AI for Drug Suitability

Challenge:
Cancer remains one of the most heterogeneous diseases, with patients showing diverse molecular and phenotypic responses to the same therapy. This variability makes it difficult to identify effective drug targets and predict treatment outcomes across individuals.

Why it matters: A “one-size-fits-all” approach to cancer treatment leads to suboptimal responses and drug resistance. Understanding patient-specific molecular profiles and drug–target interactions is essential for tailoring precise therapies and identifying opportunities for drug repurposing—especially when existing compounds could be redirected to novel cancer subtypes.

Current status:
Recent advances in multi-omics profiling and AI-based drug discovery have shown promise in modeling drug–gene interactions. However, these methods often overlook tumor heterogeneity, dynamic signaling rewiring, and population diversity, which are key to predicting individualized drug responses.

Aim:
Develop an AI-driven framework that integrates multi-omics, structural biology, and pharmacogenomic data to model tumor heterogeneity and predict patient-specific drug suitability and repurposing opportunities. By combining deep learning architectures (transformers, GNNs, and multimodal fusion networks), the system will learn cross-scale representations linking mutation profiles, protein structures, and drug mechanisms. This approach will:

· Identify repurposable drugs for resistant or rare cancer subtypes.
· Stratify patients based on molecular signatures and predicted therapeutic response.
· Accelerate precision oncology pipelines by reducing experimental screening costs.

Impact:
This research will enable data-driven, individualized cancer treatment, transforming how therapies are matched to patients and opening new pathways for targeting cancer heterogeneity with repurposed or novel drugs.

Publications

Machine Learning-Driven Insights and Predictions for CO2 Adsorption in Metal-Organic Frameworks

Skander Charni, Raeesh Muhammad, Abdulkarem I. Amhamed, Brahim Aissa, Halima Bensmail
International Conference on Thermal Engineering (ICTEA) (2025)

Tisslet: Tissues-based Learning Estimation for Transcriptomics

Ahmed Miloudi, Aisha Al-Qahtani, Thamanna Hashir, Mohamed Chikri, Halima Bensmail
BMC bioinformatics (2025)

Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia

William Villiers, Audrey Kelly, Xiaohan He, James Kaufman-Cook, Abdurrahman Elbasir, Halima Bensmail, Paul Lavender, Richard Dillon, Borbála Mifsud, Cameron S. Osborne
Nature Communications (2023)

OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values

Edin Salkovic, Abdelkader Baggag, Ahmed Gamal Rashed Salem, Halima Bensmail*, Mohammad Amin Sadeghi
Bioinformatics (2023)

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, A. Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
Briefings in Bioinformatics (2020)

Research Tools

OutSingle

A Python tool for finding outliers in RNA-Seq gene expression count data using SVD/OHT OutSingle has been tested on Windows (11). Note that OutSingle is still in alpha stage, so encountering bugs while running it is expected. If you use OutSingle in your research you can cite our paper:Edin Salkovic,…

BigQUIC: Big Quadratic Inverse Covariance Estimation

Use Newton’s method, coordinate descent, and METIS clustering to solve the L1 regularized Gaussian MLE inverse covariance matrix estimation problem. https://cran.r-project.org/web/packages/BigQuic/index.html

COUSCOus

Motivation: Current methods for predicting protein residue contacts are valuable but incomplete and do not fully agree. We developed a new method, COUSCOus, that combines advanced statistical techniques to improve accuracy. Our method consistently outperforms the established PSICOV tool across multiple benchmarks and independent tests. This demonstrates that superior statistical…

Deepsol

MotivationProtein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors.…

DeepCrystal

MotivationQCRI deep learning models for crystallization propensity prediction, DeepCrystal and B, BCrystal is ready to compute. How to get started?Perform the following steps to signup:1. Navigate to the Sign Up tab in the top navigation bar.2. Fill in your details and press register, a registration confirmation mail will be sent,…

People

DR. HALIMA BENSMAIL

PRINCIPAL SCIENTIST

View Profile

Dr. Michaël J. Aupetit

Senior Scientist

View Profile

Dr. Mohamed M. El-Shrif

Software Engineer

View Profile

Dr. Aisha M. Al-Qahtani

Research Fellow

View Profile