycan_encoder: The glycan encoder model
+            lectin_encoder: The lectin encoder model
+            le_layer_num: The number of layers to use in the lectin encoder
+            kwargs: Additional arguments
+        """
+        super().__init__()
+        self.glycan_encoder = glycan_encoder
+        self.glycan_pooling = GIFFLARPooling("global_mean")
+        self.lectin_encoder = lectin_encoder
+        self.le_layer_num = le_layer_num
+
+        self.lectin_embeddings = LectinStorage(lectin_encoder, le_layer_num)
+        self.combined_dim = glycan_encoder.hidden_dim + EMBED_SIZES[lectin_encoder]
+
+        self.head, self.loss, self.metrics = get_prediction_head(self.combined_dim, 1, "regression")
+
+    def forward(self, data: HeteroData) -> dict[str, torch.Tensor]:
+        glycan_node_embed = self.glycan_encoder(data)
+        glycan_graph_embed = self.glycan_pooling(glycan_node_embed, data.batch_dict)
+        lectin_embed = self.lectin_embeddings.query(data["aa_seq"])
+        combined = torch.cat([glycan_graph_embed, lectin_embed], dim=-1)
+        pred = self.head(combined)
+
+        return {
+            "glycan_node_embed": glycan_node_embed,
+            "glycan_graph_embed": glycan_graph_embed,
+            "lectin_embed": lectin_embed,
+            "pred": pred,
+        }
+
+    def shared_step(self, batch: HeteroData, stage: str) -> dict[str, torch.Tensor]:
+        """
+        Compute the shared step of the model.
+
+        Args:
+            data: The data to process
+            stage: The stage of the model
+
+        Returns:
+            A dictionary containing the loss and the metrics
+        """
+        fwd_dict = self(batch)
+        fwd_dict["labels"] = batch["y"]
+        fwd_dict["loss"] = self.loss(fwd_dict["pred"], fwd_dict["label"])
+        self.metrics[stage].update(fwd_dict["pred"], fwd_dict["label"])
+        self.log(f"{stage}/loss", fwd_dict["loss"])
+
+        return fwd_dict
+
+    def training_step(self, batch: HeteroData, batch_idx: int) -> dict[str, torch.Tensor]:
+        """Compute the training step of the model"""
+        return self.shared_step(batch, "train")
+
+    def validation_step(self, batch: HeteroData, batch_idx: int) -> dict[str, torch.Tensor]:
+        """Compute the validation step of the model"""
+        return self.shared_step(batch, "val")
+
+    def test_step(self, batch: HeteroData, batch_idx: int) -> dict[str, torch.Tensor]:
+        """Compute the testing step of the model"""
+        return self.shared_step(batch, "test")
+
+    def shared_end(self, stage: Literal["train", "val", "test"]):
+        """
+        Compute the shared end of the model.
+
+        Args:
+            stage: The stage of the model
+        """
+        metrics = self.metrics[stage].compute()
+        self.log_dict(metrics)
+        self.metrics[stage].reset()
+
+    def on_train_epoch_end(self) -> None:
+        """Compute the end of the training epoch"""
+        self.shared_end("train")
+
+    def on_validation_epoch_end(self) -> None:
+        """Compute the end of the validation"""
+        self.shared_end("val")
+
+    def on_test_epoch_end(self) -> None:
+        """Compute the end of the testing"""
+        self.shared_end("test")
+
+    def configure_optimizers(self):
+        """Configure the optimizer and the learning rate scheduler of the model"""
+        optimizer = torch.optim.Adam(self.parameters(), lr=1e-3)
+        return {
+            "optimizer": optimizer,
+            "lr_scheduler": torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode="min", factor=0.5, patience=5),
+            "monitor": "val/loss",
+        }

experiments/protein_encoding.py

@@ -0,0 +1,145 @@
+import re
+
+import torch
+from transformers import T5EncoderModel, AutoTokenizer, AutoModel, BertTokenizer, T5Tokenizer
+
+
+class PLMEncoder:
+    def __init__(self, layer_num: int):
+        self.layer_num = layer_num
+
+    def forward(self, seq: str) -> torch.Tensor:
+        pass
+
+    def __call__(self, *args, **kwargs):
+        self.forward(*args, **kwargs)
+
+
+class Ankh(PLMEncoder):
+    def __init__(self, layer_num: int):
+        super().__init__(layer_num)
+        self.tokenizer = AutoTokenizer.from_pretrained("ElnaggarLab/ankh-base")
+        self.model = T5EncoderModel.from_pretrained("ElnaggarLab/ankh-base")
+
+    def forward(self, seq: str) -> torch.Tensor:
+        outputs = self.tokenizer.batch_encode_plus(
+            [list(seq)],
+            add_special_tokens=True,
+            padding=True,
+            is_split_into_words=True,
+            return_tensors="pt",
+        )
+        with torch.no_grad():
+            ankh = self.model(
+                input_ids=outputs["input_ids"],
+                attention_mask=outputs["attention_mask"],
+                output_attentions=False,
+                output_hidden_states=True,
+            )
+        return ankh.hidden_states[self.layer_num][:, :-1].mean(dim=2)[0]
+
+
+class ESM(PLMEncoder):
+    def __init__(self, layer_num: int):
+        super().__init__(layer_num)
+        self.tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t33_650M_UR50D")
+        self.model = AutoModel.from_pretrained("facebook/esm2_t33_650M_UR50D")
+
+    def forward(self, seq: str) -> torch.Tensor:
+        a = self.tokenizer(seq)
+        with torch.no_grad():
+            esm = self.model(
+                torch.Tensor(a["input_ids"]).long().reshape(1, -1),
+                torch.Tensor(a["attention_mask"]).long().reshape(1, -1),
+                output_attentions=False,
+                output_hidden_states=True,
+            )
+        return esm.hidden_states[self.layer_num][:, 1:-1].mean(dim=2)[0]
+
+
+class ProtBERT(PLMEncoder):
+    def __init__(self, layer_num: int):
+        super().__init__(layer_num)
+        self.tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False)
+        self.model = AutoModel.from_pretrained("Rostlab/prot_bert")
+
+    def forward(self, seq: str) -> torch.Tensor:
+        sequence_w_spaces = ' '.join(seq)
+        encoded_input = self.tokenizer(
+            sequence_w_spaces,
+            return_tensors='pt'
+        )
+        with torch.no_grad():
+            protbert = self.model(
+                **encoded_input,
+                output_attentions=False,
+                output_hidden_states=True,
+            )
+        return protbert.hidden_states[self.layer_num][:, 1:-1].mean(dim=2)[0]
+
+
+class ProstT5(PLMEncoder):
+    def __init__(self, layer_num: int):
+        super().__init__(layer_num)
+        self.tokenizer = T5Tokenizer.from_pretrained("Rostlab/ProstT5")
+        self.model = T5EncoderModel.from_pretrained("Rostlab/ProstT5")
+
+    def forward(self, seq: str) -> torch.Tensor:
+        seq = [" ".join(list(re.sub(r"[UZOB]", "X", sequence))) for sequence in [seq]]
+        seq = ["<AA2fold>" + " " + s if s.isupper() else "<fold2AA>" + " " + s for s in seq]
+        ids = self.tokenizer.batch_encode_plus(
+            seq,
+            add_special_tokens=True,
+            padding="longest",
+            return_tensors='pt'
+        )
+        with torch.no_grad():
+            prostt5 = self.model(
+                ids.input_ids,
+                attention_mask=ids.attention_mask,
+                output_attentions=False,
+                output_hidden_states=True,
+            )
+        return prostt5.hidden_states[self.layer_num][:, 1:-1].mean(dim=2)[0]
+
+
+class AMPLIFY(PLMEncoder):
+    def __init__(self, layer_num: int):
+        super().__init__(layer_num)
+        self.tokenizer = AutoTokenizer.from_pretrained("chandar-lab/AMPLIFY_350M", trust_remote_code=True)
+        self.model = AutoModel.from_pretrained("chandar-lab/AMPLIFY_350M", trust_remote_code=True).to("cuda")
+
+    def forward(self, seq: str) -> torch.Tensor:
+        a = self.tokenizer.encode(seq, return_tensors="pt").to("cuda")
+        with torch.no_grad():
+            amplify = self.model(
+                a,
+                output_attentions=False,
+                output_hidden_states=True,
+            )
+        pass
+
+
+ENCODER_MAP = {
+    "Ankh": Ankh,
+    "ESM": ESM,
+    "ProtBert": ProtBERT,
+    "ProstT5": ProstT5,
+    "AMPLIFY": AMPLIFY,
+}
+
+EMBED_SIZES = {
+    "Ankh": 768,
+    "ESM": 1280,
+    "ProtBert": 1024,
+    "ProstT5": 1024,
+    "AMPLIFY": ...,
+}
+
+MAX_LAYERS = {
+    "Ankh": 49,
+    "ESM": 34,
+    "ProtBert": 31,
+    "ProstT5": 25,
+    "AMPLIFY": ...,
+}