from typing import Dict, List, Any
import os
import torch
from transformers import AutoTokenizer, AutoModel
import pandas as pd
import time
import numpy as np
from transformers import GenerationConfig
from P3LIB.precious3_gpt_multi_modal import Custom_MPTForCausalLM
class EndpointHandler:
def __init__(self, path="insilicomedicine/precious3-gpt", device='cuda:1'):
self.device = device
self.model = AutoModel.from_pretrained(path, trust_remote_code=True).to(self.device)
self.tokenizer = AutoTokenizer.from_pretrained(path, trust_remote_code=True)
self.model.config.pad_token_id = self.tokenizer.pad_token_id
self.model.config.bos_token_id = self.tokenizer.bos_token_id
self.model.config.eos_token_id = self.tokenizer.eos_token_id
unique_entities_p3 = pd.read_csv(
'https://huggingface.co/insilicomedicine/precious3-gpt/raw/main/all_entities_with_type.csv')
self.unique_compounds_p3 = [i.strip() for i in
unique_entities_p3[unique_entities_p3.type == 'compound'].entity.to_list()]
self.unique_genes_p3 = [i.strip() for i in
unique_entities_p3[unique_entities_p3.type == 'gene'].entity.to_list()]
def create_prompt(self, prompt_config):
prompt = "[BOS]"
multi_modal_prefix = ''
for k, v in prompt_config.items():
if k == 'instruction':
prompt += f'<{v}>' if isinstance(v, str) else "".join([f'<{v_i}>' for v_i in v])
elif k == 'up':
if v:
prompt += f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v,
str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k == 'down':
if v:
prompt += f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v,
str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k == 'age':
if isinstance(v, int):
if prompt_config['species'].strip() == 'human':
prompt += f'<{k}_individ>{v} </{k}_individ>'
elif prompt_config['species'].strip() == 'macaque':
prompt += f'<{k}_individ>Macaca-{int(v / 20)} </{k}_individ>'
else:
if v:
prompt += f'<{k}>{v.strip()} </{k}>' if isinstance(v, str) else f'<{k}>{" ".join(v)} </{k}>'
else:
prompt += f'<{k}></{k}>'
return prompt
def generate_with_generation_config(self, input_ids, generation_config, max_new_tokens, random_seed=138):
torch.manual_seed(random_seed)
with torch.no_grad():
generation_output = self.model.generate(
input_ids=input_ids,
generation_config=generation_config,
return_dict_in_generate=True,
output_scores=True,
max_new_tokens=max_new_tokens
)
return generation_output
def get_gene_probabilities(self, prompt_config, top_k=300, list_type='up', random_seed=138):
"""
Args:
top_k: how many top probable tokens to take
list_type: "up" / "down"
"""
prompt = self.create_prompt(prompt_config)
assert list_type in ["up", "down"]
if list_type == 'up':
prompt += "<up>"
print(prompt)
### Generation config https://huggingface.co/blog/how-to-generate
generation_config = GenerationConfig(temperature=0.8, num_beams=1, do_sample=True, top_p=None, top_k=3550,
pad_token_id=self.tokenizer.pad_token_id, num_return_sequences=1)
inputs = self.tokenizer(prompt, return_tensors="pt")
input_ids = inputs["input_ids"].to(self.device)
assert 3 not in input_ids[0]
max_new_tokens = self.model.config.max_seq_len - len(input_ids[0])
generation_output = self.generate_with_generation_config(input_ids=input_ids,
generation_config=generation_config,
max_new_tokens=max_new_tokens,
random_seed=random_seed)
# print(generation_output)
id_4_gene_token = list(generation_output.sequences[0][len(input_ids[0]) - 1:]).index(
self.tokenizer.convert_tokens_to_ids([f'<{list_type}>'])[0])
id_4_gene_token += 1
print('This is token index where gene should be predicted: ', id_4_gene_token)
values, indices = torch.topk(generation_output["scores"][id_4_gene_token - 1].view(-1), k=top_k)
indices_decoded = self.tokenizer.decode(indices, skip_special_tokens=True)
indices_decoded_list = indices_decoded.split(' ')
generated_genes = sorted(set(indices_decoded_list) & set(self.unique_genes_p3), key=indices_decoded_list.index)
return generated_genes
class HFEndpointHandler:
def __init__(self, path="insilicomedicine/precious3-gpt", device='cuda:1'):
self.device = device
self.model = AutoModel.from_pretrained(path, trust_remote_code=True).to(self.device)
self.tokenizer = AutoTokenizer.from_pretrained(path, trust_remote_code=True)
self.model.config.pad_token_id = self.tokenizer.pad_token_id
self.model.config.bos_token_id = self.tokenizer.bos_token_id
self.model.config.eos_token_id = self.tokenizer.eos_token_id
unique_entities_p3 = pd.read_csv('https://huggingface.co/insilicomedicine/precious3-gpt/raw/main/all_entities_with_type.csv')
self.unique_compounds_p3 = [i.strip() for i in unique_entities_p3[unique_entities_p3.type=='compound'].entity.to_list()]
self.unique_genes_p3 = [i.strip() for i in unique_entities_p3[unique_entities_p3.type=='gene'].entity.to_list()]
def create_prompt(self, prompt_config):
prompt = "[BOS]"
multi_modal_prefix = ''
for k, v in prompt_config.items():
if k=='instruction':
prompt+=f'<{v}>' if isinstance(v, str) else "".join([f'<{v_i}>' for v_i in v])
elif k=='up':
if v:
prompt+=f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v, str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k=='down':
if v:
prompt+=f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v, str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k=='age':
if isinstance(v, int):
if prompt_config['species'].strip() == 'human':
prompt+=f'<{k}_individ>{v} </{k}_individ>'
elif prompt_config['species'].strip() == 'macaque':
prompt+=f'<{k}_individ>Macaca-{int(v/20)} </{k}_individ>'
else:
if v:
prompt+=f'<{k}>{v.strip()} </{k}>' if isinstance(v, str) else f'<{k}>{" ".join(v)} </{k}>'
else:
prompt+=f'<{k}></{k}>'
return prompt
def custom_generate(self,
input_ids,
device,
max_new_tokens,
mode,
temperature=0.8,
top_p=0.2, top_k=3550,
n_next_tokens=30, num_return_sequences=1, random_seed=138):
torch.manual_seed(random_seed)
# Set parameters
# temperature - Higher value for more randomness, lower for more control
# top_p - Probability threshold for nucleus sampling (aka top-p sampling)
# top_k - Ignore logits below the top-k value to reduce randomness (if non-zero)
# n_next_tokens - Number of top next tokens when predicting compounds
# Generate sequences
outputs = []
next_token_compounds = []
next_token_up_genes = []
next_token_down_genes = []
for _ in range(num_return_sequences):
start_time = time.time()
generated_sequence = []
current_token = input_ids.clone()
for _ in range(max_new_tokens): # Maximum length of generated sequence
# Forward pass through the model
logits = self.model.forward(
input_ids=current_token
)[0]
# Apply temperature to logits
if temperature != 1.0:
logits = logits / temperature
# Apply top-p sampling (nucleus sampling)
sorted_logits, sorted_indices = torch.sort(logits, descending=True)
cumulative_probs = torch.cumsum(torch.softmax(sorted_logits, dim=-1), dim=-1)
sorted_indices_to_remove = cumulative_probs > top_p
if top_k > 0:
sorted_indices_to_remove[..., top_k:] = 1
# Set the logit values of the removed indices to a very small negative value
inf_tensor = torch.tensor(float("-inf")).type(torch.bfloat16).to(logits.device)
logits = logits.where(sorted_indices_to_remove, inf_tensor)
# Sample the next token
if current_token[0][-1] == self.tokenizer.encode('<drug>')[0] and len(next_token_compounds)==0:
next_token_compounds.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
# Sample the next token for UP genes
if current_token[0][-1] == self.tokenizer.encode('<up>')[0] and len(next_token_up_genes)==0:
next_token_up_genes.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
# Sample the next token for DOWN genes
if current_token[0][-1] == self.tokenizer.encode('<down>')[0] and len(next_token_down_genes)==0:
next_token_down_genes.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
next_token = torch.multinomial(torch.softmax(logits, dim=-1)[0], num_samples=1)[len(current_token[0])-1, :].unsqueeze(0)
# Append the sampled token to the generated sequence
generated_sequence.append(next_token.item())
# Stop generation if an end token is generated
if next_token == self.tokenizer.eos_token_id:
break
# Prepare input for the next iteration
current_token = torch.cat((current_token, next_token), dim=-1)
print(time.time()-start_time)
outputs.append(generated_sequence)
# Process generated up/down lists
processed_outputs = {"up": [], "down": []}
if mode in ['meta2diff', 'meta2diff2compound']:
predicted_up_genes_tokens = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_up_genes]
predicted_up_genes = []
for j in predicted_up_genes_tokens:
generated_up_sample = [i.strip() for i in j]
predicted_up_genes.append(sorted(set(generated_up_sample) & set(self.unique_genes_p3), key = generated_up_sample.index))
processed_outputs['up'] = predicted_up_genes
predicted_down_genes_tokens = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_down_genes]
predicted_down_genes = []
for j in predicted_down_genes_tokens:
generated_down_sample = [i.strip() for i in j]
predicted_down_genes.append(sorted(set(generated_down_sample) & set(self.unique_genes_p3), key = generated_down_sample.index))
processed_outputs['down'] = predicted_down_genes
else:
processed_outputs = outputs
predicted_compounds_ids = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_compounds]
predicted_compounds = []
for j in predicted_compounds_ids:
predicted_compounds.append([i.strip() for i in j])
return processed_outputs, predicted_compounds, random_seed
def __call__(self, data: Dict[str, Any]) -> Dict[str, str]:
"""
Args:
data (:dict:):
The payload with the text prompt and generation parameters.
"""
data = data.copy()
parameters = data.pop("parameters", None)
config_data = data.pop("inputs", None)
mode = data.pop('mode', 'Not specified')
prompt = self.create_prompt(config_data)
if mode != "diff2compound":
prompt+="<up>"
inputs = self.tokenizer(prompt, return_tensors="pt")
input_ids = inputs["input_ids"].to(self.device)
max_new_tokens = self.model.config.max_seq_len - len(input_ids[0])
try:
generated_sequence, raw_next_token_generation, out_seed = self.custom_generate(input_ids = input_ids,
max_new_tokens=max_new_tokens, mode=mode,
device=self.device, **parameters)
next_token_generation = [sorted(set(i) & set(self.unique_compounds_p3), key = i.index) for i in raw_next_token_generation]
if mode == "meta2diff":
outputs = {"up": generated_sequence['up'], "down": generated_sequence['down']}
out = {"output": outputs, "mode": mode, "message": "Done!", "input": prompt, 'random_seed': out_seed}
elif mode == "meta2diff2compound":
outputs = {"up": generated_sequence['up'], "down": generated_sequence['down']}
out = {
"output": outputs, "compounds": next_token_generation, "raw_output": raw_next_token_generation, "mode": mode,
"message": "Done!", "input": prompt, 'random_seed': out_seed}
elif mode == "diff2compound":
outputs = generated_sequence
out = {
"output": outputs, "compounds": next_token_generation, "raw_output": raw_next_token_generation, "mode": mode,
"message": "Done!", "input": prompt, 'random_seed': out_seed}
else:
out = {"message": f"Specify one of the following modes: meta2diff, meta2diff2compound, diff2compound. Your mode is: {mode}"}
except Exception as e:
print(e)
outputs, next_token_generation = [None], [None]
out = {"output": outputs, "mode": mode, 'message': f"{e}", "input": prompt, 'random_seed': 138}
return out
class MMEndpointHandler:
def __init__(self, path="insilicomedicine/precious3-gpt-multi-modal", device='cuda:3'):
self.device = device
self.path = path
# load model and processor from path
self.model = Custom_MPTForCausalLM.from_pretrained(path, torch_dtype=torch.bfloat16).to(self.device)
self.tokenizer = AutoTokenizer.from_pretrained(path, trust_remote_code=True)
self.model.config.pad_token_id = self.tokenizer.pad_token_id
self.model.config.bos_token_id = self.tokenizer.bos_token_id
self.model.config.eos_token_id = self.tokenizer.eos_token_id
unique_entities_p3 = pd.read_csv('https://huggingface.co/insilicomedicine/precious3-gpt/raw/main/all_entities_with_type.csv')
self.unique_compounds_p3 = [i.strip() for i in unique_entities_p3[unique_entities_p3.type=='compound'].entity.to_list()]
self.unique_genes_p3 = [i.strip() for i in unique_entities_p3[unique_entities_p3.type=='gene'].entity.to_list()]
self.emb_gpt_genes = pd.read_pickle('https://huggingface.co/insilicomedicine/precious3-gpt-multi-modal/resolve/main/multi-modal-data/emb_gpt_genes.pickle')
self.emb_hgt_genes = pd.read_pickle('https://huggingface.co/insilicomedicine/precious3-gpt-multi-modal/resolve/main/multi-modal-data/emb_hgt_genes.pickle')
def create_prompt(self, prompt_config):
prompt = "[BOS]"
multi_modal_prefix = '<modality0><modality1><modality2><modality3>'*3
for k, v in prompt_config.items():
if k=='instruction':
prompt+=f'<{v}>' if isinstance(v, str) else "".join([f'<{v_i}>' for v_i in v])
elif k=='up':
if v:
prompt+=f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v, str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k=='down':
if v:
prompt+=f'{multi_modal_prefix}<{k}>{v} </{k}>' if isinstance(v, str) else f'{multi_modal_prefix}<{k}>{" ".join(v)} </{k}>'
elif k=='age':
if isinstance(v, int):
if prompt_config['species'].strip() == 'human':
prompt+=f'<{k}_individ>{v} </{k}_individ>'
elif prompt_config['species'].strip() == 'macaque':
prompt+=f'<{k}_individ>Macaca-{int(v/20)} </{k}_individ>'
else:
if v:
prompt+=f'<{k}>{v.strip()} </{k}>' if isinstance(v, str) else f'<{k}>{" ".join(v)} </{k}>'
else:
prompt+=f'<{k}></{k}>'
return prompt
def custom_generate(self,
input_ids,
acc_embs_up_kg_mean,
acc_embs_down_kg_mean,
acc_embs_up_txt_mean,
acc_embs_down_txt_mean,
device,
max_new_tokens,
mode,
temperature=0.8,
top_p=0.2, top_k=3550,
n_next_tokens=50, num_return_sequences=1, random_seed=138):
torch.manual_seed(random_seed)
# Set parameters
# temperature - Higher value for more randomness, lower for more control
# top_p - Probability threshold for nucleus sampling (aka top-p sampling)
# top_k - Ignore logits below the top-k value to reduce randomness (if non-zero)
# n_next_tokens - Number of top next tokens when predicting compounds
modality0_emb = torch.unsqueeze(torch.from_numpy(acc_embs_up_kg_mean), 0).to(device) if isinstance(acc_embs_up_kg_mean, np.ndarray) else None
modality1_emb = torch.unsqueeze(torch.from_numpy(acc_embs_down_kg_mean), 0).to(device) if isinstance(acc_embs_down_kg_mean, np.ndarray) else None
modality2_emb = torch.unsqueeze(torch.from_numpy(acc_embs_up_txt_mean), 0).to(device) if isinstance(acc_embs_up_txt_mean, np.ndarray) else None
modality3_emb = torch.unsqueeze(torch.from_numpy(acc_embs_down_txt_mean), 0).to(device) if isinstance(acc_embs_down_txt_mean, np.ndarray) else None
# Generate sequences
outputs = []
next_token_compounds = []
next_token_up_genes = []
next_token_down_genes = []
for _ in range(num_return_sequences):
start_time = time.time()
generated_sequence = []
current_token = input_ids.clone()
for _ in range(max_new_tokens): # Maximum length of generated sequence
# Forward pass through the model
logits = self.model.forward(
input_ids=current_token,
modality0_emb=modality0_emb,
modality0_token_id=self.tokenizer.encode('<modality0>')[0], # 62191,
modality1_emb=modality1_emb,
modality1_token_id=self.tokenizer.encode('<modality1>')[0], # 62192,
modality2_emb=modality2_emb,
modality2_token_id=self.tokenizer.encode('<modality2>')[0], # 62193,
modality3_emb=modality3_emb,
modality3_token_id=self.tokenizer.encode('<modality3>')[0], # 62194
)[0]
# Apply temperature to logits
if temperature != 1.0:
logits = logits / temperature
# Apply top-p sampling (nucleus sampling)
sorted_logits, sorted_indices = torch.sort(logits, descending=True)
cumulative_probs = torch.cumsum(torch.softmax(sorted_logits, dim=-1), dim=-1)
sorted_indices_to_remove = cumulative_probs > top_p
if top_k > 0:
sorted_indices_to_remove[..., top_k:] = 1
# Set the logit values of the removed indices to a very small negative value
inf_tensor = torch.tensor(float("-inf")).type(torch.bfloat16).to(logits.device)
logits = logits.where(sorted_indices_to_remove, inf_tensor)
# Sample the next token
if current_token[0][-1] == self.tokenizer.encode('<drug>')[0] and len(next_token_compounds)==0:
next_token_compounds.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
# Sample the next token for UP genes
if current_token[0][-1] == self.tokenizer.encode('<up>')[0] and len(next_token_up_genes)==0:
next_token_up_genes.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
# Sample the next token for DOWN genes
if current_token[0][-1] == self.tokenizer.encode('<down>')[0] and len(next_token_down_genes)==0:
next_token_down_genes.append(torch.topk(torch.softmax(logits, dim=-1)[0][len(current_token[0])-1, :].flatten(), n_next_tokens).indices)
next_token = torch.multinomial(torch.softmax(logits, dim=-1)[0], num_samples=1)[len(current_token[0])-1, :].unsqueeze(0)
# Append the sampled token to the generated sequence
generated_sequence.append(next_token.item())
# Stop generation if an end token is generated
if next_token == self.tokenizer.eos_token_id:
break
# Prepare input for the next iteration
current_token = torch.cat((current_token, next_token), dim=-1)
print(time.time()-start_time)
outputs.append(generated_sequence)
# Process generated up/down lists
processed_outputs = {"up": [], "down": []}
if mode in ['meta2diff', 'meta2diff2compound']:
predicted_up_genes_tokens = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_up_genes]
predicted_up_genes = []
for j in predicted_up_genes_tokens:
generated_up_sample = [i.strip() for i in j]
predicted_up_genes.append(sorted(set(generated_up_sample) & set(self.unique_genes_p3), key = generated_up_sample.index))
processed_outputs['up'] = predicted_up_genes
predicted_down_genes_tokens = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_down_genes]
predicted_down_genes = []
for j in predicted_down_genes_tokens:
generated_down_sample = [i.strip() for i in j]
predicted_down_genes.append(sorted(set(generated_down_sample) & set(self.unique_genes_p3), key = generated_down_sample.index))
processed_outputs['down'] = predicted_down_genes
else:
processed_outputs = outputs
predicted_compounds_ids = [self.tokenizer.convert_ids_to_tokens(j) for j in next_token_compounds]
predicted_compounds = []
for j in predicted_compounds_ids:
predicted_compounds.append([i.strip() for i in j])
return processed_outputs, predicted_compounds, random_seed
def __call__(self, data: Dict[str, Any]) -> Dict[str, str]:
"""
Args:
data (:dict:):
The payload with the text prompt and generation parameters.
"""
data = data.copy()
parameters = data.pop("parameters", None)
config_data = data.pop("inputs", None)
mode = data.pop('mode', 'Not specified')
prompt = self.create_prompt(config_data)
if mode != "diff2compound":
prompt+="<up>"
inputs = self.tokenizer(prompt, return_tensors="pt")
input_ids = inputs["input_ids"].to(self.device)
max_new_tokens = self.model.config.max_seq_len - len(input_ids[0])
try:
if set(["up", "down"]) & set(config_data.keys()):
acc_embs_up1 = []
acc_embs_up2 = []
for gs in config_data['up']:
try:
acc_embs_up1.append(self.emb_hgt_genes[self.emb_hgt_genes.gene_symbol==gs].embs.values[0])
acc_embs_up2.append(self.emb_gpt_genes[self.emb_gpt_genes.gene_symbol==gs].embs.values[0])
except Exception as e:
pass
acc_embs_up1_mean = np.array(acc_embs_up1).mean(0) if acc_embs_up1 else None
acc_embs_up2_mean = np.array(acc_embs_up2).mean(0) if acc_embs_up2 else None
acc_embs_down1 = []
acc_embs_down2 = []
for gs in config_data['down']:
try:
acc_embs_down1.append(self.emb_hgt_genes[self.emb_hgt_genes.gene_symbol==gs].embs.values[0])
acc_embs_down2.append(self.emb_gpt_genes[self.emb_gpt_genes.gene_symbol==gs].embs.values[0])
except Exception as e:
pass
acc_embs_down1_mean = np.array(acc_embs_down1).mean(0) if acc_embs_down1 else None
acc_embs_down2_mean = np.array(acc_embs_down2).mean(0) if acc_embs_down2 else None
else:
acc_embs_up1_mean, acc_embs_up2_mean, acc_embs_down1_mean, acc_embs_down2_mean = None, None, None, None
generated_sequence, raw_next_token_generation, out_seed = self.custom_generate(input_ids = input_ids,
acc_embs_up_kg_mean=acc_embs_up1_mean,
acc_embs_down_kg_mean=acc_embs_down1_mean,
acc_embs_up_txt_mean=acc_embs_up2_mean,
acc_embs_down_txt_mean=acc_embs_down2_mean, max_new_tokens=max_new_tokens, mode=mode,
device=self.device, **parameters)
next_token_generation = [sorted(set(i) & set(self.unique_compounds_p3), key = i.index) for i in raw_next_token_generation]
if mode == "meta2diff":
outputs = {"up": generated_sequence['up'], "down": generated_sequence['down']}
out = {"output": outputs, "mode": mode, "message": "Done!", "input": prompt, 'random_seed': out_seed}
elif mode == "meta2diff2compound":
outputs = {"up": generated_sequence['up'], "down": generated_sequence['down']}
out = {
"output": outputs, "compounds": next_token_generation, "raw_output": raw_next_token_generation, "mode": mode,
"message": "Done!", "input": prompt, 'random_seed': out_seed}
elif mode == "diff2compound":
outputs = generated_sequence
out = {
"output": outputs, "compounds": next_token_generation, "raw_output": raw_next_token_generation, "mode": mode,
"message": "Done!", "input": prompt, 'random_seed': out_seed}
else:
out = {"message": f"Specify one of the following modes: meta2diff, meta2diff2compound, diff2compound. Your mode is: {mode}"}
except Exception as e:
print(e)
outputs, next_token_generation = [None], [None]
out = {"output": outputs, "mode": mode, 'message': f"{e}", "input": prompt, 'random_seed': 138}
return out
def main():
pass
if __name__=="__main__":
main()