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, Mohammad Amin Sadeghi, Abdelkader Baggag, […]
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 approaches can significantly advance protein […]
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. ModelIn this work we propose, […]
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, you will need to click […]
Deep learning, transformers and graph neural networks: a linear algebra perspective
Abdelkader Baggag, Yousef Saad
Numerical Algorithms (2025)
New Paper Published
We are pleased to announce the publication of Deep learning, transformers, and graph neural networks: a linear algebra perspective in Numerical Algorithms. Authors: Abdelkader Baggag and Yousef Saad (SIAM von Neumann Award winner). Abstract (brief): As AI permeates nearly every field of science and engineering, this article invites the numerical linear algebra (NLA) community to engage directly with the foundations of deep learning. […]
Cipherbot: A Learning Platform for AI-Augmented Education
Soon-Gyo Jung, Johanne Medina, Kholoud Aldous, Jinan Azem, Joni Salminen, Bernard J Jansen
Proceedings of the Augmented Humans International Conference (2025)
AIDR – Artificial Intelligence for Digital Response
AIDR—the Grand Prize winner of the 2015 Open Source Software System Challenge—is a free and open platform to filter and classify social media messages related to emergencies, disasters, and humanitarian crises. AIDR uses human and machine intelligence to automatically tag up to thousands of messages per minute. https://aidr.qcri.org
QCRI/CSE paper advances research and innovation by addressing limitations of AI technologies and their applications to global challenges
A research paper, originating from doctoral work at CSE and an ongoing project at QCRI, developed through collaboration between the two institutions, has been accepted for presentation at the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) 2025 in Nashville, USA. Authored by Eng. Sara A. Al-Emadi, PhD candidate, CSE, and Research Associate, QCRI, […]