arXiv Machine Learning

CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

arXiv:2608. 11269v1 Announce Type: cross Abstract: Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging.

arXiv Machine Learning

Jul 17

cGAP: Generalized Association Plots with HOMALS-Guided Heatmaps for Visualization of High-Dimensional Categorical Data

arXiv:2607. 15018v1 Announce Type: cross Abstract: High-dimensional categorical data arise in genetics, biomedicine, and the social sciences, yet visualization tools for such data remain far less developed than those for continuous variables.

By Chun-houh Chen, Shun-Chuan Chang, Chiun-How Kao, Yi-Ju Lee, Shang-Ying Shiu, Yin-Jing Tien, ShengLi Tzeng, Han-Ming Wu

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arXiv Machine Learning

Jun 5

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data

arXiv:2506. 11152v4 Announce Type: replace-cross Abstract: Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level.

By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying

llms rag benchmarks

arXiv Machine Learning

Jul 17

LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration

arXiv:2607. 14410v1 Announce Type: new Abstract: Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using single-modality pipelines.

By Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati, Kunal Rai, Tania Banerjee

rag multimodal benchmarks safety

arXiv Machine Learning

Jul 13

Uncovering smooth structures in single-cell data with PCS-guided neighbor embeddings

arXiv:2506. 22228v2 Announce Type: replace-cross Abstract: Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions.

By Rong Ma, Xi Li, Jingyuan Hu, Bin Yu

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arXiv Machine Learning

Jul 30

When One Point Is Not Enough: Addressing Ambiguous Instances in Dimensionality Reduction by Splitting

arXiv:2605. 23540v2 Announce Type: replace Abstract: Dimensionality Reduction (DR) methods are widely used to visualize high-dimensional data.

By Diede P. M. van der Hoorn, Alessio Arleo, Fernando V. Paulovich

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arXiv AI

Jun 12

scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

arXiv:2606. 13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity.

By Ping Xu, Pengjiang Li, Tian Du, Zaitian Wang, Jiawei Gu, Ziyue Qiao, Pengfei Wang, Yuanchun Zhou

llms rag diffusion multimodal benchmarks safety

arXiv AI

Jul 1

Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images

arXiv:2606. 31394v1 Announce Type: cross Abstract: Artificial intelligence is transforming our capability to solve biological challenges.

By Jisung Park, Seohyeon Kang, Daeun Yoo, Eunsu Lee, Seoin Cho, Wooyeop Choi, Ian Choi, James R. Evan, Daesoo Kim, Sonia Gandhi, Minee L. Choi

multimodal safety

arXiv Machine Learning

Aug 7

BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells

arXiv:2608. 05928v1 Announce Type: new Abstract: Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes.

By Yuhao Wang, Zelin Zang, Yuxuan Liu, Zhen Lei, Stan Z. Li

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arXiv Machine Learning

Aug 4

Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

arXiv:2608. 00985v1 Announce Type: new Abstract: The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values.

By Jiaqi Xiong, Yuntao hu, Yu Zheng, Yifei Shi, Xinyue Guo, Jiaxin Qi

arXiv AI

Jun 30

Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction

arXiv:2606. 29949v1 Announce Type: cross Abstract: H&E-stained whole-slide images offer cohort-scale availability and rich spatial context but lack molecular specificity, whereas bulk RNA-seq provides transcriptome-wide resolution at high cost with limited archival availability.

By Dominik Winter, Dominik Vonficht, Lo\"ic Le Bescond, Christian Gebbe, Marco Rosati, Richard J. Chen, Markus Schick, Ross Stewart, Nicolas Brieu

llms fine-tuning multimodal safety

arXiv AI

Jul 10

Dimensionality Reduction Meets Network Science: Sensemaking on UMAP's kNN Graph

arXiv:2607. 08746v1 Announce Type: cross Abstract: While UMAP is widely used for exploring high-dimensional data, typical workflows focus on its lower-dimensional embedding, largely overlooking the rich k-nearest-neighbor (kNN) graph that UMAP constructs internally.

By Duen Horng Chau, Donghao Ren, Fred Hohman, Dominik Moritz

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arXiv Machine Learning

Jul 2

FastUMAP: Scalable Dimensionality Reduction via Bipartite Landmark Sampling

arXiv:2605. 11428v2 Announce Type: replace Abstract: Exploratory analysis of high-dimensional data rarely stops at a single embedding.

By Hongmin Li

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