target-prediction

Protein target prediction using random forests and reliability-density neighbourhood analysis

Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence in the Life Sciences, 2022)

[CVPR 2022] Egocentric Action Target Prediction in 3D

PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)

Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022)

LigTMap currently supports prediction for 17 protein target classes that include 6000+ protein targets.

PIDGINv4

This repository contains our path generation framework Co-NNECT, in which we combine two models for establishing knowledge relations and paths between concepts from sentences, as a form of explicitation of implicit knowledge: COREC-LM (COmmonsense knowledge RElation Classification using Language Models), a relation classification system that we …

Differential expression analysis of miRNAs using edgeR and validated target retrieval with multiMiR.

De novo target prediction by chemical similarity-guided network-based inference

This repository contains our path generation framework Co-NNECT, in which we combine two models for establishing knowledge relations and paths between concepts from sentences, as a form of explicitation of implicit knowledge: COREC-LM (COmmonsense knowledge RElation Classification using Language Models), a relation classification system that we …

Semi-automated pipeline for compound data curation (PubChem API) and target prediction (SwissTargetPrediction) with logging, validation, and web automation support.

miRNA Hybrid Viewer 2 - seed, thermodynamic and null-model analysis of miRNA-mRNA interactions in a single offline HTML file

Analysis of Common Targets for circular RNAs - identifies the common target genes of the miRNAs that bind a given circRNA. Packaged as a reproducible Docker stack.

Database of pairwise consensuses for miR-mRNA target interactions

Synthetic Python demo for integrating multi-tool miRNA target predictions into consensus tables.

MD thesis' project, where I performed an In silico target prediction for small ncRNAs in Mycobacterium tuberculosis

Multi-task graph neural network predicting mechanism of action (MOA) and gene targets from molecular structure (SMILES). Trained on 755K compounds from 11 annotation sources. Encodes molecules as graphs via GINEConv with dual pooling and jointly predicts 446 MOA classes and 3,034 gene targets.