import streamlit as st import numpy as np import pandas as pd import os os.environ["CUDA_VISIBLE_DEVICES"]="-1" ### load on cpu if GPU is making issue os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' from tensorflow.keras.models import load_model import time # from PIL import Image st.set_page_config(page_title="TCR-ESM",page_icon="dna") hide_streamlit_style = """ """ st.markdown(hide_streamlit_style, unsafe_allow_html=True) # image = Image.open('TCR-ESM.png') # st.image(image) st.title('TCR-ESM') st.subheader('a webserver accompanying our work on predicting TCR-peptide-MHC binding with large protein model (ESM1v) embeddings') dataset = st.radio("Please select the Training Databse",('MCPAS', 'VDJDB'), horizontal=True) task = st.radio("Please select the Prediction Task",("TCR\u03B1-TCR\u03B2-Peptide-MHC", "TCR\u03B1-TCR\u03B2-Peptide", "TCR\u03B1-Peptide-MHC", "TCR\u03B2-Peptide-MHC", "TCR\u03B1-Peptide", "TCR\u03B2-Peptide"), horizontal=True) with open("sample_input_data.zip", "rb") as file: btn = st.download_button(label="Download Sample Input Data",data=file,file_name="sample_input_data.zip", mime="application/octet-stream") # st.download_button('Download Sample Input Data', open('tcresm_sample_input.zip')) ############## get numpy files if task == "TCR\u03B1-TCR\u03B2-Peptide-MHC": alpha = st.file_uploader("Choose the .npy file containing TCR\u03B1 Embeddings", key=101) beta = st.file_uploader("Choose the .npy file containing TCR\u03B2 Embeddings", key=103) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=109) mhc = st.file_uploader("Choose the .npy file containing MHC Embeddings", key=113) shorttask = 'abpm' group = (alpha,beta,pepti,mhc) elif task == "TCR\u03B1-TCR\u03B2-Peptide": alpha = st.file_uploader("Choose the .npy file containing TCR\u03B1 Embeddings", key=127) beta = st.file_uploader("Choose the .npy file containing TCR\u03B2 Embeddings", key=131) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=137) shorttask = 'abp' group = (alpha,beta,pepti) elif task == "TCR\u03B1-Peptide-MHC": alpha = st.file_uploader("Choose the .npy file containing TCR\u03B1 Embeddings", key=139) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=149) mhc = st.file_uploader("Choose the .npy file containing MHC Embeddings", key=151) shorttask = 'apm' group = (alpha,pepti,mhc) elif task == "TCR\u03B2-Peptide-MHC": beta = st.file_uploader("Choose the .npy file containing TCR\u03B2 Embeddings", key=157) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=163) mhc = st.file_uploader("Choose the .npy file containing MHC Embeddings", key=167) shorttask = 'bpm' group = (beta,pepti,mhc) elif task == "TCR\u03B1-Peptide": alpha = st.file_uploader("Choose the .npy file containing TCR\u03B1 Embeddings", key=173) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=179) shorttask = 'ap' group = (alpha,pepti) elif task == "TCR\u03B2-Peptide": beta = st.file_uploader("Choose the .npy file containing TCR\u03B2 Embeddings", key=181) pepti = st.file_uploader("Choose the .npy file containing Peptide Embeddings", key=191) shorttask = 'bp' group = (beta,pepti) ##################### ML predict function # @st.cache_data def predict_on_batch_output(dataset,shorttask,group): if dataset == 'MCPAS': dataset='mcpas' elif dataset== 'VDJDB': dataset ='vdjdb' if dataset=='mcpas' and shorttask=='abp': #load data alpha, beta, pep = group alpha_np, beta_np, pep_np = np.load(alpha), np.load(beta), np.load(pep) #load model model = load_model('models/mcpas/bestmodel_alphabetapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, beta_np, pep_np]) elif dataset=='mcpas' and shorttask=='abpm': #load data alpha, beta, pep, mhc = group alpha_np, beta_np, pep_np, mhc_np = np.load(alpha), np.load(beta), np.load(pep), np.load(mhc) #load model model = load_model('models/mcpas/bestmodel_alphabetaptptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, beta_np, pep_np, mhc_np]) elif dataset=='mcpas' and shorttask=='ap': #load data alpha, pep, = group alpha_np, pep_np, = np.load(alpha), np.load(pep) #load model model = load_model('models/mcpas/bestmodel_alphapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np,pep_np]) elif dataset=='mcpas' and shorttask=='bp': #load data beta, pep = group beta_np, pep_np = np.load(beta), np.load(pep) #load model model = load_model('models/mcpas/bestmodel_betapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([beta_np, pep_np]) elif dataset=='mcpas' and shorttask=='apm': #load data alpha, pep, mhc = group alpha_np, pep_np, mhc_np = np.load(alpha), np.load(pep), np.load(mhc) #load model model = load_model('models/mcpas/bestmodel_alphapeptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, pep_np, mhc_np]) elif dataset=='mcpas' and shorttask=='bpm': #load data beta, pep, mhc = group beta_np, pep_np, mhc_np = np.load(beta), np.load(pep), np.load(mhc) #load model model = load_model('models/mcpas/bestmodel_betapeptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([beta_np, pep_np, mhc_np]) elif dataset=='vdjdb' and shorttask=='abp': #load data alpha, beta, pep = group alpha_np, beta_np, pep_np = np.load(alpha), np.load(beta), np.load(pep) #load model model = load_model('models/vdjdb/bestmodel_alphabetapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, beta_np, pep_np]) elif dataset=='vdjdb' and shorttask=='abpm': #load data alpha, beta, pep, mhc = group alpha_np, beta_np, pep_np, mhc_np = np.load(alpha), np.load(beta), np.load(pep), np.load(mhc) #load model model = load_model('models/vdjdb/bestmodel_alphabetapeptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, beta_np, pep_np, mhc_np]) elif dataset=='vdjdb' and shorttask=='ap': #load data alpha, pep, = group alpha_np, pep_np, = np.load(alpha), np.load(pep) #load model model = load_model('models/vdjdb/bestmodel_alphapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, pep_np]) elif dataset=='vdjdb' and shorttask=='bp': #load data beta, pep = group beta_np, pep_np = np.load(beta), np.load(pep) #load model model = load_model('models/vdjdb/bestmodel_betapeptide.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([beta_np, pep_np]) elif dataset=='vdjdb' and shorttask=='apm': #load data alpha, pep, mhc = group alpha_np, pep_np, mhc_np = np.load(alpha), np.load(pep), np.load(mhc) #load model model = load_model('models/vdjdb/bestmodel_alphapeptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([alpha_np, pep_np, mhc_np]) elif dataset=='vdjdb' and shorttask=='bpm': #load data beta, pep, mhc = group beta_np, pep_np, mhc_np = np.load(beta), np.load(pep), np.load(mhc) #load model model = load_model('models/vdjdb/bestmodel_betapeptidemhc.hdf5',compile=False) #predict_on_batch output = model.predict_on_batch([beta_np, pep_np, mhc_np]) # return np.around(output.squeeze(), 4) val = np.squeeze(output) return val # @st.cache_data def convert_df(df): # IMPORTANT: Cache the conversion to prevent computation on every rerun return df.to_csv().encode('utf-8') ##################### if st.button('Submit'): # with st.spinner('Wait for it...'): # time.sleep(0.5) # res = predict_on_batch_output(dataset,shorttask,group) # st.write("Binding Probabilities") # st.dataframe((np.round(res, 4))) # csv = convert_df(pd.DataFrame(np.round(res, 4), columns=['output'])) # st.download_button(label="Download Predictions",data=csv,file_name='tcresm_predictions.csv', mime='text/csv') try: res = predict_on_batch_output(dataset,shorttask,group) with st.spinner('Calculating ...'): time.sleep(0.5) st.write("Binding Probabilities") st.dataframe((np.round(res, 4)), use_container_width=500, height=500) csv = convert_df(pd.DataFrame(np.round(res, 4), columns=['output'])) st.download_button(label="Download Predictions",data=csv,file_name='tcresm_predictions.csv', mime='text/csv') except: st.error('Please ensure you have uploaded the files and chosen the correct model before pressing the Submit button', icon="🚨") # if st.button("Clear All"): # # Clear values from *all* all in-memory and on-disk data caches: # # i.e. clear values from both square and cube # st.cache.clear() st.caption('Developed By: Shashank Yadav : shashank[at]arizona.edu', unsafe_allow_html=True)