import os import torch import torch.nn as nn import pandas as pd import torch.nn.functional as F from lavis.models.protein_models.protein_function_opt import Blip2ProteinMistral from lavis.models.base_model import FAPMConfig import spaces import gradio as gr from esm_scripts.extract import run_demo from esm import pretrained, FastaBatchedDataset model_esm, alphabet = pretrained.load_model_and_alphabet('esm2_t36_3B_UR50D') model_esm.to('cuda') # Load the model # model = Blip2ProteinMistral(config=FAPMConfig(), esm_size='3b') # model.load_checkpoint("model/checkpoint_mf2.pth") # model.to('cuda') @spaces.GPU def generate_caption(protein, prompt): # Process the image and the prompt # with open('/home/user/app/example.fasta', 'w') as f: # f.write('>{}\n'.format("protein_name")) # f.write('{}\n'.format(protein.strip())) # os.system("python esm_scripts/extract.py esm2_t36_3B_UR50D /home/user/app/example.fasta /home/user/app --repr_layers 36 --truncation_seq_length 1024 --include per_tok") # esm_emb = run_demo(protein_name='protein_name', protein_seq=protein, # model=model_esm, alphabet=alphabet, # include='per_tok', repr_layers=[36], truncation_seq_length=1024) protein_name='protein_name' protein_seq=protein include='per_tok' repr_layers=[36] truncation_seq_length=1024 toks_per_batch=4096 print("start") dataset = FastaBatchedDataset([protein_name], [protein_seq]) print("dataset prepared") batches = dataset.get_batch_indices(toks_per_batch, extra_toks_per_seq=1) print("batches prepared") data_loader = torch.utils.data.DataLoader( dataset, collate_fn=alphabet.get_batch_converter(truncation_seq_length), batch_sampler=batches ) print(f"Read sequences") return_contacts = "contacts" in include assert all(-(model_esm.num_layers + 1) <= i <= model_esm.num_layers for i in repr_layers) repr_layers = [(i + model_esm.num_layers + 1) % (model_esm.num_layers + 1) for i in repr_layers] model_esm.eval() with torch.no_grad(): for batch_idx, (labels, strs, toks) in enumerate(data_loader): print( f"Processing {batch_idx + 1} of {len(batches)} batches ({toks.size(0)} sequences)" ) if torch.cuda.is_available(): toks = toks.to(device="cuda", non_blocking=True) out = model_esm(toks, repr_layers=repr_layers, return_contacts=return_contacts) logits = out["logits"].to(device="cpu") representations = { layer: t.to(device="cpu") for layer, t in out["representations"].items() } if return_contacts: contacts = out["contacts"].to(device="cpu") for i, label in enumerate(labels): result = {"label": label} truncate_len = min(truncation_seq_length, len(strs[i])) # Call clone on tensors to ensure tensors are not views into a larger representation # See https://github.com/pytorch/pytorch/issues/1995 if "per_tok" in include: result["representations"] = { layer: t[i, 1 : truncate_len + 1].clone() for layer, t in representations.items() } if "mean" in include: result["mean_representations"] = { layer: t[i, 1 : truncate_len + 1].mean(0).clone() for layer, t in representations.items() } if "bos" in include: result["bos_representations"] = { layer: t[i, 0].clone() for layer, t in representations.items() } if return_contacts: result["contacts"] = contacts[i, : truncate_len, : truncate_len].clone() esm_emb = result['representations'][36] print("esm embedding generated") esm_emb = F.pad(esm_emb.t(), (0, 1024 - len(esm_emb))).t().to('cuda') print("esm embedding processed") samples = {'name': ['protein_name'], 'image': torch.unsqueeze(esm_emb, dim=0), 'text_input': ['none'], 'prompt': [prompt]} # Generate the output # prediction = model.generate(samples, length_penalty=0., num_beams=15, num_captions=10, temperature=1., repetition_penalty=1.0) # return prediction return "test" # Define the FAPM interface description = """Quick demonstration of the FAPM model for protein function prediction. Upload an protein sequence to generate a function description. Modify the Prompt to provide the taxonomy information. The model used in this app is available at [Hugging Face Model Hub](https://huggingface.co/wenkai/FAPM) and the source code can be found on [GitHub](https://github.com/xiangwenkai/FAPM/tree/main).""" iface = gr.Interface( fn=generate_caption, inputs=[gr.Textbox(type="text", label="Upload sequence"), gr.Textbox(type="text", label="Prompt")], outputs=gr.Textbox(label="Generated description"), description=description ) # Launch the interface iface.launch()