Smita Krishnaswamy

While data diffusion-based embeddings are widely used in unsupervised learning to reveal the intrinsic geometry of data, they are fundamenta… (voir plus)lly constrained by their discrete nature and inability to generalize beyond training points. This limitation ob

2025-10-20

TechRxiv (accepté)

RNAGenScape: Property-guided Optimization and Interpolation of mRNA Sequences with Manifold Langevin Dynamics

Danqi Liao

Chen Liu

Xingzhi Sun

Di'e Tang

Haochen Wang

Scott E. Youlten

Srikar Krishna Gopinath

Haejeong Lee

Ethan C. Strayer

Antonio J. Giraldez

2025-10-13

ArXiv (prépublication)

CTR-LoRA: Curvature-Aware and Trust-Region Guided Low-Rank Adaptation for Large Language Models

Zhuxuanzi Wang

Mingqiao Mo

Xi Xiao

Chen Liu

Chenrui Ma

Yunbei Zhang

Xiao Wang

Tianyang Wang

Parameter-efficient fine-tuning (PEFT) has become the standard approach for adapting large language models under limited compute and memory … (voir plus)budgets. Although previous methods improve efficiency through low-rank updates, quantization, or heuristic budget reallocation, they often decouple the allocation of capacity from the way updates evolve during training. In this work, we introduce CTR-LoRA, a framework guided by curvature trust region that integrates rank scheduling with stability-aware optimization. CTR-LoRA allocates parameters based on marginal utility derived from lightweight second-order proxies and constrains updates using a Fisher/Hessian-metric trust region. Experiments on multiple open-source backbones (7B-13B), evaluated on both in-distribution and out-of-distribution benchmarks, show consistent improvements over strong PEFT baselines. In addition to increased accuracy, CTR-LoRA enhances training stability, reduces memory requirements, and achieves higher throughput, positioning it on the Pareto frontier of performance and efficiency. These results highlight a principled path toward more robust and deployable PEFT.

2025-10-10

ArXiv (prépublication)

Equivariant Geometric Scattering Networks via Vector Diffusion Wavelets

David R. Johnson

Rishabh Anand

Michael Perlmutter

2025-09-30

ArXiv (prépublication)

VDW-GNNs: Vector diffusion wavelets for geometric graph neural networks

David R. Johnson

Alexander Sietsema

Rishabh Anand

Deanna Needell

Michael Perlmutter

We introduce vector diffusion wavelets (VDWs), a novel family of wavelets inspired by the vector diffusion maps algorithm that was introduce… (voir plus)d to analyze data lying in the tangent bundle of a Riemannian manifold. We show that these wavelets may be effectively incorporated into a family of geometric graph neural networks, which we refer to as VDW-GNNs. We demonstrate that such networks are effective on synthetic point cloud data, as well as on real-world data derived from wind-field measurements and neural activity data. Theoretically, we prove that these new wavelets have desirable frame theoretic properties, similar to traditional diffusion wavelets. Additionally, we prove that these wavelets have desirable symmetries with respect to rotations and translations.

2025-09-30

ArXiv (prépublication)

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

Hiren Madhu

João Felipe Rocha

Tinglin Huang

Siddharth Viswanath

Rex Ying

2025-09-24

ArXiv (prépublication)

César Miguel Valdez Cordova

Measure Before You Look: Grounding Embeddings Through Manifold Metrics

Simon Gravel

2025-09-22

NeurIPS.cc/2025/Workshop/UniReps (publié)

openreview.net

Learning Laplacian Eigenvectors: a Pre-training Method for Graph Neural Networks

Howard Dai

Nyambura Njenga

Catherine Ma

Siddharth Viswanath

Ryan Pellico

Ian Adelstein

2025-09-01

ArXiv (prépublication)

Low-dimensional embeddings of high-dimensional data

Cyril de Bodt

Alex Diaz-Papkovich

Michael Bleher

Kerstin Bunte

Corinna Coupette

Sebastian Damrich

Enrique Fita Sanmartin

Fred Hamprecht

EmHoke-'Agnes Horv'at

Dhruv Kohli

John A. Lee 0001

Boudewijn P. F. Lelieveldt

Leland McInnes

Ian T. Nabney

Maximilian Noichl

Pavlin G. Polivcar

Bastian Rieck

Guy Wolf

Gal Mishne … (voir 1 de plus)

Dmitry Kobak

Large collections of high-dimensional data have become nearly ubiquitous across many academic fields and application domains, ranging from b… (voir plus)iology to the humanities. Since working directly with high-dimensional data poses challenges, the demand for algorithms that create low-dimensional representations, or embeddings, for data visualization, exploration, and analysis is now greater than ever. In recent years, numerous embedding algorithms have been developed, and their usage has become widespread in research and industry. This surge of interest has resulted in a large and fragmented research field that faces technical challenges alongside fundamental debates, and it has left practitioners without clear guidance on how to effectively employ existing methods. Aiming to increase coherence and facilitate future work, in this review we provide a detailed and critical overview of recent developments, derive a list of best practices for creating and using low-dimensional embeddings, evaluate popular approaches on a variety of datasets, and discuss the remaining challenges and open problems in the field.

2025-08-20

ArXiv (prépublication)

Revealing dynamic temporal trajectories and underlying regulatory networks with
<i>Cflows</i>

Alexander Tong

Manik Kuchroo

Shabarni Gupta

Aarthi Venkat

Chen Liu

Beatriz P. San Juan

Laura Rangel

Brandon Zhu

John G. Lock

Christine L. Chaffer

While single-cell technologies provide snapshots of tumor states, building continuous trajectories and uncovering causative gene regulatory … (voir plus)networks remains a significant challenge. We present Cflows , an AI framework that combines neural ODE networks with Granger causality to infer continuous cell state transitions and gene regulatory interactions from static scRNA-seq data. In a new 5-time point dataset capturing tumorsphere development over 30 days, Cflows reconstructs two types of trajectories leading to tumorsphere formation or apoptosis. Trajectory-based cell-of-origin analysis delineated a novel cancer stem cell profile characterized by CD44 hi EPCAM + CAV1 + , and uncovered a cell cycle–dependent enrichment of tumorsphere-initiating potential in G2/M or S-phase cells. Cflows uncovers ESRRA as a crucial causal driver of the tumor-forming gene regulatory network. Indeed, ESRRA inhibition significantly reduces tumor growth and metastasis in vivo. Cflows offers a powerful framework for uncovering cellular transitions and dynamic regulatory networks from static single-cell data.

2025-08-06

bioRxiv (prépublication)

Manifold Filter-Combine Networks

Joyce Chew

Edward De Brouwer

Deanna Needell

Michael Perlmutter

In order to better understand manifold neural networks (MNNs), we introduce Manifold Filter-Combine Networks (MFCNs). Our filter-combine fra… (voir plus)mework parallels the popular aggregate-combine paradigm for graph neural networks (GNNs) and naturally suggests many interesting families of MNNs which can be interpreted as manifold analogues of various popular GNNs. We propose a method for implementing MFCNs on high-dimensional point clouds that relies on approximating an underlying manifold by a sparse graph. We then prove that our method is consistent in the sense that it converges to a continuum limit as the number of data points tends to infinity, and we numerically demonstrate its effectiveness on real-world and synthetic data sets.

2025-08-04

Sampling Theory, Signal Processing, and Data Analysis (publié)

CellForge: Agentic Design of Virtual Cell Models

Xiangru Tang

Zhuoyun Yu

Jiapeng Chen

Yan Cui

Yanjun Shao

Weixu Wang

Fang Wu

Yuchen Zhuang

Wenqi Shi

Zhi Huang

Arman Cohan

Xihong Lin

Fabian Theis

Mark B. Gerstein

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantiti… (voir plus)es such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

2025-08-03

ArXiv (prépublication)