2 citations · 7 across the 9 of their papers we have counts for
12 papers
Geometric Relevance Is Not Sufficient: Evaluating Focused Post-Training Supervision in Diffusion Docking
Michael Brown, Maryam Rahimimovassagh, Mehdi Yazdani-Jahromi +2
Diffusion-based molecular docking requires learning a corrective score field across a broad corruption distribution, yet individual pose errors can differ substantially in their st…
MIRAGE: Measuring Interpolation and Redundancy in Affinity GEneralization
Mehdi Yazdani-Jahromi, Sanjay Padhi, Ivan Garibay
Deep learning now underpins structure-based drug design, from complex and affinity prediction to ligand ranking and pose generation. Recent co-folding models reportedly approach fr…
FairContrast: Enhancing Fairness through Contrastive learning and Customized Augmenting Methods on Tabular Data
Aida Tayebi, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi +1
As AI systems become more embedded in everyday life, the development of fair and unbiased models becomes more critical. Considering the social impact of AI systems is not merely a…
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Ozmen Garibay
The growing importance of mRNA therapeutics and synthetic biology highlights the need for models that capture the latent structure of synonymous codon (different triplets encoding…
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay
Structure-based drug design (SBDD) leverages the 3D structure of biomolecular targets to guide the creation of new therapeutic agents. Recent advances in generative models, includi…
Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi +3
The persistent challenge of bias in machine learning models necessitates robust solutions to ensure parity and equal treatment across diverse groups, particularly in classification…
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi +2
Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in…
Agent-Based Modeling of C. Difficile Spread in Hospitals: Assessing Contribution of High-Touch vs. Low-Touch Surfaces and Inoculations' Containment Impact
Sina Abdidizaji, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi +2
Health issues and pandemics remain paramount concerns in the contemporary era. Clostridioides Difficile Infection (CDI) stands out as a critical healthcare-associated infection wit…
Controlling the Misinformation Diffusion in Social Media by the Effect of Different Classes of Agents
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Sina Abdidizaji +2
The rapid and widespread dissemination of misinformation through social networks is a growing concern in today's digital age. This study focused on modeling fake news diffusion, di…
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi +3
Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel tran…
Through a fair looking-glass: mitigating bias in image datasets
Amirarsalan Rajabi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay +1
With the recent growth in computer vision applications, the question of how fair and unbiased they are has yet to be explored. There is abundant evidence that the bias present in t…
Distraction is All You Need for Fairness
Mehdi Yazdani-Jahromi, AmirArsalan Rajabi, Ali Khodabandeh Yalabadi +2
Bias in training datasets must be managed for various groups in classification tasks to ensure parity or equal treatment. With the recent growth in artificial intelligence models a…