Title
When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes Marina Popova Iaroslav Chelombitko Aleksey Komissarov 25 0 0 13 May 2025
Efficient Unstructured Pruning of Mamba State-Space Models for Resource-Constrained Environments Ibne Farabi Shihab Sanjeda Akter Anuj Sharma Mamba 54 0 0 13 May 2025
DNAZEN: Enhanced Gene Sequence Representations via Mixed Granularities of Coding Units Lei Mao Yuanhe Tian Yan Song 23 0 0 04 May 2025
Fast and Low-Cost Genomic Foundation Models via Outlier Removal Haozheng Luo Chenghao Qiu Maojiang Su Zhihan Zhou Zoe Mehta Guo Ye Jerry Yao-Chieh Hu Han Liu AAML 55 1 0 01 May 2025
Beating Transformers using Synthetic Cognition Alfredo Ibias Miguel Rodriguez-Galindo Hector Antona Guillem Ramirez-Miranda Enric Guinovart 36 0 0 10 Apr 2025
Leveraging State Space Models in Long Range Genomics Matvei Popov Aymen Kallala Anirudha Ramesh Narimane Hennouni Shivesh Khaitan Rick Gentry Alain-Sam Cohen Mamba 65 0 0 07 Apr 2025
Gene42: Long-Range Genomic Foundation Model With Dense Attention Kirill Vishniakov Boulbaba Ben Amor Engin Tekin Nancy A. ElNaker Karthik Viswanathan ... Tiago Magalhaes Natalia Vassilieva Dwarikanath Mahapatra Marco Pimentel and Shadab Khan 3DV 44 0 0 20 Mar 2025
Transformers without Normalization Jiachen Zhu Xinlei Chen Kaiming He Yann LeCun Zhuang Liu ViT OffRL 65 8 0 13 Mar 2025
Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning and RAG for Interpretable Classification Nathaniel Lesperance S. Ratnasingham Graham W. Taylor VLM 79 0 0 13 Mar 2025
HELM: Hierarchical Encoding for mRNA Language Modeling Mehdi Yazdani-Jahromi Mangal Prakash Tommaso Mansi Artem Moskalev Rui Liao 99 2 0 13 Mar 2025
Regulatory DNA sequence Design with Reinforcement Learning Zhao-Qing Yang Bing-Huang Su Chuan Cao Ji-Rong Wen 58 0 0 11 Mar 2025
Revisiting Convolution Architecture in the Realm of DNA Foundation Models Yu Bo Weian Mao Yanjun Shao Weiqiang Bai Peng Ye Xinzhu Ma Junbo Zhao Hao Chen Chunhua Shen 3DV 60 1 0 25 Feb 2025
Learning to Discover Regulatory Elements for Gene Expression Prediction Xingyu Su Haiyang Yu D. Zhi Shuiwang Ji 36 0 0 19 Feb 2025
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification Zicheng Liu Siyuan Li Zhiyuan Chen Lei Xin Fang Wu Chang Yu Qirong Yang Yucheng Guo Yifan Yang Stan Z. Li SyDa AI4CE 94 0 0 11 Feb 2025
Accelerating Linear Recurrent Neural Networks for the Edge with Unstructured Sparsity Alessandro Pierro Steven Abreu Jonathan Timcheck Philipp Stratmann Andreas Wild S. Shrestha 75 0 0 03 Feb 2025
Longer Attention Span: Increasing Transformer Context Length with Sparse Graph Processing Techniques Nathaniel Tomczak Sanmukh Kuppannagari 98 0 0 31 Jan 2025
BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity Zahra Gharaee Scott C. Lowe ZeMing Gong Pablo Millán Arias Nicholas Pellegrino ... Lila Kari Dirk Steinke Graham W. Taylor Paul Fieguth Angel X. Chang 56 8 0 28 Jan 2025
State-space models are accurate and efficient neural operators for dynamical systems Zheyuan Hu Nazanin Ahmadi Daryakenari Qianli Shen Kenji Kawaguchi George Karniadakis Mamba AI4CE 75 13 0 28 Jan 2025
Can linguists better understand DNA? Wang Liang 92 1 0 20 Jan 2025
Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA Lifeng Qiao Peng Ye Yuchen Ren Weiqiang Bai Chaoqi Liang Xinzhu Ma Nanqing Dong W. Ouyang 91 2 0 18 Dec 2024
BarcodeMamba: State Space Models for Biodiversity Analysis Tiancheng Gao Graham W. Taylor Mamba 82 2 0 15 Dec 2024
Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHRs Michael Wornow Suhana Bedi Miguel Angel Fuentes Hernandez E. Steinberg Jason Alan Fries Christopher Ré Sanmi Koyejo N. Shah 100 4 0 09 Dec 2024
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA Aman Patel Arpita Singhal Austin Wang Anusri Pampari Maya Kasowski Anshul Kundaje ELM 66 2 0 06 Dec 2024
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter Günter Klambauer MedIm 63 4 0 06 Nov 2024
Specialized Foundation Models Struggle to Beat Supervised Baselines Zongzhe Xu Ritvik Gupta Wenduo Cheng Alexander Shen Junhong Shen Ameet Talwalkar M. Khodak AI4CE 54 7 0 05 Nov 2024
Revisiting K-mer Profile for Effective and Scalable Genome Representation Learning Abdulkadir Celikkanat A. Masegosa Thomas D. Nielsen 26 1 0 04 Nov 2024
NIMBA: Towards Robust and Principled Processing of Point Clouds With SSMs Nursena Köprücü Destiny Okpekpe Antonio Orvieto Mamba 44 1 0 31 Oct 2024
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences Zehui Li Yuhao Ni Guoxuan Xia W. Beardall Akashaditya Das Guy-Bart Stan Yiren Zhao 18 0 0 28 Oct 2024
Taipan: Efficient and Expressive State Space Language Models with Selective Attention Chien Van Nguyen Huy Huu Nguyen Thang M. Pham Ruiyi Zhang Hanieh Deilamsalehy ... Ryan A. Rossi Trung Bui Viet Dac Lai Franck Dernoncourt Thien Huu Nguyen Mamba RALM 37 1 0 24 Oct 2024
ST-MoE-BERT: A Spatial-Temporal Mixture-of-Experts Framework for Long-Term Cross-City Mobility Prediction Haoyu He Haozheng Luo Qi Wang 33 0 0 18 Oct 2024
BSM: Small but Powerful Biological Sequence Model for Genes and Proteins Weixi Xiang Xueting Han Xiujuan Chai Jing Bai 26 1 0 15 Oct 2024
OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models Heng Yang Jack Cole Ke Li 28 0 0 02 Oct 2024
dnaGrinder: a lightweight and high-capacity genomic foundation model Qihang Zhao Chi Zhang Weixiong Zhang 31 0 0 24 Sep 2024
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities Charlotte Bunne Yusuf Roohani Yanay Rosen Ankit Gupta Xikun Zhang ... Theofanis Karaletsos Aviv Regev Emma Lundberg J. Leskovec Stephen R. Quake 48 20 0 18 Sep 2024
GP-GPT: Large Language Model for Gene-Phenotype Mapping Yanjun Lyu Zihao Wu Lu Zhang Jing Zhang Yiwei Li ... Rongjie Liu Chao Huang Wentao Li Tianming Liu Dajiang Zhu LM&MA 25 3 0 15 Sep 2024
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials Yizhen Zheng Huan Yee Koh M. Yang Li Li Lauren T. May Geoffrey I. Webb Shirui Pan George Church LM&MA 49 11 0 06 Sep 2024
Differentially Private Kernel Density Estimation Erzhi Liu Jerry Yao-Chieh Hu Alex Reneau Zhao Song Han Liu 69 3 0 03 Sep 2024
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions Sully F. Chen Robert J. Steele Beakal Lemeneh S. Lad Eric Oermann Eric K. Oermann AI4CE 47 0 0 29 Aug 2024
Unlocking Efficiency: Adaptive Masking for Gene Transformer Models Soumyadeep Roy S. Sural Niloy Ganguly MedIm 43 0 0 13 Aug 2024
Genomic Language Models: Opportunities and Challenges Gonzalo Benegas Chengzhong Ye C. Albors Jianan Canal Li Yun S. Song AI4CE LM&MA ELM 53 18 0 16 Jul 2024
Mamba Hawkes Process Anningzhe Gao Shan Dai Yan Hu Mamba 31 1 0 07 Jul 2024
M5: A Whole Genome Bacterial Encoder at Single Nucleotide Resolution Agust Egilsson 39 0 0 03 Jul 2024
Multi-modal Transfer Learning between Biological Foundation Models Juan Jose Garau-Luis Patrick Bordes Liam Gonzalez Masa Roller Bernardo P. de Almeida ... Stefan Laurent Jan Grzegorzewski Maren Lang Thomas Pierrot Guillaume Richard AI4CE 41 3 0 20 Jun 2024
A Scalable and Effective Alternative to Graph Transformers Kaan Sancak Zhigang Hua Jin Fang Yan Xie Andrey Malevich Bo Long M. F. Balin Ümit V. Çatalyürek 50 1 0 17 Jun 2024
QTIP: Quantization with Trellises and Incoherence Processing Albert Tseng Qingyao Sun David Hou Christopher De Sa MQ 40 11 0 17 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 46 29 0 16 Jun 2024
Enhancing Cross-Modal Fine-Tuning with Gradually Intermediate Modality Generation Lincan Cai Shuang Li Wenxuan Ma Jingxuan Kang Binhui Xie Zixun Sun Chengwei Zhu MoE MoMe 42 0 0 13 Jun 2024
Simple and Effective Masked Diffusion Language Models S. Sahoo Marianne Arriola Yair Schiff Aaron Gokaslan Edgar Marroquin Justin T Chiu Alexander M. Rush Volodymyr Kuleshov DiffM 58 70 0 11 Jun 2024
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models Zicheng Liu Jiahui Li Siyuan Li Z. Zang Cheng Tan Yufei Huang Yajing Bai Stan Z. Li ELM 34 8 0 01 Jun 2024
Language Models Need Inductive Biases to Count Inductively Yingshan Chang Yonatan Bisk LRM 34 6 0 30 May 2024