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b/iterative_alignment_experiment_megascale/TrpB4/base_model_96/trpb_post_rd_2_9.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:23b7d0d4e167c24e773fa56ec97063f006d6b28f2246205df82a5da2373b7c65 +size 645912 diff --git a/iterative_alignment_experiment_megascale/automated_experiment.sh b/iterative_alignment_experiment_megascale/automated_experiment.sh new file mode 100644 index 0000000000000000000000000000000000000000..c6b6a9757590fadca26152405aff1f3b6cf60446 --- /dev/null +++ b/iterative_alignment_experiment_megascale/automated_experiment.sh @@ -0,0 +1,270 @@ +#!/bin/bash +#SBATCH -N 1 +#SBATCH -G 4 +#SBATCH -C GPU_MEM:80GB +#SBATCH -p rotskoff +#SBATCH -t 04-20:00:00 +#SBATCH --mem=320GB +#SBATCH -J alignment + +#source /home/groups/nsgray01/anaconda3/etc/profile.d/conda.sh +#conda activate proera +source /home/groups/nsgray01/MoLE/.venv/bin/activate + +target="DHFR" +base_model_path="/scratch/groups/rotskoff/sebastian/era/protein_era/111225BenchmarkWithMegascalePretrain/megascale_ckpts/best_model.ckpt" +round=0 + +# sample from the base model (in this case the Megascale pretrained model) 10 times +for i in {0..9}; do + echo "Running iteration $i for target $target" + # Run the Python script with the specified arguments + python sample_esm_first_round.py \ + --target $target \ + --num_samples 96 \ + --replicate "$i" +done + +# Make the first round alignment datasets for each model +echo "Creating alignment dataset for target $target" +python create_alignment_dataset_first_round.py --target $target + +# Train the first round models +cd $target + +for i in {0..9}; do + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "++train.lightning_model_args.better_energy=lower" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=${base_model_path}" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. + +# sample from the first round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) + +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# Make the second round alignment datasets for each model +round=1 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_second_round.py --target $target + +# Train the second round models +cd $target +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "++train.lightning_model_args.better_energy=lower" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=lightning_logs_round_0/${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. + +# sample from the second round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) + +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# Make the third round alignment datasets for each model +round=2 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_third_round.py --target $target + +# Train the third round models +cd $target +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "++train.lightning_model_args.better_energy=lower" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=lightning_logs_round_1/${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. +# sample from the third round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# make the fourth round alignment datasets for each model +round=3 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_fourth_round.py --target $target +# Train the fourth round models +cd $target +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "++train.lightning_model_args.better_energy=lower" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=lightning_logs_round_2/${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. +# sample from the fourth round trained models +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +echo "All rounds completed for target $target" diff --git a/iterative_alignment_experiment_megascale/compute_updated_logps.py b/iterative_alignment_experiment_megascale/compute_updated_logps.py new file mode 100644 index 0000000000000000000000000000000000000000..d2d2bb8307b0fe4d4ae1a722843a441786baf21f --- /dev/null +++ b/iterative_alignment_experiment_megascale/compute_updated_logps.py @@ -0,0 +1,160 @@ +import os +import torch +import numpy as np +import pandas as pd +import h5py +import re +from omegaconf import OmegaConf +import h5py +import lightning as L +from pera.nn import BidirectionalModel, sample_components_from_bidirectional_transformer, sample_perturbations, sample_embedding_perturbations +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +sequence_tokenizer = EsmSequenceTokenizer() + +import argparse +# set up parser +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +parser.add_argument('--num_samples', type=int, required=False, default=384, help='Number of samples to process (default: 100000)') +parser.add_argument('--alignment_round', type=int, required=False, default=1, help='Alignment round as an integer') +parser.add_argument('--version_number', type=str, required=False, default=1, help='Version number as a string') +parser.add_argument('--replicate', type=int, required=False, default=1, help='Replicate number as an integer') +args = parser.parse_args() + +target = args.target +alignment_round = args.alignment_round +version_number = args.version_number +num_samples = args.num_samples +replicate = args.replicate + +datasets = [f"{target}/base_model_{num_samples}"] +for i in range(alignment_round): + datasets.append(f"{target}/aligned_{i}_{num_samples}_{replicate}") + +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +sequence_tokenizer = EsmSequenceTokenizer() + +cfg_filename = f"{target}/lightning_logs_round_{alignment_round}/{version_number}/config.yaml" +network_filename = f"{target}/lightning_logs_round_{alignment_round}/{version_number}/checkpoints/best_model.ckpt" + +cfg = OmegaConf.load(cfg_filename) +# sampling_temperature = cfg["train"]["lightning_model_args"]["sampling_temperature"] +sampling_temperature=1 +OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) +esm_model = BidirectionalModel(cfg["nn"]["model"], + cfg["nn"]["model_args"], + **cfg["train"]["lightning_model_args"]).to(device) +esm_model.load_model_from_ckpt(network_filename) +esm_model.eval() +print("") +mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] +bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] +eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] +pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + +for data in datasets: + save_folder_name = data + + data = data.split("/")[0] + data = data.split("_")[0] + + os.makedirs(save_folder_name, exist_ok=True) + if not data.startswith("TrpB") and not data.startswith("DHFR"): + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + elif data.startswith("DHFR"): + print("Loading DHFR data...") + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + else: + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + if data != "GB1": + muts = df["muts"].iloc[0] + else: + muts = df["muts"].iloc[100000] + + numbers = re.findall(r'\d+', muts) + mask_indices = list(map(int, numbers)) + num_masks_per_sequence = num_samples // 4 + num_to_generate_per_mask = 4 + + + parent_sequence = torch.tensor(sequence_tokenizer.encode(parent_sequence_decoded, + add_special_tokens=True), device=device).unsqueeze(0).long() + sequence_length = parent_sequence.shape[1] + print(sequence_length, parent_sequence.shape, parent_sequence_decoded) + + print(save_folder_name) + + trpb = torch.load(f"./{save_folder_name}/trpb_{replicate}.pt") + all_unmasked_sequences_decoded = trpb["all_unmasked_sequences_decoded"] + all_unmasked_sequences = trpb["all_unmasked_sequences"] + all_masked_sequences = trpb["all_masked_sequences"] + all_unmasked_sequences = all_unmasked_sequences.reshape(-1, all_unmasked_sequences.shape[-1]) + + all_logps = [] + + print(all_masked_sequences.shape) + + for i in range(0, all_masked_sequences.shape[0], num_to_generate_per_mask): + masked_sequences = all_masked_sequences[i:i+num_to_generate_per_mask] + unmasked_sequences = all_unmasked_sequences[i:i+num_to_generate_per_mask] + + sequence_id = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((num_to_generate_per_mask, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((num_to_generate_per_mask), device=device) + + per_res_plddt = torch.zeros((num_to_generate_per_mask, sequence_length), device=device) + ss8_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + sasa_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + + function_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 16), device=device).long() + masked_indices = (masked_sequences == mask_token_sequence).float() + + with torch.no_grad(): + logits = esm_model.nn(sequence_tokens=masked_sequences, + structure_tokens=structure_tokens, + average_plddt=average_plddt, + per_res_plddt=per_res_plddt, + ss8_tokens=ss8_tokens, + sasa_tokens=sasa_tokens, + function_tokens=function_tokens, + residue_annotation_tokens=residue_annotation_tokens, + sequence_id=sequence_id, + bb_coords=coords)["sequence_logits"].detach() + logps = torch.nn.functional.log_softmax(logits/sampling_temperature, dim=-1) + logps = torch.gather(logps, dim=-1, index=unmasked_sequences.unsqueeze(-1)).squeeze(-1) + logps = (logps * masked_indices).sum(-1).detach() + + all_logps.append(logps) + + all_logps = torch.cat(all_logps).view(-1) + + print(all_logps.shape) + + + to_save = {"parent_sequence": parent_sequence, + "all_masked_sequences": all_masked_sequences, + "all_unmasked_sequences": all_unmasked_sequences, + "all_unmasked_sequences_decoded": all_unmasked_sequences_decoded, + "all_logps": all_logps} + torch.save(to_save, f"{save_folder_name}/trpb_post_rd_{alignment_round}_{replicate}.pt") \ No newline at end of file diff --git a/iterative_alignment_experiment_megascale/create_alignment_dataset_first_round.py b/iterative_alignment_experiment_megascale/create_alignment_dataset_first_round.py new file mode 100644 index 0000000000000000000000000000000000000000..79ee9b80d73152258091c695aaeedc10493328a8 --- /dev/null +++ b/iterative_alignment_experiment_megascale/create_alignment_dataset_first_round.py @@ -0,0 +1,165 @@ +import torch +import re +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +import h5py +import argparse +from omegaconf import OmegaConf +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +num_replicates = 10 +campaign_number = 0 # change this according to the campaign we are interested in +dataset_size = 96 # change this according to the dataset size we are interested in + +sequence_tokenizer = EsmSequenceTokenizer() + +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +args = parser.parse_args() +data = args.target + +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +print(data) +for i in range(num_replicates): + cfg_filename = f"./config.yaml" + cfg = OmegaConf.load(cfg_filename) + sampling_temperature=1 + OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) + mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] + bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] + eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] + pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + + else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + if data != "GB1": + muts = df["muts"].iloc[0] + else: + muts = df["muts"].iloc[100000] + + numbers = re.findall(r'\d+', muts) + mask_indices = list(map(int, numbers)) + # mask_indices = [i-1 for i in mask_indices] #convert to 0-based indexing + + fitness_scores = [] + + # Load from base_model_{dataset_size} + trpb_base = torch.load(f"./{data}/base_model_{dataset_size}/trpb_{i}.pt") + all_unmasked_sequences_decoded_base = trpb_base["all_unmasked_sequences_decoded"] + all_unmasked_sequences_base = trpb_base["all_unmasked_sequences"] + all_masked_sequences_base = trpb_base["all_masked_sequences"] + all_unmasked_sequences_base = all_unmasked_sequences_base.reshape(-1, all_unmasked_sequences_base.shape[-1]) + all_logps_base = trpb_base["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_base, all_unmasked_sequences_base): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + + # Concatenate the sequences and logps from all models + all_unmasked_sequences = all_unmasked_sequences_base.clone() + all_masked_sequences = all_masked_sequences_base.clone() + all_logps = all_logps_base.clone() + + all_fitness_scores = fitness_scores + + # Check for duplicates in all_unmasked_sequences + unique_sequences, counts = torch.unique(all_unmasked_sequences, dim=0, return_counts=True) + num_duplicates = torch.sum(counts > 1).item() + print(f"Number of duplicate sequences: {num_duplicates}") + + all_fitness_scores = np.array(all_fitness_scores) + all_fitness_scores = np.where(all_fitness_scores > 0, -np.log(all_fitness_scores), 10) + + sampling_temperature = 1 # hard-coding a sampling temperature of 1 for mixed-temperature alignment + + sequence_length = all_unmasked_sequences.shape[1] + + sequence_id = torch.ones((all_unmasked_sequences.shape[0], sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((1, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((all_unmasked_sequences.shape[0], sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((1), device=device) + + per_res_plddt = torch.zeros((1, sequence_length), device=device) + ss8_tokens = torch.zeros((1, sequence_length), device=device).long() + sasa_tokens = torch.zeros((1, sequence_length), device=device).long() + + function_tokens = torch.zeros((1, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((1, sequence_length, 16), device=device).long() + + + with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3_{i}.hdf5", "w") as f: + masked_sequence_tokens = f.create_dataset("masked_sequence_tokens", data=all_masked_sequences.cpu().numpy()) + unmasked_sequence_tokens = f.create_dataset("unmasked_sequence_tokens", data=all_unmasked_sequences.cpu().numpy()) + sequence_id = f.create_dataset("sequence_id", data=sequence_id.cpu().numpy()) + structure_tokens = f.create_dataset("structural_tokens", data=structure_tokens.cpu().numpy()) + coords = f.create_dataset("bb_coords", data=coords.cpu().numpy()) + average_plddt = f.create_dataset("average_plddt", data=average_plddt.cpu().numpy()) + per_res_plddt = f.create_dataset("per_res_plddt", data=per_res_plddt.cpu().numpy()) + ss8_tokens = f.create_dataset("ss8_tokens", data=ss8_tokens.cpu().numpy()) + sasa_tokens = f.create_dataset("sasa_tokens", data=sasa_tokens.cpu().numpy()) + function_tokens = f.create_dataset("function_tokens", data=function_tokens.cpu().numpy()) + residue_annotation_tokens = f.create_dataset("residue_annotation_tokens", data=residue_annotation_tokens.cpu().numpy()) + + ref_logps = f.create_dataset("ref_logps", data=all_logps.cpu().numpy()) + energies = f.create_dataset("energies", data=all_fitness_scores) + + + f.attrs["num_prompts"] = 1 + f.attrs["num_examples_per_prompt"] = masked_sequence_tokens.shape[0] + f.attrs["fixed_bb_coords"] = True + f.attrs["fixed_average_plddt"] = True + f.attrs["fixed_per_res_plddt"] = True + f.attrs["fixed_ss8_tokens"] = True + f.attrs["fixed_sasa_tokens"] = True + f.attrs["fixed_function_tokens"] = True + f.attrs["fixed_residue_annotation_tokens"] = True + f.attrs["fixed_structural_tokens"] = True + f.attrs["sampling_temperature"] = sampling_temperature + diff --git a/iterative_alignment_experiment_megascale/make_alignment_dataset_fourth_round.py b/iterative_alignment_experiment_megascale/make_alignment_dataset_fourth_round.py new file mode 100644 index 0000000000000000000000000000000000000000..5cd33beba111be167f4ad98de90c995a0d24ce9b --- /dev/null +++ b/iterative_alignment_experiment_megascale/make_alignment_dataset_fourth_round.py @@ -0,0 +1,268 @@ +import torch +import re +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +import h5py +import argparse +from omegaconf import OmegaConf +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +num_replicates = 10 +campaign_number = 3 # change this according to the campaign we are interested in +dataset_size = 96 # change this according to the dataset size we are interested in + +sequence_tokenizer = EsmSequenceTokenizer() + +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +args = parser.parse_args() +data = args.target + +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +print(data) +for i in range(num_replicates): + cfg_filename = f"./config.yaml" + cfg = OmegaConf.load(cfg_filename) + sampling_temperature=1 + OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) + mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] + bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] + eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] + pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + + else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + if data != "GB1": + muts = df["muts"].iloc[0] + else: + muts = df["muts"].iloc[100000] + + numbers = re.findall(r'\d+', muts) + mask_indices = list(map(int, numbers)) + # mask_indices = [i-1 for i in mask_indices] #convert to 0-based indexing + + fitness_scores = [] + + # Load from base_model_{dataset_size} + trpb_base = torch.load(f"./{data}/base_model_{dataset_size}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_base = trpb_base["all_unmasked_sequences_decoded"] + all_unmasked_sequences_base = trpb_base["all_unmasked_sequences"] + all_masked_sequences_base = trpb_base["all_masked_sequences"] + all_unmasked_sequences_base = all_unmasked_sequences_base.reshape(-1, all_unmasked_sequences_base.shape[-1]) + all_logps_base = trpb_base["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_base, all_unmasked_sequences_base): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_0_{dataset_size} + trpb_aligned = torch.load(f"./{data}/aligned_{campaign_number-3}_{dataset_size}_{i}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_aligned_0 = trpb_aligned["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_0 = trpb_aligned["all_unmasked_sequences"] + all_masked_sequences_aligned_0 = trpb_aligned["all_masked_sequences"] + all_unmasked_sequences_aligned_0 = all_unmasked_sequences_aligned_0.reshape(-1, all_unmasked_sequences_aligned_0.shape[-1]) + all_logps_aligned_0 = trpb_aligned["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_0, all_unmasked_sequences_aligned_0): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_1_{dataset_size} + trpb_aligned_1 = torch.load(f"./{data}/aligned_{campaign_number-2}_{dataset_size}_{i}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_aligned_1 = trpb_aligned_1["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_1 = trpb_aligned_1["all_unmasked_sequences"] + all_masked_sequences_aligned_1 = trpb_aligned_1["all_masked_sequences"] + all_unmasked_sequences_aligned_1 = all_unmasked_sequences_aligned_1.reshape(-1, all_unmasked_sequences_aligned_1.shape[-1]) + all_logps_aligned_1 = trpb_aligned_1["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_1, all_unmasked_sequences_aligned_1): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_2_{dataset_size} + trpb_aligned_2 = torch.load(f"./{data}/aligned_{campaign_number-1}_{dataset_size}_{i}/trpb_{i}.pt") + all_unmasked_sequences_decoded_aligned_2 = trpb_aligned_2["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_2 = trpb_aligned_2["all_unmasked_sequences"] + all_masked_sequences_aligned_2 = trpb_aligned_2["all_masked_sequences"] + all_unmasked_sequences_aligned_2 = all_unmasked_sequences_aligned_2.reshape(-1, all_unmasked_sequences_aligned_2.shape[-1]) + all_logps_aligned_2 = trpb_aligned_2["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_2, all_unmasked_sequences_aligned_2): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + + # Concatenate the sequences and logps from all models + all_unmasked_sequences = torch.cat((all_unmasked_sequences_base, all_unmasked_sequences_aligned_0, all_unmasked_sequences_aligned_1, all_unmasked_sequences_aligned_2),dim=0)# + all_masked_sequences = torch.cat((all_masked_sequences_base, all_masked_sequences_aligned_0, all_masked_sequences_aligned_1, all_masked_sequences_aligned_2),dim=0)# + print(all_logps_base.shape, all_logps_aligned_0.shape, all_logps_aligned_1.shape, all_logps_aligned_2.shape)# + all_logps = torch.cat((all_logps_base, all_logps_aligned_0, all_logps_aligned_1, all_logps_aligned_2),dim=0)# + + all_fitness_scores = fitness_scores + + # Check for duplicates in all_unmasked_sequences + unique_sequences, counts = torch.unique(all_unmasked_sequences, dim=0, return_counts=True) + num_duplicates = torch.sum(counts > 1).item() + print(f"Number of duplicate sequences: {num_duplicates}") + + all_fitness_scores = np.array(all_fitness_scores) + all_fitness_scores = np.where(all_fitness_scores > 0, -np.log(all_fitness_scores), 10) + + sampling_temperature = 1 # hard-coding a sampling temperature of 1 for mixed-temperature alignment + + sequence_length = all_unmasked_sequences.shape[1] + + sequence_id = torch.ones((all_unmasked_sequences.shape[0], sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((1, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((1, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((1), device=device) + + per_res_plddt = torch.zeros((1, sequence_length), device=device) + ss8_tokens = torch.zeros((1, sequence_length), device=device).long() + sasa_tokens = torch.zeros((1, sequence_length), device=device).long() + + function_tokens = torch.zeros((1, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((1, sequence_length, 16), device=device).long() + + + with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3_{i}.hdf5", "w") as f: + masked_sequence_tokens = f.create_dataset("masked_sequence_tokens", data=all_masked_sequences.cpu().numpy()) + unmasked_sequence_tokens = f.create_dataset("unmasked_sequence_tokens", data=all_unmasked_sequences.cpu().numpy()) + sequence_id = f.create_dataset("sequence_id", data=sequence_id.cpu().numpy()) + structure_tokens = f.create_dataset("structural_tokens", data=structure_tokens.cpu().numpy()) + coords = f.create_dataset("bb_coords", data=coords.cpu().numpy()) + average_plddt = f.create_dataset("average_plddt", data=average_plddt.cpu().numpy()) + per_res_plddt = f.create_dataset("per_res_plddt", data=per_res_plddt.cpu().numpy()) + ss8_tokens = f.create_dataset("ss8_tokens", data=ss8_tokens.cpu().numpy()) + sasa_tokens = f.create_dataset("sasa_tokens", data=sasa_tokens.cpu().numpy()) + function_tokens = f.create_dataset("function_tokens", data=function_tokens.cpu().numpy()) + residue_annotation_tokens = f.create_dataset("residue_annotation_tokens", data=residue_annotation_tokens.cpu().numpy()) + + ref_logps = f.create_dataset("ref_logps", data=all_logps.cpu().numpy()) + energies = f.create_dataset("energies", data=all_fitness_scores) + + + f.attrs["num_prompts"] = 1 + f.attrs["num_examples_per_prompt"] = masked_sequence_tokens.shape[0] + f.attrs["fixed_bb_coords"] = True + f.attrs["fixed_average_plddt"] = True + f.attrs["fixed_per_res_plddt"] = True + f.attrs["fixed_ss8_tokens"] = True + f.attrs["fixed_sasa_tokens"] = True + f.attrs["fixed_function_tokens"] = True + f.attrs["fixed_residue_annotation_tokens"] = True + f.attrs["fixed_structural_tokens"] = True + f.attrs["sampling_temperature"] = sampling_temperature + +# with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3.hdf5", "r") as f: +# for key in f.keys(): +# print(key, f[key].shape) \ No newline at end of file diff --git a/iterative_alignment_experiment_megascale/make_alignment_dataset_second_round.py b/iterative_alignment_experiment_megascale/make_alignment_dataset_second_round.py new file mode 100644 index 0000000000000000000000000000000000000000..0e72e4370b6d628aec1fac047cb559ef6b6a1ca7 --- /dev/null +++ b/iterative_alignment_experiment_megascale/make_alignment_dataset_second_round.py @@ -0,0 +1,200 @@ +import argparse +import torch +import re +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +import h5py +from omegaconf import OmegaConf +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +num_replicates = 10 +campaign_number = 1 # change this according to the campaign we are interested in +dataset_size = 96 # change this according to the dataset size we are interested in + +sequence_tokenizer = EsmSequenceTokenizer() + +parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +args = parser.parse_args() +data = args.target + +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + + +print(data) +for i in range(num_replicates): + cfg_filename = f"./config.yaml" + cfg = OmegaConf.load(cfg_filename) + sampling_temperature=1 + OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) + mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] + bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] + eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] + pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + + else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + if data != "GB1": + muts = df["muts"].iloc[0] + else: + muts = df["muts"].iloc[100000] + + numbers = re.findall(r'\d+', muts) + mask_indices = list(map(int, numbers)) + # mask_indices = [i-1 for i in mask_indices] #convert to 0-based indexing + + fitness_scores = [] + + # Load from base_model_{dataset_size} + trpb_base = torch.load(f"./{data}/base_model_{dataset_size}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_base = trpb_base["all_unmasked_sequences_decoded"] + all_unmasked_sequences_base = trpb_base["all_unmasked_sequences"] + all_masked_sequences_base = trpb_base["all_masked_sequences"] + all_unmasked_sequences_base = all_unmasked_sequences_base.reshape(-1, all_unmasked_sequences_base.shape[-1]) + all_logps_base = trpb_base["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_base, all_unmasked_sequences_base): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_0_{dataset_size} + trpb_aligned = torch.load(f"./{data}/aligned_{campaign_number-1}_{dataset_size}_{i}/trpb_{i}.pt") + all_unmasked_sequences_decoded_aligned_0 = trpb_aligned["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_0 = trpb_aligned["all_unmasked_sequences"] + all_masked_sequences_aligned_0 = trpb_aligned["all_masked_sequences"] + all_unmasked_sequences_aligned_0 = all_unmasked_sequences_aligned_0.reshape(-1, all_unmasked_sequences_aligned_0.shape[-1]) + all_logps_aligned_0 = trpb_aligned["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_0, all_unmasked_sequences_aligned_0): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + + # Concatenate the sequences and logps from all models + all_unmasked_sequences = torch.cat((all_unmasked_sequences_base, all_unmasked_sequences_aligned_0),dim=0)# + all_masked_sequences = torch.cat((all_masked_sequences_base, all_masked_sequences_aligned_0),dim=0)# + print(all_logps_base.shape, all_logps_aligned_0.shape)# + all_logps = torch.cat((all_logps_base, all_logps_aligned_0),dim=0)# + + all_fitness_scores = fitness_scores + + # Check for duplicates in all_unmasked_sequences + unique_sequences, counts = torch.unique(all_unmasked_sequences, dim=0, return_counts=True) + num_duplicates = torch.sum(counts > 1).item() + print(f"Number of duplicate sequences: {num_duplicates}") + + all_fitness_scores = np.array(all_fitness_scores) + all_fitness_scores = np.where(all_fitness_scores > 0, -np.log(all_fitness_scores), 10) + + sampling_temperature = 1 # hard-coding a sampling temperature of 1 for mixed-temperature alignment + + sequence_length = all_unmasked_sequences.shape[1] + + sequence_id = torch.ones((all_unmasked_sequences.shape[0], sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((1, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((1, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((1), device=device) + + per_res_plddt = torch.zeros((1, sequence_length), device=device) + ss8_tokens = torch.zeros((1, sequence_length), device=device).long() + sasa_tokens = torch.zeros((1, sequence_length), device=device).long() + + function_tokens = torch.zeros((1, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((1, sequence_length, 16), device=device).long() + + + with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3_{i}.hdf5", "w") as f: + masked_sequence_tokens = f.create_dataset("masked_sequence_tokens", data=all_masked_sequences.cpu().numpy()) + unmasked_sequence_tokens = f.create_dataset("unmasked_sequence_tokens", data=all_unmasked_sequences.cpu().numpy()) + sequence_id = f.create_dataset("sequence_id", data=sequence_id.cpu().numpy()) + structure_tokens = f.create_dataset("structural_tokens", data=structure_tokens.cpu().numpy()) + coords = f.create_dataset("bb_coords", data=coords.cpu().numpy()) + average_plddt = f.create_dataset("average_plddt", data=average_plddt.cpu().numpy()) + per_res_plddt = f.create_dataset("per_res_plddt", data=per_res_plddt.cpu().numpy()) + ss8_tokens = f.create_dataset("ss8_tokens", data=ss8_tokens.cpu().numpy()) + sasa_tokens = f.create_dataset("sasa_tokens", data=sasa_tokens.cpu().numpy()) + function_tokens = f.create_dataset("function_tokens", data=function_tokens.cpu().numpy()) + residue_annotation_tokens = f.create_dataset("residue_annotation_tokens", data=residue_annotation_tokens.cpu().numpy()) + + ref_logps = f.create_dataset("ref_logps", data=all_logps.cpu().numpy()) + energies = f.create_dataset("energies", data=all_fitness_scores) + + + f.attrs["num_prompts"] = 1 + f.attrs["num_examples_per_prompt"] = masked_sequence_tokens.shape[0] + f.attrs["fixed_bb_coords"] = True + f.attrs["fixed_average_plddt"] = True + f.attrs["fixed_per_res_plddt"] = True + f.attrs["fixed_ss8_tokens"] = True + f.attrs["fixed_sasa_tokens"] = True + f.attrs["fixed_function_tokens"] = True + f.attrs["fixed_residue_annotation_tokens"] = True + f.attrs["fixed_structural_tokens"] = True + f.attrs["sampling_temperature"] = sampling_temperature + \ No newline at end of file diff --git a/iterative_alignment_experiment_megascale/make_alignment_dataset_third_round.py b/iterative_alignment_experiment_megascale/make_alignment_dataset_third_round.py new file mode 100644 index 0000000000000000000000000000000000000000..48096f2821a4104d4d224e5fb3e44782eec2323b --- /dev/null +++ b/iterative_alignment_experiment_megascale/make_alignment_dataset_third_round.py @@ -0,0 +1,234 @@ +import torch +import re +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +import h5py +import argparse +from omegaconf import OmegaConf +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +num_replicates = 10 +campaign_number = 2 # change this according to the campaign we are interested in +dataset_size = 96 # change this according to the dataset size we are interested in + +sequence_tokenizer = EsmSequenceTokenizer() + +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +args = parser.parse_args() +data = args.target +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +print(data) +for i in range(num_replicates): + cfg_filename = f"./config.yaml" + cfg = OmegaConf.load(cfg_filename) + sampling_temperature=1 + OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) + mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] + bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] + eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] + pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + + else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + + if data != "GB1": + muts = df["muts"].iloc[0] + else: + muts = df["muts"].iloc[100000] + + numbers = re.findall(r'\d+', muts) + mask_indices = list(map(int, numbers)) + # mask_indices = [i-1 for i in mask_indices] #convert to 0-based indexing + + fitness_scores = [] + + # Load from base_model_{dataset_size} + trpb_base = torch.load(f"./{data}/base_model_{dataset_size}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_base = trpb_base["all_unmasked_sequences_decoded"] + all_unmasked_sequences_base = trpb_base["all_unmasked_sequences"] + all_masked_sequences_base = trpb_base["all_masked_sequences"] + all_unmasked_sequences_base = all_unmasked_sequences_base.reshape(-1, all_unmasked_sequences_base.shape[-1]) + all_logps_base = trpb_base["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_base, all_unmasked_sequences_base): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_0_{dataset_size} + trpb_aligned = torch.load(f"./{data}/aligned_{campaign_number-2}_{dataset_size}_{i}/trpb_post_rd_{campaign_number-1}_{i}.pt") + all_unmasked_sequences_decoded_aligned_0 = trpb_aligned["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_0 = trpb_aligned["all_unmasked_sequences"] + all_masked_sequences_aligned_0 = trpb_aligned["all_masked_sequences"] + all_unmasked_sequences_aligned_0 = all_unmasked_sequences_aligned_0.reshape(-1, all_unmasked_sequences_aligned_0.shape[-1]) + all_logps_aligned_0 = trpb_aligned["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_0, all_unmasked_sequences_aligned_0): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + # Load from aligned_1_{dataset_size} + trpb_aligned_1 = torch.load(f"./{data}/aligned_{campaign_number-1}_{dataset_size}_{i}/trpb_{i}.pt") + all_unmasked_sequences_decoded_aligned_1 = trpb_aligned_1["all_unmasked_sequences_decoded"] + all_unmasked_sequences_aligned_1 = trpb_aligned_1["all_unmasked_sequences"] + all_masked_sequences_aligned_1 = trpb_aligned_1["all_masked_sequences"] + all_unmasked_sequences_aligned_1 = all_unmasked_sequences_aligned_1.reshape(-1, all_unmasked_sequences_aligned_1.shape[-1]) + all_logps_aligned_1 = trpb_aligned_1["all_logps"] + + for unmasked_sequence_decoded, unmasked_sequence in zip(all_unmasked_sequences_decoded_aligned_1, all_unmasked_sequences_aligned_1): + index_residue_0 = unmasked_sequence_decoded[mask_indices[0]-1] + index_residue_1 = unmasked_sequence_decoded[mask_indices[1]-1] + index_residue_2 = unmasked_sequence_decoded[mask_indices[2]-1] + try: + index_residue_3 = unmasked_sequence_decoded[mask_indices[3]-1] + mutations = [index_residue_0, index_residue_1, index_residue_2, index_residue_3] + muts = ''.join(mutations) + except: + mutations = [index_residue_0, index_residue_1, index_residue_2] + muts = ''.join(mutations) + + df_filtered = df[df["AAs"] == muts] + + if len(df_filtered) == 0: + if torch.any((unmasked_sequence[1:-1] > 23) | (unmasked_sequence[1:-1] < 4)): + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + print(f"Invalid sequence {muts}") + fitness_score = -2 + else: + fitness_score = df_filtered["fitness"].values[0] + fitness_scores.append(fitness_score) + + + # Concatenate the sequences and logps from all models + all_unmasked_sequences = torch.cat((all_unmasked_sequences_base, all_unmasked_sequences_aligned_0, all_unmasked_sequences_aligned_1),dim=0)# + all_masked_sequences = torch.cat((all_masked_sequences_base, all_masked_sequences_aligned_0, all_masked_sequences_aligned_1),dim=0)# + print(all_logps_base.shape, all_logps_aligned_0.shape, all_logps_aligned_1.shape)# + all_logps = torch.cat((all_logps_base, all_logps_aligned_0, all_logps_aligned_1),dim=0)# + + all_fitness_scores = fitness_scores + + # Check for duplicates in all_unmasked_sequences + unique_sequences, counts = torch.unique(all_unmasked_sequences, dim=0, return_counts=True) + num_duplicates = torch.sum(counts > 1).item() + print(f"Number of duplicate sequences: {num_duplicates}") + + all_fitness_scores = np.array(all_fitness_scores) + all_fitness_scores = np.where(all_fitness_scores > 0, -np.log(all_fitness_scores), 10) + + sampling_temperature = 1 # hard-coding a sampling temperature of 1 for mixed-temperature alignment + + sequence_length = all_unmasked_sequences.shape[1] + + sequence_id = torch.ones((all_unmasked_sequences.shape[0], sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((1, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((1, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((1), device=device) + + per_res_plddt = torch.zeros((1, sequence_length), device=device) + ss8_tokens = torch.zeros((1, sequence_length), device=device).long() + sasa_tokens = torch.zeros((1, sequence_length), device=device).long() + + function_tokens = torch.zeros((1, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((1, sequence_length, 16), device=device).long() + + + with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3_{i}.hdf5", "w") as f: + masked_sequence_tokens = f.create_dataset("masked_sequence_tokens", data=all_masked_sequences.cpu().numpy()) + unmasked_sequence_tokens = f.create_dataset("unmasked_sequence_tokens", data=all_unmasked_sequences.cpu().numpy()) + sequence_id = f.create_dataset("sequence_id", data=sequence_id.cpu().numpy()) + structure_tokens = f.create_dataset("structural_tokens", data=structure_tokens.cpu().numpy()) + coords = f.create_dataset("bb_coords", data=coords.cpu().numpy()) + average_plddt = f.create_dataset("average_plddt", data=average_plddt.cpu().numpy()) + per_res_plddt = f.create_dataset("per_res_plddt", data=per_res_plddt.cpu().numpy()) + ss8_tokens = f.create_dataset("ss8_tokens", data=ss8_tokens.cpu().numpy()) + sasa_tokens = f.create_dataset("sasa_tokens", data=sasa_tokens.cpu().numpy()) + function_tokens = f.create_dataset("function_tokens", data=function_tokens.cpu().numpy()) + residue_annotation_tokens = f.create_dataset("residue_annotation_tokens", data=residue_annotation_tokens.cpu().numpy()) + + ref_logps = f.create_dataset("ref_logps", data=all_logps.cpu().numpy()) + energies = f.create_dataset("energies", data=all_fitness_scores) + + + f.attrs["num_prompts"] = 1 + f.attrs["num_examples_per_prompt"] = masked_sequence_tokens.shape[0] + f.attrs["fixed_bb_coords"] = True + f.attrs["fixed_average_plddt"] = True + f.attrs["fixed_per_res_plddt"] = True + f.attrs["fixed_ss8_tokens"] = True + f.attrs["fixed_sasa_tokens"] = True + f.attrs["fixed_function_tokens"] = True + f.attrs["fixed_residue_annotation_tokens"] = True + f.attrs["fixed_structural_tokens"] = True + f.attrs["sampling_temperature"] = sampling_temperature + +# with h5py.File(f"./{data}/alignment_dataset_{campaign_number}_{dataset_size}_from_ESM3.hdf5", "r") as f: +# for key in f.keys(): +# print(key, f[key].shape) \ No newline at end of file diff --git a/iterative_alignment_experiment_megascale/resume_experiment.sh b/iterative_alignment_experiment_megascale/resume_experiment.sh new file mode 100644 index 0000000000000000000000000000000000000000..d9435217404966ba9a7ee9d25957d9f79e3b4726 --- /dev/null +++ b/iterative_alignment_experiment_megascale/resume_experiment.sh @@ -0,0 +1,68 @@ +#!/bin/bash +#SBATCH -N 1 +#SBATCH -G 4 +#SBATCH -C GPU_MEM:80GB +#SBATCH -p rotskoff +#SBATCH -t 01-12:00:00 +#SBATCH --mem=320GB +#SBATCH -J alignment + +#source /home/groups/nsgray01/anaconda3/etc/profile.d/conda.sh +#conda activate proera +source /home/groups/nsgray01/MoLE/.venv/bin/activate + +target="TrpB4" +BASE_DIR="./${target}/lightning_logs_round_2" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +round=3 + +# Train the fourth round models +cd $target +for i in {7..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "++train.lightning_model_args.better_energy=lower" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=lightning_logs_round_2/${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. +# sample from the fourth round trained models +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +for i in {7..9}; do + version_number=$(basename "${subdirs[$i]}") + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +echo "All rounds completed for target $target" diff --git a/iterative_alignment_experiment_megascale/sample_esm.py b/iterative_alignment_experiment_megascale/sample_esm.py new file mode 100644 index 0000000000000000000000000000000000000000..66473ec909b25b6dd5dea86ce33268e7c70d7187 --- /dev/null +++ b/iterative_alignment_experiment_megascale/sample_esm.py @@ -0,0 +1,208 @@ +import os +import torch +import numpy as np +import pandas as pd +import h5py +import re +from omegaconf import OmegaConf +import h5py +import lightning as L +from pera.nn import BidirectionalModel, sample_components_from_bidirectional_transformer, sample_perturbations, sample_embedding_perturbations +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +sequence_tokenizer = EsmSequenceTokenizer() + +import argparse + +# set up parser +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +parser.add_argument('--num_samples', type=int, required=False, default=384, help='Number of samples to process (default: 100000)') +parser.add_argument('--alignment_round', type=int, required=False, default=1, help='Alignment round as an integer') +parser.add_argument('--version_number', type=str, required=False, default=1, help='Version number as a string') +parser.add_argument('--replicate', type=int, required=False, default=1, help='Replicate number as an integer') +args = parser.parse_args() + +target = args.target +alignment_round = args.alignment_round +version_number = args.version_number +num_samples = args.num_samples +replicate = args.replicate + +cfg_filename = f"{target}/lightning_logs_round_{alignment_round}/{version_number}/config.yaml" +network_filename = f"{target}/lightning_logs_round_{alignment_round}/{version_number}/checkpoints/best_model.ckpt" +save_folder_name = f"{target}/aligned_{alignment_round}_{num_samples}_{replicate}" + +cfg = OmegaConf.load(cfg_filename) +sampling_temperature=1 +OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) +OmegaConf.update(cfg, "train.lightning_model_args.better_energy", "lower") +esm_model = BidirectionalModel(cfg["nn"]["model"], + cfg["nn"]["model_args"], + **cfg["train"]["lightning_model_args"]).to(device) +esm_model.load_model_from_ckpt(network_filename) +esm_model.eval() +print("") +mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] +bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] +eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] +pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + +os.makedirs(save_folder_name, exist_ok=True) + +past_generations =[f"{target}/base_model_{num_samples}"] +for i in range(alignment_round): + past_generations.append(f"{target}/aligned_{i}_{num_samples}_{replicate}") + +previous_unmasked_sequences_decoded = [] + +for round in past_generations: + trpb = torch.load(f"{round}/trpb_{replicate}.pt") + previous_unmasked_sequences_decoded.extend(trpb['all_unmasked_sequences_decoded']) + +assert len(previous_unmasked_sequences_decoded) == len(set(previous_unmasked_sequences_decoded)), "There are duplicate sequences in previous_unmasked_sequences_decoded" +print("All elements in previous_unmasked_sequences_decoded are unique.") + +data = target # "GB1", "ParD2", "TEV", "TrpB3F", "TrpB3I", "TrpB4" +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +sequence_tokenizer = EsmSequenceTokenizer() + +if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + +elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + +else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + +if data != "GB1": + muts = df["muts"].iloc[0] +else: + muts = df["muts"].iloc[100000] + +numbers = re.findall(r'\d+', muts) +mask_indices = list(map(int, numbers)) +num_masks_per_sequence = num_samples // 4 +num_to_generate_per_mask = 4 + + +parent_sequence = torch.tensor(sequence_tokenizer.encode(parent_sequence_decoded, + add_special_tokens=True), device=device).unsqueeze(0).long() +sequence_length = parent_sequence.shape[1] + + +all_masked_sequences = [] +all_unmasked_sequences_decoded = [] +all_unmasked_sequences = [] +all_logps = [] + + +while len(all_unmasked_sequences_decoded) < num_samples: + + print(len(all_unmasked_sequences_decoded)) + + masked_sequences = parent_sequence.clone().repeat(num_to_generate_per_mask, 1) + masked_sequences[:, mask_indices] = mask_token_sequence + + + + + + sequence_id = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((num_to_generate_per_mask, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((num_to_generate_per_mask), device=device) + + per_res_plddt = torch.zeros((num_to_generate_per_mask, sequence_length), device=device) + ss8_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + sasa_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + + function_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 16), device=device).long() + + + + + with torch.no_grad(): + unmasked_sequences = sample_components_from_bidirectional_transformer(transformer_model=esm_model, + masked_sequence_tokens=masked_sequences, + structure_tokens=structure_tokens, + average_plddt=average_plddt, + per_res_plddt=per_res_plddt, + ss8_tokens=ss8_tokens, + sasa_tokens=sasa_tokens, + function_tokens=function_tokens, + residue_annotation_tokens=residue_annotation_tokens, + bb_coords=coords, + sequence_id=sequence_id, + mask_token_sequence=mask_token_sequence, + bos_token_sequence=bos_token_sequence, + eos_token_sequence=eos_token_sequence, + pad_token_sequence=pad_token_sequence, + inference_batch_size=1) + + + + masked_indices = (masked_sequences == mask_token_sequence).float() + logits = esm_model.nn(sequence_tokens=masked_sequences, + structure_tokens=structure_tokens, + average_plddt=average_plddt, + per_res_plddt=per_res_plddt, + ss8_tokens=ss8_tokens, + sasa_tokens=sasa_tokens, + function_tokens=function_tokens, + residue_annotation_tokens=residue_annotation_tokens, + sequence_id=sequence_id, + bb_coords=coords)["sequence_logits"].detach() + logps = torch.nn.functional.log_softmax(logits/sampling_temperature, dim=-1) + logps = torch.gather(logps, dim=-1, index=unmasked_sequences.unsqueeze(-1)).squeeze(-1) + logps = (logps * masked_indices).sum(-1).detach() + + decoded_seqs = [sequence.replace(" ", "") for sequence in sequence_tokenizer.batch_decode(unmasked_sequences[:, 1:-1])] + for seq, logp, masked_seq, unmasked_seq in zip(decoded_seqs, logps, masked_sequences, unmasked_sequences): + if seq in all_unmasked_sequences_decoded or seq in previous_unmasked_sequences_decoded: + continue + else: + all_unmasked_sequences_decoded.append(seq) + all_logps.append(logp) + all_masked_sequences.append(masked_seq) + all_unmasked_sequences.append(unmasked_seq) + + + +all_unmasked_sequences_decoded = all_unmasked_sequences_decoded[:num_samples] +all_masked_sequences = all_masked_sequences[:num_samples] +all_unmasked_sequences = all_unmasked_sequences[:num_samples] +all_logps = all_logps[:num_samples] + +all_masked_sequences = torch.stack(all_masked_sequences, dim=0) +all_unmasked_sequences = torch.stack(all_unmasked_sequences, dim=0) +all_logps = torch.stack(all_logps, dim=0) + + + +to_save = {"parent_sequence": parent_sequence, + "all_masked_sequences": all_masked_sequences, + "all_unmasked_sequences": all_unmasked_sequences, + "all_unmasked_sequences_decoded": all_unmasked_sequences_decoded, + "all_logps": all_logps} +torch.save(to_save, f"{save_folder_name}/trpb_{replicate}.pt") diff --git a/iterative_alignment_experiment_megascale/sample_esm_first_round.py b/iterative_alignment_experiment_megascale/sample_esm_first_round.py new file mode 100644 index 0000000000000000000000000000000000000000..b7961c25d0890a071e920ae69cc31d47c04428dc --- /dev/null +++ b/iterative_alignment_experiment_megascale/sample_esm_first_round.py @@ -0,0 +1,192 @@ +import os +import torch +import numpy as np +import pandas as pd +import h5py +import re +from omegaconf import OmegaConf +import h5py +import lightning as L +from pera.nn import BidirectionalModel, sample_components_from_bidirectional_transformer, sample_perturbations, sample_embedding_perturbations +from esm.tokenization.sequence_tokenizer import EsmSequenceTokenizer +from Bio.Seq import Seq + +device = torch.device("cuda:0") + +sequence_tokenizer = EsmSequenceTokenizer() + +import argparse + +# set up parser +parser = parser = argparse.ArgumentParser(description="Calculating the log-likelihood of a sequence") +parser.add_argument('--target', type=str, required=True, help='Dataset as a string') +parser.add_argument('--num_samples', type=int, required=False, default=384, help='Number of samples to process (default: 100000)') +parser.add_argument('--version_number', type=str, required=False, default=1, help='Version number as a string') +parser.add_argument('--replicate', type=int, required=False, default=1, help='Replicate number as an integer') +args = parser.parse_args() + +target = args.target +num_samples = args.num_samples +replicate = args.replicate + +cfg_filename = "./config.yaml" +network_filename = "./megascale_ckpts/step_step_100000.ckpt" +save_folder_name = f"{target}/base_model_{num_samples}" + +cfg = OmegaConf.load(cfg_filename) +sampling_temperature=1 +OmegaConf.update(cfg, "train.lightning_model_args.sampling_temperature", sampling_temperature) +OmegaConf.update(cfg, "train.lightning_model_args.better_energy", "lower") +esm_model = BidirectionalModel(cfg["nn"]["model"], + cfg["nn"]["model_args"], + **cfg["train"]["lightning_model_args"]).to(device) +esm_model.load_model_from_ckpt(network_filename) +esm_model.eval() +print("") +mask_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["mask"] +bos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["bos"] +eos_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["eos"] +pad_token_sequence = cfg["nn"]["model_args"]["residue_token_info"]["pad"] + + +os.makedirs(save_folder_name, exist_ok=True) + +data = target # "GB1", "ParD2", "TEV", "TrpB3F", "TrpB3I", "TrpB4" +data_root_path = "/scratch/groups/rotskoff/sebastian/era/protein_era/data" + +sequence_tokenizer = EsmSequenceTokenizer() + +if data.startswith("TrpB"): + df = pd.read_csv(f"{data_root_path}/TrpB/scale2max/{data}.csv") + with open(f"{data_root_path}/TrpB/TrpB.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + +elif data == "DHFR": + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + nucleotide_seq = file.readlines()[1].strip() + nucleotide_seq = Seq(nucleotide_seq) + parent_sequence_decoded = str(nucleotide_seq.translate()) # Translate to amino acid sequence + +else: + df = pd.read_csv(f"{data_root_path}/{data}/scale2max/{data}.csv") + with open(f"{data_root_path}/{data}/{data}.fasta", "r") as file: + parent_sequence_decoded = file.readlines()[1].strip() + +if data != "GB1": + muts = df["muts"].iloc[0] +else: + muts = df["muts"].iloc[100000] + +numbers = re.findall(r'\d+', muts) +mask_indices = list(map(int, numbers)) +num_masks_per_sequence = num_samples // 4 +num_to_generate_per_mask = 4 + + +parent_sequence = torch.tensor(sequence_tokenizer.encode(parent_sequence_decoded, + add_special_tokens=True), device=device).unsqueeze(0).long() +sequence_length = parent_sequence.shape[1] + + +all_masked_sequences = [] +all_unmasked_sequences_decoded = [] +all_unmasked_sequences = [] +all_logps = [] + + +while len(all_unmasked_sequences_decoded) < num_samples: + + print(len(all_unmasked_sequences_decoded)) + + masked_sequences = parent_sequence.clone().repeat(num_to_generate_per_mask, 1) + masked_sequences[:, mask_indices] = mask_token_sequence + + + + + + sequence_id = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 1 + + structure_tokens = torch.ones((num_to_generate_per_mask, sequence_length), device=device).long() * 4096 + structure_tokens[:, 0] = 4098 + structure_tokens[:, -1] = 4097 + + coords = torch.inf * torch.ones((num_to_generate_per_mask, sequence_length, 3, 3), device=device) + + average_plddt = torch.ones((num_to_generate_per_mask), device=device) + + per_res_plddt = torch.zeros((num_to_generate_per_mask, sequence_length), device=device) + ss8_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + sasa_tokens = torch.zeros((num_to_generate_per_mask, sequence_length), device=device).long() + + function_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 8), device=device).long() + residue_annotation_tokens = torch.zeros((num_to_generate_per_mask, sequence_length, 16), device=device).long() + + + + + with torch.no_grad(): + unmasked_sequences = sample_components_from_bidirectional_transformer(transformer_model=esm_model, + masked_sequence_tokens=masked_sequences, + structure_tokens=structure_tokens, + average_plddt=average_plddt, + per_res_plddt=per_res_plddt, + ss8_tokens=ss8_tokens, + sasa_tokens=sasa_tokens, + function_tokens=function_tokens, + residue_annotation_tokens=residue_annotation_tokens, + bb_coords=coords, + sequence_id=sequence_id, + mask_token_sequence=mask_token_sequence, + bos_token_sequence=bos_token_sequence, + eos_token_sequence=eos_token_sequence, + pad_token_sequence=pad_token_sequence, + inference_batch_size=1) + + + + masked_indices = (masked_sequences == mask_token_sequence).float() + logits = esm_model.nn(sequence_tokens=masked_sequences, + structure_tokens=structure_tokens, + average_plddt=average_plddt, + per_res_plddt=per_res_plddt, + ss8_tokens=ss8_tokens, + sasa_tokens=sasa_tokens, + function_tokens=function_tokens, + residue_annotation_tokens=residue_annotation_tokens, + sequence_id=sequence_id, + bb_coords=coords)["sequence_logits"].detach() + logps = torch.nn.functional.log_softmax(logits/sampling_temperature, dim=-1) + logps = torch.gather(logps, dim=-1, index=unmasked_sequences.unsqueeze(-1)).squeeze(-1) + logps = (logps * masked_indices).sum(-1).detach() + + decoded_seqs = [sequence.replace(" ", "") for sequence in sequence_tokenizer.batch_decode(unmasked_sequences[:, 1:-1])] + for seq, logp, masked_seq, unmasked_seq in zip(decoded_seqs, logps, masked_sequences, unmasked_sequences): + if seq in all_unmasked_sequences_decoded: + continue + else: + all_unmasked_sequences_decoded.append(seq) + all_logps.append(logp) + all_masked_sequences.append(masked_seq) + all_unmasked_sequences.append(unmasked_seq) + + + +all_unmasked_sequences_decoded = all_unmasked_sequences_decoded[:num_samples] +all_masked_sequences = all_masked_sequences[:num_samples] +all_unmasked_sequences = all_unmasked_sequences[:num_samples] +all_logps = all_logps[:num_samples] + +all_masked_sequences = torch.stack(all_masked_sequences, dim=0) +all_unmasked_sequences = torch.stack(all_unmasked_sequences, dim=0) +all_logps = torch.stack(all_logps, dim=0) + + + +to_save = {"parent_sequence": parent_sequence, + "all_masked_sequences": all_masked_sequences, + "all_unmasked_sequences": all_unmasked_sequences, + "all_unmasked_sequences_decoded": all_unmasked_sequences_decoded, + "all_logps": all_logps} +torch.save(to_save, f"{save_folder_name}/trpb_{replicate}.pt") diff --git a/iterative_alignment_experiment_megascale/test.sh b/iterative_alignment_experiment_megascale/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..1a0834f06dee5ab8badc0d263a065f8da83f560d --- /dev/null +++ b/iterative_alignment_experiment_megascale/test.sh @@ -0,0 +1,271 @@ +#!/bin/bash +#SBATCH -N 1 +#SBATCH -G 4 +#SBATCH -C GPU_MEM:80GB +#SBATCH -p rotskoff +#SBATCH -t 07-00:00:00 +#SBATCH --mem=320GB +#SBATCH -J alignment + +#source /home/groups/nsgray01/anaconda3/etc/profile.d/conda.sh +#conda activate proera +source /home/groups/nsgray01/MoLE/.venv/bin/activate + +target="GB1" +base_model_path="/scratch/groups/rotskoff/sebastian/era/protein_era/111225BenchmarkWithMegascalePretrain/megascale_ckpts/step_step_100000.ckpt" +round=0 + +# sample from the base model (in this case the Megascale pretrained model) 10 times +for i in {0..1}; do + echo "Running iteration $i for target $target" + # Run the Python script with the specified arguments + python sample_esm_first_round.py \ + --target $target \ + --num_samples 96 \ + --replicate "$i" +done + +# Make the first round alignment datasets for each model +echo "Creating alignment dataset for target $target" +python create_alignment_dataset_first_round.py --target $target + +# Train the first round models +cd $target + +for i in {0..1}; do + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=2" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.trainer_args.enable_progress_bar=True" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=${base_model_path}" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. + +# sample from the first round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) + +for i in {0..1}; do + version_number=$(basename "${subdirs[$i]}") + echo "$version_number" + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# Make the second round alignment datasets for each model +round=1 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_second_round.py --target $target + +# Train the second round models +cd $target +for i in {0..1}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i, version_number $version_number" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.trainer_args.enable_progress_bar=True" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=lightning_logs_round_0/${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. + +# sample from the second round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) + +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# Make the third round alignment datasets for each model +round=2 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_third_round.py --target $target + +# Train the third round models +cd $target +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.trainer_args.enable_progress_bar=True" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. +# sample from the third round trained models and update the logps +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" + + python compute_updated_logps.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +# make the fourth round alignment datasets for each model +round=3 +echo "Creating alignment dataset for target $target, round $round" +python make_alignment_dataset_fourth_round.py --target $target --alignment_round $round +# Train the fourth round models +cd $target +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + echo "Training model for target $target, round $round, replicate $i" + pera_train \ + "train.lightning_model_args.eval_type=era" \ + "train.lightning_model_args.beta=10.0" \ + "train.lightning_model_args.gamma=0" \ + "train.trainer_args.devices=4" \ + "train.trainer_args.max_epochs=25" \ + "train.trainer_args.log_every_n_steps=1" \ + "train.trainer_args.enable_progress_bar=True" \ + "train.logger.logger_args.version=${i}" \ + "train.lightning_model_args.interval=epoch" \ + "train.lightning_model_args.monitor=train/ERALoss" \ + "train.best_checkpoint_args.monitor=train/ERALoss" \ + "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \ + "++train.lightning_model_args.lr_scheduler_args.patience=5" \ + "train.lightning_model_args.optimizer=AdamW" \ + "train.lightning_model_args.optimizer_args.lr=1.0e-6" \ + "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \ + "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \ + "train.lightning_model_args.on_step=false" \ + "global_args.dataset_filename=alignment_dataset_${round}_96_from_ESM3_${i}.hdf5" \ + "nn.batch_size=4" \ + "nn.load_model=${version_number}/checkpoints/best_model.ckpt" \ + "nn.dataset_split_args.train=1.0" \ + "nn.dataset_split_args.val=0.0" \ + "nn.dataset_split_args.test=0.0" \ + "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" +done + +# move lightning_logs to be specific to this round +mv lightning_logs lightning_logs_round_${round} +cd .. +# sample from the fourth round trained models +BASE_DIR="./${target}/lightning_logs_round_${round}" +subdirs=($(ls -d "$BASE_DIR"/*/ | sort)) +for i in {0..9}; do + version_number=$(basename "${subdirs[$i]}") + python sample_esm.py \ + --target $target \ + --num_samples 96 \ + --alignment_round $round \ + --version_number "$version_number" \ + --replicate "$i" +done + +echo "All rounds completed for target $target"