Character based String Kernels for Bio-Entity Relation Detection. - Ritambhara Singh; Yanjun Qi (BioNLP@ACL, 2016)

DeepChrome: deep-learning for predicting gene expression from histone modifications. - Ritambhara Singh; Jack Lanchantin; Gabriel Robins; Yanjun Qi (Bioinform., 2016)

Deep Motif: Visualizing Genomic Sequence Classifications. - Jack Lanchantin; Ritambhara Singh; Zeming Lin; Yanjun Qi (CoRR, 2016)

Deep GDashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks. - Jack Lanchantin; Ritambhara Singh; Beilun Wang; Yanjun Qi (CoRR, 2016)

A constrained L1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models. - Beilun Wang; Ritambhara Singh; Yanjun Qi (CoRR, 2016)

Memory Matching Networks for Genomic Sequence Classification. - Jack Lanchantin; Ritambhara Singh; Yanjun Qi (ICLR (Workshop), 2017)

Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin. - Ritambhara Singh; Jack Lanchantin; Arshdeep Sekhon; Yanjun Qi (NIPS, 2017)

GaKCo: A Fast Gapped k-mer String Kernel Using Counting. - Ritambhara Singh; Arshdeep Sekhon; Kamran Kowsari; Jack Lanchantin; Beilun Wang; Yanjun Qi (ECML/PKDD (1), 2017)

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks. - Jack Lanchantin; Ritambhara Singh; Beilun Wang; Yanjun Qi (PSB, 2017)

Prototype Matching Networks for Large-Scale Multi-label Genomic Sequence Classification. - Jack Lanchantin; Arshdeep Sekhon; Ritambhara Singh; Yanjun Qi (CoRR, 2017)

A constrained $$ ell $$ ℓ 1 minimization approach for estimating multiple sparse Gaussian or nonparanormal graphical models. - Beilun Wang; Ritambhara Singh; Yanjun Qi (Mach. Learn., 2017)

DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications. - Arshdeep Sekhon; Ritambhara Singh; Yanjun Qi (Bioinform., 2018)

Jointly Embedding Multiple Single-Cell Omics Measurements. - Jie Liu 045; Yuanhao Huang; Ritambhara Singh; Jean-Philippe Vert; William Stafford Noble (WABI, 2019)

Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction. - Ritambhara Singh; Jack Lanchantin; Gabriel Robins; Yanjun Qi (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Unsupervised manifold alignment for single-cell multi-omics data. - Ritambhara Singh; Pinar Demetci; Giancarlo Bonora; Vijay Ramani; Choli Lee; He Fang; Zhi-jun Duan; Xinxian Deng; Jay Shendure; Christine Disteche; William Stafford Noble (BCB, 2020)

Exploring Graph-Based Neural Networks for Automatic Brain Tumor Segmentation. - Camillo Saueressig; Adam Berkley; Elliot Kang; Reshma Munbodh; Ritambhara Singh (DataMod@CIKM, 2020)

FastSK: fast sequence analysis with gapped string kernels. - Derrick Blakely; Eamon Collins; Ritambhara Singh; Andrew P. Norton; Jack Lanchantin; Yanjun Qi (Bioinform., 2020)

A Joint Graph and Image Convolution Network for Automatic Brain Tumor Segmentation. - Camillo Saueressig; Adam Berkley; Reshma Munbodh; Ritambhara Singh (BrainLes@MICCAI (1), 2021)

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. - Ashley Mae Conard; Nathaniel Goodman; Yanhui Hu; Norbert Perrimon; Ritambhara Singh; Charles Lawrence; Erica Larschan (Nucleic Acids Res., 2021)

Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation. - Pinar Demetci; Rebecca Santorella; Björn Sandstede; Ritambhara Singh (RECOMB, 2022)

Multimodal attention-based deep learning for Alzheimer's disease diagnosis. - Michal Golovanevsky; Carsten Eickhoff; Ritambhara Singh (J. Am. Medical Informatics Assoc., 2022)

Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks. - Jeremy Bigness; Xavier Loinaz; Shalin Patel; Erica Larschan; Ritambhara Singh (J. Comput. Biol., 2022)

SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation. - Pinar Demetci; Rebecca Santorella; Manav Chakravarthy; Björn Sandstede; Ritambhara Singh (J. Comput. Biol., 2022)

SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. - Pinar Demetci; Rebecca Santorella; Björn Sandstede; William Stafford Noble; Ritambhara Singh (J. Comput. Biol., 2022)

Single-Cell Multiomics Integration by SCOT. - Pinar Demetci; Rebecca Santorella; Björn Sandstede; William Stafford Noble; Ritambhara Singh (J. Comput. Biol., 2022)

An automated COVID-19 triage pipeline using artificial intelligence based on chest radiographs and clinical data. - Chris K. Kim; Ji Whae Choi; Zhicheng Jiao; Dongcui Wang; Jing Wu; Thomas Y. Yi; Kasey C. Halsey; Feyisope Eweje; Thi My Linh Tran; Chang Liu 082; Robin Wang; John Sollee; et al. (npj Digit. Medicine, 2022)

Unbalanced CO-optimal Transport. - Quang Huy Tran; Hicham Janati; Nicolas Courty; Rémi Flamary; Ievgen Redko; Pinar Demetci; Ritambhara Singh (AAAI, 2023)

One-Versus-Others Attention: Scalable Multimodal Integration. - Michal Golovanevsky; Eva Schiller; Akira Nair; Ritambhara Singh; Carsten Eickhoff (CoRR, 2023)

Revisiting invariances and introducing priors in Gromov-Wasserstein distances. - Pinar Demetci; Quang Huy Tran; Ievgen Redko; Ritambhara Singh (CoRR, 2023)

Breaking isometric ties and introducing priors in Gromov-Wasserstein distances. - Pinar Demetci; Quang Huy Tran; Ievgen Redko; Ritambhara Singh (AISTATS, 2024)

Retrieval Augmented Zero-Shot Text Classification. - Tassallah Abdullahi; Ritambhara Singh; Carsten Eickhoff (ICTIR, 2024)

scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression. - Ghulam Murtaza; Byron Butaney; Justin Wagner; Ritambhara Singh (Bioinform., 2024)

scNODE : generative model for temporal single cell transcriptomic data prediction. - Jiaqi Zhang; Erica Larschan; Jeremy Bigness; Ritambhara Singh (Bioinform., 2024)

On the Effect of Image Resolution on Semantic Segmentation. - Ritambhara Singh; Abhishek Jain; Pietro Perona; Shivani Agarwal 006; Junfeng Yang (CoRR, 2024)

What Do VLMs NOTICE? A Mechanistic Interpretability Pipeline for Noise-free Text-Image Corruption and Evaluation. - Michal Golovanevsky; William Rudman; Vedant Palit; Ritambhara Singh; Carsten Eickhoff (CoRR, 2024)

BetaExplainer: A Probabilistic Method to Explain Graph Neural Networks. - Whitney Sloneker; Shalin Patel; Michael Wang; Lorin Crawford; Ritambhara Singh (CoRR, 2024)

Forgotten Polygons: Multimodal Large Language Models are Shape-Blind. - William Rudman; Michal Golovanevsky; Amir Bar; Vedant Palit; Yann LeCun; Carsten Eickhoff; Ritambhara Singh (ACL (Findings), 2025)

What Do VLMs NOTICE? A Mechanistic Interpretability Pipeline for Gaussian-Noise-free Text-Image Corruption and Evaluation. - Michal Golovanevsky; William Rudman; Vedant Palit; Carsten Eickhoff; Ritambhara Singh (NAACL (Long Papers), 2025)

K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction. - Tassallah Abdullahi; Ioanna Gemou; Nihal V. Nayak; Ghulam Murtaza; Stephen H. Bach; Carsten Eickhoff; Ritambhara Singh (CoRR, 2025)

Forgotten Polygons: Multimodal Large Language Models are Shape-Blind. - William Rudman; Michal Golovanesky; Amir Bar; Vedant Palit; Yann LeCun; Carsten Eickhoff; Ritambhara Singh (CoRR, 2025)

Pixels Versus Priors: Controlling Knowledge Priors in Vision-Language Models through Visual Counterfacts. - Michal Golovanevsky; William Rudman; Michael Lepori; Amir Bar; Ritambhara Singh; Carsten Eickhoff (CoRR, 2025)

PiCME: Pipeline for Contrastive Modality Evaluation and Encoding in the MIMIC Dataset. - Michal Golovanevsky; Pranav Mahableshwarkar; Carsten Eickhoff; Ritambhara Singh (CoRR, 2025)