Pinned Repositories
50_layer_Resnet
50 Layer Resnet to predict the regression values of Tetrahymena pyriformis IGC50 from 2d molecular images only
ALALI
Automated Loading assuming Atomic Level Interactions (ALALI): A python tool to map atoms to qubits, including IBM Q topologies. GPL-3.0-or-later.
CardioTox
Chemception
CNN model based on Google Inception model to predict regression values of regression values of Tetrahymena pyriformis IGC50 from 2D images of molcules
HPE
Heterogeneous Predictors Ensembling for Quantitative Toxicity Prediction
HybridTox2D
In recent times, toxicological classification of chemical compounds is considered to be a grand challenge for pharma-ceutical and environment regulators. Advancement in machine learning techniques enabled efficient toxicity predic-tion pipelines. Random forests (RF), support vector machines (SVM) and deep neural networks (DNN) are often ap-plied to model the toxic effects of chemical compounds. However, complexity-accuracy tradeoff still needs to be ac-counted in order to improve the efficiency and commercial deployment of these methods. In this study, we implement a hybrid framework consists of a shallow neural network and a decision classifier for toxicity prediction of chemicals that interrupt nuclear receptor (NR) and stress response (SR) signaling pathways. A model based on proposed hybrid framework is trained on Tox21 data using 2D chemical descriptors that are less multifarious in nature and easy to calcu-late. Our method achieved the highest accuracy of 0.847 AUC (area under the curve) using a shallow neural network with only one hidden layer consisted of 10 neurons. Furthermore, our hybrid model enabled us to elucidate the inter-pretation of most important descriptors responsible for NR and SR toxicity.
Intent_classification
My demo code and a report for Intent classification
New_molecules_generation
Character level RNN to generate new molecules
QuantitativeTox
Smiles2vec
Proof of the concept implementation of smiles2vec paper
Abdulk084's Repositories
Abdulk084/Chemception
CNN model based on Google Inception model to predict regression values of regression values of Tetrahymena pyriformis IGC50 from 2D images of molcules
Abdulk084/50_layer_Resnet
50 Layer Resnet to predict the regression values of Tetrahymena pyriformis IGC50 from 2d molecular images only
Abdulk084/New_molecules_generation
Character level RNN to generate new molecules
Abdulk084/Intro-to-probability-and-data-project
Exploratory data analysis for Behavioral Risk Factor Surveillance System (BRFSS) dataset
Abdulk084/awesome-cheminformatics
A curated list of awesome Cheminformatics libraries and software.
Abdulk084/Leander_colab
Next_Project
Abdulk084/Algorithms-for-DNA-sequencing
Codes from Coursera's course Algorithms for DNA sequencing, part of genomic data science specialization offered by Johns Hopkins University
Abdulk084/augmented-GCN
Abdulk084/DeepSynergy
Abdulk084/drug-synergy-modeling
Machine learning analysis for prediction of synergistic drug behavior
Abdulk084/eToxPred
Abdulk084/interpretable-research
I collected some papers about interpretable CNN and reorganized them here.
Abdulk084/keras-attention-mechanism
Attention mechanism Implementation for Keras.
Abdulk084/keras_attention
Contains an implementation of the attention mechanism and a keras text classifier wrapper.
Abdulk084/minimum-area-bounding-rectangle
Find the minimum area bounding box that can be fitted to a set of points. Self-contained implementations in Python & Matlab.
Abdulk084/Publications
Supporting information of publications from Structural Bioinformatics Group
Abdulk084/sepsisrl
Reinforcement Learning for optimal sepsis treatment policies
Abdulk084/SMILES-enumeration
SMILES enumeration for QSAR modelling using LSTM recurrent neural networks
Abdulk084/SmileViz
A SMILES visualizer
Abdulk084/the-unix-workbench
:house_with_garden: A Book for Anyone to Get Started with Unix