SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
Fuente:
arXiv
Saved in:
| Main Authors: | Tsui, Darin, Musharaf, Aryan, Erginbas, Yigit Efe, Kang, Justin Singh, Aghazadeh, Amirali |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
by: Yang, Qirong, et al.
Published: (2025)
by: Yang, Qirong, et al.
Published: (2025)
Gene and RNA Editing: Methods, Enabling Technologies, Applications, and Future Directions
by: Aledhari, Mohammed, et al.
Published: (2024)
by: Aledhari, Mohammed, et al.
Published: (2024)
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
by: Walton, Thomas, et al.
Published: (2025)
by: Walton, Thomas, et al.
Published: (2025)
scVGAE: A Novel Approach using ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation
by: Inoue, Yoshitaka
Published: (2024)
by: Inoue, Yoshitaka
Published: (2024)
From In Silico to In Vitro: A Comprehensive Guide to Validating Bioinformatics Findings
by: Wang, Tianyang, et al.
Published: (2025)
by: Wang, Tianyang, et al.
Published: (2025)
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
by: Kim, Jeremie S., et al.
Published: (2019)
by: Kim, Jeremie S., et al.
Published: (2019)
Unlocking Noisy Real-World Corpora for Foundation Model Pre-Training via Quality-Aware Tokenization
by: Gollwitzer, Arvid E., et al.
Published: (2026)
by: Gollwitzer, Arvid E., et al.
Published: (2026)
A Linear Time Quantum Algorithm for Pairwise Sequence Alignment
by: Khan, Md. Rabiul Islam, et al.
Published: (2023)
by: Khan, Md. Rabiul Islam, et al.
Published: (2023)
AntigenLM: Structure-Aware DNA Language Modeling for Influenza
by: Pei, Yue, et al.
Published: (2026)
by: Pei, Yue, et al.
Published: (2026)
RNA-GPT: Multimodal Generative System for RNA Sequence Understanding
by: Xiao, Yijia, et al.
Published: (2024)
by: Xiao, Yijia, et al.
Published: (2024)
Beyond the Alphabet: Deep Signal Embedding for Enhanced DNA Clustering
by: Abraham, Hadas, et al.
Published: (2024)
by: Abraham, Hadas, et al.
Published: (2024)
Efficient Algorithm for Sparse Fourier Transform of Generalized $q$-ary Functions
by: Tsui, Darin, et al.
Published: (2025)
by: Tsui, Darin, et al.
Published: (2025)
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome
by: Zhou, Zhihan, et al.
Published: (2023)
by: Zhou, Zhihan, et al.
Published: (2023)
dnaGrinder: a lightweight and high-capacity genomic foundation model
by: Zhao, Qihang, et al.
Published: (2024)
by: Zhao, Qihang, et al.
Published: (2024)
DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings
by: Zhou, Zhihan, et al.
Published: (2024)
by: Zhou, Zhihan, et al.
Published: (2024)
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
by: Kong, Yong
Published: (2014)
by: Kong, Yong
Published: (2014)
Revisiting K-mer Profile for Effective and Scalable Genome Representation Learning
by: Celikkanat, Abdulkadir, et al.
Published: (2024)
by: Celikkanat, Abdulkadir, et al.
Published: (2024)
ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data
by: Jiao, Yifeng, et al.
Published: (2025)
by: Jiao, Yifeng, et al.
Published: (2025)
On Recovering Higher-order Interactions from Protein Language Models
by: Tsui, Darin, et al.
Published: (2024)
by: Tsui, Darin, et al.
Published: (2024)
Large Language Models in Plant Biology
by: Lam, Hilbert Yuen In, et al.
Published: (2024)
by: Lam, Hilbert Yuen In, et al.
Published: (2024)
Bridging Sequence-Structure Alignment in RNA Foundation Models
by: Yang, Heng, et al.
Published: (2024)
by: Yang, Heng, et al.
Published: (2024)
GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding
by: Long, Weicai, et al.
Published: (2026)
by: Long, Weicai, et al.
Published: (2026)
GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction
by: Inoue, Yoshitaka, et al.
Published: (2025)
by: Inoue, Yoshitaka, et al.
Published: (2025)
Motif Caller: Sequence Reconstruction for Motif-Based DNA Storage
by: Agarwal, Parv, et al.
Published: (2024)
by: Agarwal, Parv, et al.
Published: (2024)
Biological Sequence Clustering: A Survey
by: Zhang, Simeng, et al.
Published: (2026)
by: Zhang, Simeng, et al.
Published: (2026)
Generative Language Models on Nucleotide Sequences of Human Genes
by: Ihtiyar, Musa Nuri, et al.
Published: (2023)
by: Ihtiyar, Musa Nuri, et al.
Published: (2023)
The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.
by: May, Samuel A, et al.
Published: (2025)
by: May, Samuel A, et al.
Published: (2025)
DNAMotifTokenizer: Towards Biologically Informed Tokenization of Genomic Sequences
by: Zhou, Xiaoxiao, et al.
Published: (2025)
by: Zhou, Xiaoxiao, et al.
Published: (2025)
Single-cell spatial (scs) omics: Recent developments in data analysis
by: Camacho, José, et al.
Published: (2024)
by: Camacho, José, et al.
Published: (2024)
Design Principles Developed through User-Centered and Socio-Technical Methods Improve Clinician Satisfaction, Speed, and Confidence in Pharmacogenomic Clinical Decision Support
by: Herr, Timothy M., et al.
Published: (2020)
by: Herr, Timothy M., et al.
Published: (2020)
Deep Neural Network: An Efficient and Optimized Machine Learning Paradigm for Reducing Genome Sequencing Error
by: Kartriku, Ferdinand, et al.
Published: (2020)
by: Kartriku, Ferdinand, et al.
Published: (2020)
Sparse Autoencoders for Low-$N$ Protein Function Prediction and Design
by: Tsui, Darin, et al.
Published: (2025)
by: Tsui, Darin, et al.
Published: (2025)
Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.
by: Li, Yunlong, et al.
Published: (2026)
by: Li, Yunlong, et al.
Published: (2026)
An Imbalanced Dataset with Multiple Feature Representations for Studying Quality Control of Next-Generation Sequencing
by: Röchner, Philipp, et al.
Published: (2026)
by: Röchner, Philipp, et al.
Published: (2026)
Cancer-inspired Genomics Mapper Model for the Generation of Synthetic DNA Sequences with Desired Genomics Signatures
by: Lazebnik, Teddy, et al.
Published: (2023)
by: Lazebnik, Teddy, et al.
Published: (2023)
ProxySPEX: Inference-Efficient Interpretability via Sparse Feature Interactions in LLMs
by: Butler, Landon, et al.
Published: (2025)
by: Butler, Landon, et al.
Published: (2025)
DNACHUNKER: Learnable Tokenization for DNA Language Models
by: Kim, Taewon, et al.
Published: (2026)
by: Kim, Taewon, et al.
Published: (2026)
Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data
by: Liu, Junhao, et al.
Published: (2024)
by: Liu, Junhao, et al.
Published: (2024)
PhageBench: Can LLMs Understand Raw Bacteriophage Genomes?
by: Hou, Yusen, et al.
Published: (2026)
by: Hou, Yusen, et al.
Published: (2026)
Mind the Gap No More: Achieving Zero-Gap Multimodal Integration via One Tokenizer
by: Li, Yanan, et al.
Published: (2026)
by: Li, Yanan, et al.
Published: (2026)
Similar Items
-
TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
by: Yang, Qirong, et al.
Published: (2025) -
Gene and RNA Editing: Methods, Enabling Technologies, Applications, and Future Directions
by: Aledhari, Mohammed, et al.
Published: (2024) -
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
by: Walton, Thomas, et al.
Published: (2025) -
scVGAE: A Novel Approach using ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation
by: Inoue, Yoshitaka
Published: (2024) -
From In Silico to In Vitro: A Comprehensive Guide to Validating Bioinformatics Findings
by: Wang, Tianyang, et al.
Published: (2025)