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{
"cells": [
{
"cell_type": "markdown",
"id": "b1b4e507-0ca2-4309-ac5c-0461f99edc72",
"metadata": {},
"source": [
"# Phosformer-ST Example Code"
]
},
{
"cell_type": "markdown",
"id": "3a23dd26-2060-4cb1-a1a0-dd97b168a329",
"metadata": {},
"source": [
"## imports"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ec3bd89c-8aa1-408c-b569-c89dc2bb768d",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import sys\n",
"import hashlib\n",
"import warnings\n",
"sys.dont_write_bytecode=True\n",
"\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt\n",
"\n",
"import torch\n",
"\n",
"from tokenization_esm import EsmTokenizer\n",
"from modeling_esm import EsmForSequenceClassificationMHACustom\n",
"#for versioning spesfics see ReadMe \n"
]
},
{
"cell_type": "markdown",
"id": "a42e87fc-bd23-4b7b-8234-06cbdcb25bc0",
"metadata": {},
"source": [
"## loading in pre-trained model"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "9def3d4b-822d-44b8-a896-3e6ee5aca13d",
"metadata": {},
"outputs": [],
"source": [
"model_dir = 'multitask_MHA_esm2_t30_150M_UR50D_neg_ratio_8+8_shift_30_mask_0.2_2023-03-25_90'\n",
"\n",
"tokenizer = EsmTokenizer.from_pretrained(model_dir)\n",
"model = EsmForSequenceClassificationMHACustom.from_pretrained(model_dir, num_labels=2)\n",
"\n"
]
},
{
"cell_type": "markdown",
"id": "ff3f7f18-6cb2-4818-9583-bb729e848b81",
"metadata": {},
"source": [
"## configureing paramaters of the Phos-ST model\n",
"\n",
"## also orginizing the data for the input into Phos-ST "
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "1dbece0a-39a3-4932-8781-a679dd699587",
"metadata": {},
"outputs": [],
"source": [
"def run_model(peptides, kinases, model=model, tokenizer=tokenizer, device='cuda', batch_size=50, output_hidden_states=True, output_attentions=True):\n",
" torch.cuda.empty_cache()\n",
" \n",
" model.eval()\n",
" model = model.to(device)\n",
" \n",
" size = len(peptides)\n",
" breaks = set(np.cumsum([batch_size]*(size//batch_size)+[size%batch_size])-1)\n",
"\n",
" pairs = []\n",
" for n, pair in enumerate(zip(peptides, kinases)):\n",
" sys.stderr.write(f'{1+n}\\r')\n",
" pairs += [pair]\n",
" if n in breaks:\n",
" \n",
" output = dict(zip(('peptide','kinase'),zip(*pairs)))\n",
" ids = tokenizer(pairs, padding=True, return_tensors='pt')\n",
" ids = ids.to(device)\n",
" \n",
" with torch.no_grad():\n",
" results, classifier_attn_outputs, classifier_attn_output_weights = model(ids['input_ids'], \n",
" attention_mask=ids['attention_mask'], \n",
" output_hidden_states=output_hidden_states, \n",
" output_attentions=output_attentions)\n",
" \n",
" attention_mask = ids['attention_mask'].cpu().type(torch.bool)\n",
"\n",
" output['probability'] = results['logits'].softmax(1)[:,1].cpu().numpy()\n",
" \n",
" if output_hidden_states:\n",
" last_embeddings = results['hidden_states'][-1].cpu().numpy()\n",
" output['embedding'] = [i[m] for i, m in zip(last_embeddings, attention_mask)]\n",
" \n",
" if output_attentions:\n",
" last_attentions = results['attentions'][-1].cpu().numpy()\n",
" output['attention'] = [i[:,m,:][:,:,m] for i, m in zip(last_attentions, attention_mask)]\n",
" \n",
" classifier_attn_outputs = classifier_attn_outputs.cpu()\n",
" output['classifier_attn_outputs'] = classifier_attn_outputs\n",
"\n",
" classifier_attn_output_weights = classifier_attn_output_weights.cpu()\n",
" output['classifier_attn_output_weights'] = [i[:,m[16:]] for i, m in zip(classifier_attn_output_weights, attention_mask)]\n",
" \n",
" keys = output.keys()\n",
" for data in zip(*(output[k] for k in keys)):\n",
" yield dict(zip(keys, data))\n",
" \n",
" pairs = []\n"
]
},
{
"cell_type": "markdown",
"id": "3fbfc05d-970c-4db9-bae8-61ea2ffb06af",
"metadata": {},
"source": [
"## helper funtion to use Phos-ST"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "98e90bc6-28db-449c-8a0b-805ef22cd9ec",
"metadata": {},
"outputs": [],
"source": [
"# this could be modified to take in a list of substrate and kinase domains\n",
"# just drop the square brackets on the kinaseDomainSeq variable and substrate15mer variable around the job fuction's 1st and 2nd argument\n",
"def phosST(kinaseDomainSeq,substrate15mer):\n",
" job = run_model(\n",
" [substrate15mer],\n",
" [kinaseDomainSeq],\n",
" model=model, \n",
" tokenizer=tokenizer, \n",
" device='cuda', \n",
" batch_size=10,\n",
" output_hidden_states=False,\n",
" output_attentions=False,\n",
" )\n",
" \n",
" #total = dataset.shape[0]\n",
" results = {\n",
" 'kinase' : [],\n",
" 'peptide' : [],\n",
" 'prob' : [],\n",
" }\n",
"\n",
" \n",
" for n, i in enumerate(job):\n",
" #sys.stderr.write(f'{n+1} / {total}\\r')\n",
" results['kinase' ] += [i['kinase']]\n",
" results['peptide'] += [i['peptide']]\n",
" results['prob' ] += [i['probability']]\n",
" \n",
" result = pd.DataFrame(results)\n",
" print(\"The Predictive score is \"+str(i['probability']))\n",
" \n",
" return result\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "151c217b-1ee1-4cf7-b41f-b52f5ce22719",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"\n"
]
},
{
"cell_type": "markdown",
"id": "ee511f8b-5d9e-4c8a-8191-bd2a7fd3a5e9",
"metadata": {},
"source": [
"# Postive Example"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5bd6e8ee-444e-49d5-a617-d2343759759a",
"metadata": {},
"outputs": [],
"source": [
"# P17612 KAPCA_HUMAN\n",
"kinDomain=\"FERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWF\"\n",
"# P53602_S96_LARKRRNSRDGDPLP\n",
"substrate=\"LARKRRNSRDGDPLP\"\n",
"\n",
"phosST(kinDomain,substrate).to_csv('PostiveExample.csv')\n",
"#the score should be listed in the csv file aswell"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f1f27f0f-5bda-4107-adef-a8712ace540c",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"id": "f432840c-f56e-40f2-959f-157dc65f57d6",
"metadata": {},
"source": [
"# Negitive Example"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "41e2c0de-9088-4cf1-a744-a451ce19d7a6",
"metadata": {},
"outputs": [],
"source": [
"# P17612 KAPCA_HUMAN\n",
"kinDomain=\"FERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWF\"\n",
"# 'Q01831_T169_PVEIEIETPEQAKTR'\n",
"substrate=\"PVEIEIETPEQAKTR\"\n",
"\n",
"phosST(kinDomain,substrate).to_csv('NegitiveExample.csv')\n",
"#the score should be listed in the csv file aswell"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ac3b5b10-3cde-4f66-ba7a-f137538fa880",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "85509eea-3217-492f-bf77-9da8ee123b76",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "9bfe47df-7e6b-487b-92b6-33ba2d9c6eb7",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "c6c2b239-f7d1-418b-bd1d-916fb1db8933",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "5af09564-6b23-4dea-a0a3-76bc8362b7b4",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
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"file_extension": ".py",
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