Aly A. Khan

16 papers A* 2B 1C 1Misc 1Journal 10Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Cell-JEPA: Latent Representation Learning for Single-Cell Transcriptomics.
CoRR
Ali ElSheikh, Rui-Xi Wang, Weimin Wu, Yibo Wen, Payam Dibaeinia, Jennifer Yuntong Zhang, Jerry Yao-Chieh Hu, Mei Knudson, Sudarshan Babu, Shao-Hua Sun, Aly A. Khan, Han Liu
2025 J jnl
HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields.
CoRR
Sudarshan Babu, Phillip Lo, Xiao Zhang, Aadi Srivastava, Ali Davariashtiyani, Jason Perera, Michael Maire, Aly A. Khan
2025 J jnl
Scalable Single-Cell Gene Expression Generation with Latent Diffusion Models.
CoRR
Giovanni Palla, Sudarshan Babu, Payam Dibaeinia, James D. Pearce, Donghui Li, Aly A. Khan, Theofanis Karaletsos, Jakub M. Tomczak
2024 J jnl
Computational prediction of protein interactions in single cells by proximity sequencing.
PLoS Comput. Biol.
Junjie Xia, Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savas Tay
2024 A* conf
Enhancing Instance-Level Image Classification with Set-Level Labels.
ICLR
Renyu Zhang, Aly A. Khan, Yuxin Chen, Robert L. Grossman
2024 B conf
TRIBAL: Tree Inference of B Cell Clonal Lineages.
RECOMB
Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan
2023 J jnl
Enhancing Instance-Level Image Classification with Set-Level Labels.
CoRR
Renyu Zhang, Aly A. Khan, Yuxin Chen, Robert L. Grossman
2023 A* conf
Scalable Batch-Mode Deep Bayesian Active Learning via Equivalence Class Annealing.
ICLR
Renyu Zhang, Aly A. Khan, Robert L. Grossman, Yuxin Chen
2022 J jnl
Privacy preserving validation for multiomic prediction models.
Briefings Bioinform.
Talal Ahmed, Mark A. Carty, Stephane Wenric, Jonathan R. Dry, Ameen A. Salahudeen, Aly A. Khan, Eric Lefkofsky, Martin C. Stumpe, Raphael Pelossof
2021 J jnl
BALanCe: Deep Bayesian Active Learning via Equivalence Class Annealing.
CoRR
Renyu Zhang, Aly A. Khan, Robert L. Grossman, Yuxin Chen
2021 J jnl
Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination.
PLoS Comput. Biol.
Derek Reiman, Godhev Kumar Manakkat Vijay, Heping Xu, Andrew Sonin, Dianyu Chen, Nathan Salomonis, Harinder Singh, Aly A. Khan
2020 — conf
Evaluating and interpreting caption prediction for histopathology images.
MLHC
Renyu Zhang, Christopher Weber, Robert L. Grossman, Aly A. Khan
2020 C conf
Evaluation of Hyperbolic Attention in Histopathology Images.
BIBE
Renyu Zhang, Aly A. Khan, Robert L. Grossman
2019 Misc conf
Integrating RNA expression and visual features for immune infiltrate prediction.
PSB
Derek Reiman, Lingdao Sha, Irvin Ho, Timothy Tan, Denise Lau, Aly A. Khan
2018 J jnl
Predicting protein-protein interactions through sequence-based deep learning.
Bioinform.
Somaye Hashemifar, Behnam Neyshabur, Aly A. Khan, Jinbo Xu
2017 J jnl
BASIC: BCR assembly from single cells.
Bioinform.
Stefan Canzar, Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly A. Khan