Ritambhara Singh

64 papers A* 2A 1B 1C 1Misc 2Journal 44Unranked 13
YearRankTypeTitle / Venue / Authors
2026 J jnl
Identifying and timing patient outcomes in clinician notes using large language models.
Artif. Intell. Medicine
Tassallah Abdullahi, Ali Hamzeh, Isaac Sears, Neelia Abadi, Ritambhara Singh, Carsten Eickhoff, Adeel Abbasi
2026 J jnl
Mechanisms of Prompt-Induced Hallucination in Vision-Language Models.
CoRR
William Rudman, Michal Golovanevsky, Dana Arad, Yonatan Belinkov, Ritambhara Singh, Carsten Eickhoff, Kyle Mahowald
2026 J jnl
The Persona Paradox: Medical Personas as Behavioral Priors in Clinical Language Models.
CoRR
Tassallah Abdullahi, Shrestha Ghosh, Hamish S. Fraser, Daniel León Tramontini, Adeel Abbasi, Ghada Bourjeily, Carsten Eickhoff, Ritambhara Singh
2026 J jnl
UbuntuGuard: A Culturally-Grounded Policy Benchmark for Equitable AI Safety in African Languages.
CoRR
Tassallah Abdullahi, Macton Mgonzo, Mardiyyah Oduwole, Paul Okewunmi, Abraham Toluwase Owodunni, Ritambhara Singh, Carsten Eickhoff
2025 — conf
Extending Fairness in Single-Cell AI: Evaluating Age, Sex, and Ethnicity Bias with Synthetic Data Augmentation.
BCB
Fernando Peralta Castro, Jiaqi Zhang, Ritambhara Singh
2025 — conf
Forgotten Polygons: Multimodal Large Language Models are Shape-Blind.
ACL (Findings)
William Rudman, Michal Golovanevsky, Amir Bar, Vedant Palit, Yann LeCun, Carsten Eickhoff, Ritambhara Singh
2025 J jnl
Forgotten Polygons: Multimodal Large Language Models are Shape-Blind.
CoRR
William Rudman, Michal Golovanesky, Amir Bar, Vedant Palit, Yann LeCun, Carsten Eickhoff, Ritambhara Singh
2025 J jnl
GrapHiC: An Integrative Graph Based Approach for Imputing Missing Hi-C Reads.
IEEE Trans. Comput. Biol. Bioinform.
Ghulam Murtaza, Justin Wagner, Justin M. Zook, Ritambhara Singh
2025 — conf
Improved Spatial Transcriptomics Clustering with Nested Graph Neural Networks.
BCB
Atishay Jain, David H. Laidlaw, Ying Ma, Ritambhara Singh
2025 — conf
K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction.
KDD (2)
Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak, Ghulam Murtaza, Stephen H. Bach, Carsten Eickhoff, Ritambhara Singh
2025 J jnl
K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction.
CoRR
Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak, Ghulam Murtaza, Stephen H. Bach, Carsten Eickhoff, Ritambhara Singh
2025 J jnl
Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.
PLoS Comput. Biol.
Yusuke Suita, Hardy Bright, Yuan Pu, Merih Deniz Toruner, Jordan Idehen, Nikos Tapinos, Ritambhara Singh
2025 J jnl
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation.
PLoS Comput. Biol.
Wenjun Zhao, Erica Larschan, Björn Sandstede, Ritambhara Singh
2025 J jnl
PiCME: Pipeline for Contrastive Modality Evaluation and Encoding in the MIMIC Dataset.
CoRR
Michal Golovanevsky, Pranav Mahableshwarkar, Carsten Eickhoff, Ritambhara Singh
2025 A* conf
Pixels Versus Priors: Controlling Knowledge Priors in Vision-Language Models through Visual Counterfacts.
EMNLP
Michal Golovanevsky, William Rudman, Michael A. Lepori, Amir Bar, Ritambhara Singh, Carsten Eickhoff
2025 J jnl
Pixels Versus Priors: Controlling Knowledge Priors in Vision-Language Models through Visual Counterfacts.
CoRR
Michal Golovanevsky, William Rudman, Michael A. Lepori, Amir Bar, Ritambhara Singh, Carsten Eickhoff
2025 — conf
What Do VLMs NOTICE? A Mechanistic Interpretability Pipeline for Gaussian-Noise-free Text-Image Corruption and Evaluation.
NAACL (Long Papers)
Michal Golovanevsky, William Rudman, Vedant Palit, Carsten Eickhoff, Ritambhara Singh
2025 — conf
scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data.
BCB
Jiaqi Zhang, Manav Chakravarthy, Ritambhara Singh
2024 J jnl
<tt> scNODE </tt>: generative model for temporal single cell transcriptomic data prediction.
Bioinform.
Jiaqi Zhang, Erica Larschan, Jeremy Bigness, Ritambhara Singh
2024 J jnl
BetaExplainer: A Probabilistic Method to Explain Graph Neural Networks.
CoRR
Whitney Sloneker, Shalin Patel, Michael Wang, Lorin Crawford, Ritambhara Singh
2024 A conf
Breaking isometric ties and introducing priors in Gromov-Wasserstein distances.
AISTATS
Pinar Demetci, Quang Huy Tran, Ievgen Redko, Ritambhara Singh
2024 J jnl
On the Effect of Image Resolution on Semantic Segmentation.
CoRR
Ritambhara Singh, Abhishek Jain, Pietro Perona, Shivani Agarwal, Junfeng Yang
2024 Misc conf
Retrieval Augmented Zero-Shot Text Classification.
ICTIR
Tassallah Abdullahi, Ritambhara Singh, Carsten Eickhoff
2024 J jnl
Retrieval Augmented Zero-Shot Text Classification.
CoRR
Tassallah Abdullahi, Ritambhara Singh, Carsten Eickhoff
2024 J jnl
What Do VLMs NOTICE? A Mechanistic Interpretability Pipeline for Noise-free Text-Image Corruption and Evaluation.
CoRR
Michal Golovanevsky, William Rudman, Vedant Palit, Ritambhara Singh, Carsten Eickhoff
2024 J jnl
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression.
Bioinform.
Ghulam Murtaza, Byron Butaney, Justin Wagner, Ritambhara Singh
2023 J jnl
One-Versus-Others Attention: Scalable Multimodal Integration.
CoRR
Michal Golovanevsky, Eva Schiller, Akira Nair, Ritambhara Singh, Carsten Eickhoff
2023 J jnl
Revisiting invariances and introducing priors in Gromov-Wasserstein distances.
CoRR
Pinar Demetci, Quang Huy Tran, Ievgen Redko, Ritambhara Singh
2023 A* conf
Unbalanced CO-optimal Transport.
AAAI
Quang Huy Tran, Hicham Janati, Nicolas Courty, Rémi Flamary, Ievgen Redko, Pinar Demetci, Ritambhara Singh
2022 J jnl
An automated COVID-19 triage pipeline using artificial intelligence based on chest radiographs and clinical data.
npj Digit. Medicine
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, Robin Wang, John Sollee, Celina Hsieh, Ken Chang, Fang-Xue Yang, Ritambhara Singh, Jie-Lin Ou, Raymond Y. Huang, Cai Feng, Michael D. Feldman, Tao Liu, Ji Sheng Gong, Shaolei Lu, Carsten Eickhoff, Xue Feng, Ihab Kamel, Ronnie Sebro, Michael Atalay, Terrance Healey, Yong Fan, Wei-hua Liao, Jianxin Wang, Harrison X. Bai
2022 J jnl
Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks.
J. Comput. Biol.
Jeremy Bigness, Xavier Loinaz, Shalin Patel, Erica Larschan, Ritambhara Singh
2022 J jnl
Multimodal Attention-based Deep Learning for Alzheimer's Disease Diagnosis.
CoRR
Michal Golovanevsky, Carsten Eickhoff, Ritambhara Singh
2022 J jnl
Multimodal attention-based deep learning for Alzheimer's disease diagnosis.
J. Am. Medical Informatics Assoc.
Michal Golovanevsky, Carsten Eickhoff, Ritambhara Singh
2022 J jnl
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.
J. Comput. Biol.
Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
2022 J jnl
SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation.
J. Comput. Biol.
Pinar Demetci, Rebecca Santorella, Manav Chakravarthy, Björn Sandstede, Ritambhara Singh
2022 J jnl
Single-Cell Multiomics Integration by SCOT.
J. Comput. Biol.
Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
2022 J jnl
Unbalanced CO-Optimal Transport.
CoRR
Quang Huy Tran, Hicham Janati, Nicolas Courty, Rémi Flamary, Ievgen Redko, Pinar Demetci, Ritambhara Singh
2022 B conf
Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation.
RECOMB
Pinar Demetci, Rebecca Santorella, Björn Sandstede, Ritambhara Singh
2021 — conf
A Joint Graph and Image Convolution Network for Automatic Brain Tumor Segmentation.
BrainLes@MICCAI (1)
Camillo Saueressig, Adam Berkley, Reshma Munbodh, Ritambhara Singh
2021 J jnl
A Joint Graph and Image Convolution Network for Automatic Brain Tumor Segmentation.
CoRR
Camillo Saueressig, Adam Berkley, Reshma Munbodh, Ritambhara Singh
2021 J jnl
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
Nucleic Acids Res.
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan
2020 — conf
Exploring Graph-Based Neural Networks for Automatic Brain Tumor Segmentation.
DataMod@CIKM
Camillo Saueressig, Adam Berkley, Elliot Kang, Reshma Munbodh, Ritambhara Singh
2020 J jnl
FastSK: fast sequence analysis with gapped string kernels.
Bioinform.
Derrick Blakely, Eamon Collins, Ritambhara Singh, Andrew P. Norton, Jack Lanchantin, Yanjun Qi
2020 — conf
Unsupervised manifold alignment for single-cell multi-omics data.
BCB
Ritambhara Singh, Pinar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhi-jun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, William Stafford Noble
2019 C conf
Jointly Embedding Multiple Single-Cell Omics Measurements.
WABI
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
2019 J jnl
Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi
2018 J jnl
DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications.
Bioinform.
Arshdeep Sekhon, Ritambhara Singh, Yanjun Qi
2018 J jnl
DeepDiff: Deep-learning for predicting Differential gene expression from histone modifications.
CoRR
Arshdeep Sekhon, Ritambhara Singh, Yanjun Qi
2017 J jnl
A constrained $$\ell $$ ℓ 1 minimization approach for estimating multiple sparse Gaussian or nonparanormal graphical models.
Mach. Learn.
Beilun Wang, Ritambhara Singh, Yanjun Qi
2017 — conf
Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin.
NIPS
Ritambhara Singh, Jack Lanchantin, Arshdeep Sekhon, Yanjun Qi
2017 J jnl
Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin.
CoRR
Ritambhara Singh, Jack Lanchantin, Arshdeep Sekhon, Yanjun Qi
2017 Misc conf
Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks.
PSB
Jack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi
2017 — conf
GaKCo: A Fast Gapped k-mer String Kernel Using Counting.
ECML/PKDD (1)
Ritambhara Singh, Arshdeep Sekhon, Kamran Kowsari, Jack Lanchantin, Beilun Wang, Yanjun Qi
2017 J jnl
GaKCo: a Fast GApped k-mer string Kernel using COunting.
CoRR
Ritambhara Singh, Arshdeep Sekhon, Kamran Kowsari, Jack Lanchantin, Beilun Wang, Yanjun Qi
2017 — conf
Memory Matching Networks for Genomic Sequence Classification.
ICLR (Workshop)
Jack Lanchantin, Ritambhara Singh, Yanjun Qi
2017 J jnl
Memory Matching Networks for Genomic Sequence Classification.
CoRR
Jack Lanchantin, Ritambhara Singh, Yanjun Qi
2017 J jnl
Prototype Matching Networks for Large-Scale Multi-label Genomic Sequence Classification.
CoRR
Jack Lanchantin, Arshdeep Sekhon, Ritambhara Singh, Yanjun Qi
2016 J jnl
A constrained L1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models.
CoRR
Beilun Wang, Ritambhara Singh, Yanjun Qi
2016 — conf
Character based String Kernels for Bio-Entity Relation Detection.
BioNLP@ACL
Ritambhara Singh, Yanjun Qi
2016 J jnl
Deep GDashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks.
CoRR
Jack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi
2016 J jnl
Deep Motif: Visualizing Genomic Sequence Classifications.
CoRR
Jack Lanchantin, Ritambhara Singh, Zeming Lin, Yanjun Qi
2016 J jnl
DeepChrome: Deep-learning for predicting gene expression from histone modifications.
CoRR
Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi
2016 J jnl
DeepChrome: deep-learning for predicting gene expression from histone modifications.
Bioinform.
Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi
2016 J jnl
Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.
CoRR
Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi