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PreprintU ZurichU PalermoUniversitat Pompeu FabraInstitut de Biologia EvolutivaBarcelona School of EconomicsGenomics & single-cell

Agta hunter-gatherer oral microbiomes are shaped by contact network structure

Agta hunter-gatherer oral microbiomes resemble Central African foragers more than neighbors, with contact networks predicting bacterial transmission and central individuals as supersharers.

Federico Musciotto, Begoña Dobón, Michael John Greenacre, Álex Mira and 12 more

Published Dec 31, 2030 · 0 citations

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NeurIPS 2026SichuanCollege of Computer Science, SicGenomics & single-cell

scMAF: Single-Cell Multi-Omics Clustering via Adaptive Modality Fusion

Jun Fu, Yiding Lu, Ruohong Yang, Xi Peng and 1 more

Sydney Poster Session 4, Wed, Dec 9, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026FudanGenomics & single-cell

Causally Structured Differential Network Modeling for Single-Cell Perturbation Prediction

Jiayi Dong, Xinyue Gu, Fei Wang

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026U Electronic Science and TechnolAlpaca AI LabGroup 42Sichuan AgriculturalSouthwest JiaotongGenomics & single-cell

Layout Before Pixels: Topology-Anchored Transcriptome-to-Histology Generation

Jianwei Zhao, Xin Li, Fan Yang, Qiang Zhai and 2 more

Sydney Poster Session 1, Tue, Dec 8, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Scienta LabMines ParisNeuralk AIGenomics & single-cell

When Transcriptomic Foundation Models Scale: Domain-Focused Pretraining for Drug Development in Immunology and Inflammation

Karim El Kanbi, Yannis Cattan, Aziz Fouché, Charlotte Claye and 2 more

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026SUN YAT-SEN UNIVERSITYTencent AI for Life Sciences LabTencentTsinghua University, TsinghuaThe Hong Kong University of ScieGenomics & single-cell

WaveSem: Frequency-Adaptive Tokenization for Disentangling Semantics and Noise in Genomics

Shou Z Chen, Bing He, Zhenchao Tang, Jun Zhu and 8 more

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026SpotlightNew YorkLabs For HumanityGenomics & single-cell

Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processes

Ethan Baron, Alan Amin, Andrew Wilson

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026DukeDuke University / KAUSTGenomics & single-cell

Learning Biological Hierarchies in Single-Cell Foundation Models

Xiangyu Guo, Ricardo Henao

Atlanta Poster Session 2, Wed, Dec 9, 4:30 PM–7:30 PM, Hall C1 · Published 2026

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NeurIPS 2026U Missouri ColumbiaU Missouri - ColumbiaU MissouriGenomics & single-cell

GRNAgent: A Multimodal Graph Reasoning Agent for Gene Regulatory Network Inference

Akshata Hegde, Kyler Zook, Yanli Wang, Jianlin Cheng

Atlanta Poster Session 3, Thu, Dec 10, 10:00 AM–1:00 PM, Hall C1 · Published 2026

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NeurIPS 2026CMU, Carnegie MellonCMU & MBZUAIGenomics & single-cell

Identifiable Feedback-Controlled Latent Flow for Unpaired Single-cell Spatio-Temporal Dynamics

Jianle Sun, Kun Zhang

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Texas A&MTexas A&M University - ColleGenomics & single-cell

PerturbReason: A Knowledge-Grounded Benchmark and Framework for Cell-State–Conditioned Mechanistic Reasoning of Perturbation Effects

Dongkwan Kim, Yiming Gao, Yining Yang, Yang Shen

Atlanta Poster Session 6, Fri, Dec 11, 4:30 PM–7:30 PM, Hall C1 · Published 2026

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NeurIPS 2026PurdueCytognosis FoundationGenomics & single-cell

Spectral Adaptive Repositioning for Flow-Based Single-Cell Perturbation Modeling

Shourya Verma, Mengbo Wang, Simran Kadadi, Shahin Mohammadi and 2 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026The University of ManchesterU ManchesterGenomics & single-cell

Benchmarks Design under Data Scarcity: From Coarse Labels to Diagnostic Evaluation of Biosynthetic Gene Cluster Models

Hanlin Xiao, Eriko Takano, Mauricio A Álvarez, Rainer Breitling

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Weizmann Institute of ScienceGenomics & single-cell

LeCellModel: Interpretable Density Estimation over the Gene Expression Manifold

Gil Karin, Artemy Bakulin, Nir Yosef

Sydney Poster Session 4, Wed, Dec 9, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Nagoya Institute of Technology /Genomics & single-cell

Adapting Vision Transformers to Organoid Imaging

Yu Takagi

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026U WarsawUniwersytet Warszawski ul. KrakoCMU, Carnegie MellonMerck Healthcare KGaAHelmholtz Munich GmbHGenomics & single-cell

ImmuVis: Hyperconvolutional Foundation Models for Imaging Mass Cytometry

Dawid Uchal, Marcin Możejko, Krzysztof Gogolewski, Piotr Kupidura and 13 more

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026KAISTGenentechHITSKorea Advanced Institute of ScieAI-CRED, KAISTGenomics & single-cell

scTrilemma: Balancing Identity, Invariance, and Reconstruction in Single-Cell Representation Learning

Yunhak Oh, Yoonho Lee, Junseok Lee, Namkyeong Lee and 8 more

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026ETH ZurichETHZ - ETH ZurichInstitute of Science and TechnolHelmholtz AIETHZGenomics & single-cell

Forecasting Microbial Dynamics: Evaluation Protocol and Prior-Spectrum Benchmark

Fedor Sergeev, Anna Győrffy-Kerekes, Tristan Gollmart, Vincent Fortuin and 2 more

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026ShanxiGenomics & single-cell

Dynamic Regulatory Graph Learning for Histology-to-Spatial Transcriptomics

Yikai Luo, Peng Zhang, Heyang Zhao, Hongming Shan and 1 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026WestlakeTencent AI LabTencentTencent AI for Life Sciences LabThe Hong Kong University of ScieGenomics & single-cell

UGM: Unified Multi-scale Genomic Event Modeling with Site-level Joint Prediction

Jiayang Wu, Chenchen Qin, Xu YANG, Yu Zhao and 7 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Altos LabsInstitute of Tokyo ScienceTokyo University of Agriculture Genomics & single-cell

TraceSim: A Generative Simulator and Benchmark for Joint scRNA-seq and Lineage Tracing

Mehrshad Sadria, Katsuki Fujisawa, Xun Shen

Sydney Poster Session 4, Wed, Dec 9, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026U California, IrvineComputer Science and EngineeringYaleUCIGenomics & single-cell

sMMC-22M: A Context-Aware Dataset and Benchmark for Single-Cell Spatial Transcriptomics

Xi Li, Yaqi Hu, Ziheng Duan, Xinyi Wang and 4 more

Atlanta Poster Session 4, Thu, Dec 10, 4:30 PM–7:30 PM, Hall C1 · Published 2026

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NeurIPS 2026U California, IrvineIFLYTEK Co.,LtdNEC Laboratories AmericaUCIGenomics & single-cell

TargetSage: Identifying Therapeutic Target Genes with Interpretable and Robust LLM Reasoning

Ziheng Duan, Tong Wu, Xi Li, Simon D Sun and 4 more

Atlanta Poster Session 3, Thu, Dec 10, 10:00 AM–1:00 PM, Hall C1 · Published 2026

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NeurIPS 2026Evoscape BioscienceEvoscape BioEvoscape Bioscience Co LtdEvoscapeGenomics & single-cell

Toward in Silico Strain Evaluation: A Multimodal Surrogate for Fermentation Dynamics with Metabolic Graph Pretraining

Yunxiao Li, Difeng Gao, Yubin Zheng, JIJIAO ZENG

Atlanta Poster Session 4, Thu, Dec 10, 4:30 PM–7:30 PM, Hall C1 · Published 2026

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NeurIPS 2026CeMM & Medical University ofMines ParisTechCeMM Research Center for MoleculStanfordGenomics & single-cell

Designing Cell-Type-Specific Regulatory DNA with Guided Discrete Diffusion

Animesh Awasthi, Martin Stoll, Raphael Bednarsky, Moritz Schaefer and 1 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026AntGroupShanghai Academy of Artificial IFudanGenomics & single-cell

Nüwa.RNA: An RNA Foundation Model for Unified Representation with Deep Structure Infusion

Kun Huang, Jiyang Li, Xin Guo, LIMEI HAN and 1 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026U Cambridge Sanger InstituteU StellenboschCarnegie MellonU CambridgeWelcome Sanger Genomics & single-cell

PRISM: Phenotype-Resolved Inference in Single-Cell Mixed Models via Latent Disease States and Contextualized Differential Expression

Andrea Rubbi, Lama Salem, Caleb Ellington, Pietro Lió and 3 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026U FlorenceGenomics & single-cell

What DNA Foundation Models Learn Beyond Sequence Composition

Vincenzo Y. Civale, Andrew Bagdanov, Alberto Magi

Paris Poster Session 5, Fri, Dec 11, 11:30 AM–1:30 PM, Paris Poster Hall · Published 2026

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NeurIPS 2026Wellcome Sanger Institute / UnivSanger instituteWellcome Sanger Institutewellcome sanger instituteNewcastle University, UKGenomics & single-cell

MUSS: A Multi-scale and Sequence-based Model for Single-cell Gene Regulation

Kangjie Zheng, Amirhossein Vahidi, Liying Jin, Joseph Clarke and 6 more

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026AalborgGenomics & single-cell

UncertainGen: Scalable Uncertainty-Aware Representation Learning of DNA Sequences

Abdulkadir Celikkanat, Andres Masegosa, Mads Albertsen, Thomas Nielsen

Paris Poster Session 5, Fri, Dec 11, 11:30 AM–1:30 PM, Paris Poster Hall · Published 2026

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NeurIPS 2026Department of Computer Science aThe Chinese University of Hong KTencentChinese University of Hong KongGenomics & single-cell

Cross-Cell-Line Perturbation Prediction Needs Controls

Xingyu Fan, Jinghao Wang, kim hsieh, Chunbin Gu and 1 more

Atlanta Poster Session 1, Wed, Dec 9, 10:00 AM–1:00 PM, Hall C1 · Published 2026

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NeurIPS 2026The Chinese University of Hong KThe Hong Kong University of ScieThe Chinese University of Hong KGenomics & single-cell

ATLAS: Adaptive Temporal Learning for Single-Cell Multi-Omics Alignment and Dynamics

Ye Zhang, Zijie Fang, Zhixiang Lin

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Pohang university of Science andDGISTGenomics & single-cell

Pathway-Aligned Regulator Tokens for Interpretable Spatial Gene Expression Prediction from Histologyatial Transcriptomics Prediction from Histology

Hyun Namgung, Sanghyun Park

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026DAMO Academy, Alibaba GroupAlibaba GroupGenomics & single-cell

Multi-Scale Representation Learning for Single-Cell Multi-Omics

Zhijie Zheng, Meng Lan, Fei Gu

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026KyushuThe University of OsakaNational Cancer Center JapanKyushu University, Faculty of IGenomics & single-cell

Preserving DEG Rankings for Gene Discovery in Histology-Based Spatial Gene Expression Prediction

IDER formulates image-based differential expression ranking to evaluate whether predicted spatial gene expression preserves contrast-specific DEG rankings, improving agreement and pathway overlap over reconstruction objectives.

Kaito Shiku, Kazuya Nishimura, Yasuhiro Kojima, Ryoma Bise

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Department of Computer Science aChinese University of Hong KongStanfordThe Chinese University of Hong KGenomics & single-cell

Towards Scalable Context-Aware Single-Cell Spatial Transcriptomics Prediction from Histology Images

CELLO predicts single-cell spatial transcriptomics from histology via grid sampling and distance-decay cross-attention, achieving 14x faster inference than DeepSpot2Cell without upstream segmentation.

Zijun Gao, Chunbin Gu, Xiangde Luo, Jinxi Xiang and 1 more

Sydney Poster Session 4, Wed, Dec 9, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Mila - Quebec AI Institute / UniMila - Quebec Artificial IntelliUniversité de MontréalMila - Quebec AI InstituteU OttawaGenomics & single-cell

Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

LLM-based cellular perturbation reasoning relies on intrinsic gene tendencies rather than true perturbation effects, and contrastive evidence organization improves prediction accuracy substantially.

XINYU YUAN, Xixian Liu, Jianan Zhao, Ya Shi Zhang and 2 more

Sydney Poster Session 1, Tue, Dec 8, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026PekingSchool of mathematical Science, Genomics & single-cell

Simulation-free Unbalanced Dynamic Optimal Transport with General Growth Penalty

SUDO enables simulation-free unbalanced dynamic optimal transport for general convex growth penalties, matching WFR accuracy with faster speed while supporting asymmetric biological priors.

Junda Ying, Yuxuan Wang, Bowen Yang, Peijie Zhou and 1 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Aalto University & OpenProteAaltoMIT —> Aalto University/YaiYaGenomics & single-cell

Flexible Flows for Biological Sequence Design

Flexible Flows for Biological Sequence Design proposes structured couplings and latent edit-based rate parameterization to achieve state-of-the-art results across diverse biological sequence generation tasks.

Yogesh Verma, Dani Korpela, Harri Lähdesmäki, Vikas Garg

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Harvard University, HarvardHarvardCarnegie MellonGoogle DeepMindGoogle ResearchGenomics & single-cell

How Post-Training Shapes Biological Reasoning Models

Continued pre-training aligns biological language, supervised fine-tuning improves in-domain but harms out-of-domain reasoning, and reinforcement learning recovers generalization when rewards align.

Lukas Fesser, Hanlin Zhang, Michelle M Li, Eric Wang and 4 more

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026 · ▲ 3 on Hugging Face

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