Research

We make our research visible to both the computational biology and machine learning community. See the overview of our research and recent publications below.

2025

Interactive Training: Feedback-Driven Neural Network Optimization

W Zhang, YY Lu, Y Deng

Empirical Methods in Natural Language Processing (System Demonstration Track)  ·  02 Oct 2025

Large Language Model

PaperCodeDemo

Error-controlled non-additive interaction discovery in machine learning models

W Chen*, Y Jiang*, WS Noble, YY Lu#

Nature Machine Intelligence  ·  22 Sep 2025

Error-controlled Machine LearningHypothesis Generation

PaperCodeSlides

Fast and memory efficient searching of large-scale mass spectrometry data using Tide

A Kertesz-Farkas, FLA Acquaye, V Ostapenko, RH Locon, YY Lu, CE Grant, WS Noble

Journal of Proteome Research  ·  12 Aug 2025

Computational Proteomics

PaperCode

Securing diagonal integration of multimodal single-cell data against ambiguous mapping

H Zhou, K Cao, YY Lu#

Bioinformatics  ·  14 Jun 2025

Error-controlled Machine LearningComputational GenomicsMulti-omics Integration

PaperCodePosterDatasets

Programmatic design and editing of cis-regulatory elements

J Schreiber, FK Lorbeer, M Heinzl, YY Lu, A Stark, WS Noble

Cold Spring Harbor Laboratory  ·  23 Apr 2025

Computational Genomics

Preprint

MIOSTONE: Modeling microbiome-trait associations with taxonomy-adaptive neural networks

Y Jiang, M Atton, Q Zhu, YY Lu#

Microbiome  ·  29 Mar 2025

Computational Microbiomics

PaperCodeSlidesDatasets

PhyloMix: Enhancing microbiome-trait association prediction through phylogeny-mixing augmentation

Y Jiang*, D Liao*, Q Zhu, YY Lu#

Bioinformatics  ·  12 Jan 2025

Computational MicrobiomicsData Augmentation

PaperCodeDatasets

2024

DeepROCK: Error-controlled interaction detection in deep neural networks

W Chen, WS Noble#, YY Lu#

NeurIPS Intepretable AI Workshop  ·  15 Dec 2024

Error-controlled Machine LearningHypothesis Generation

PaperCodePoster

A BLAST from the past: revisiting BLAST E-value

YY Lu, WS Noble, U Keich

Bioinformatics  ·  04 Dec 2024

BioinformaticsComputational Genomics

PaperCodeSlides

Retrieved Sequence Augmentation for Protein Representation Learning

C Ma, H Zhao, L Zheng, J Xin, Q Li, L Wu, Z Deng, YY Lu, Q Liu, L Kong

Empirical Methods in Natural Language Processing (EMNLP)  ·  12 Nov 2024

Computational ProteomicsLarge Language Model

Paper

Leveraging machine learning for taxonomic classification of emerging astroviruses

F Alipour, C Holmes, YY Lu, KA Hill, L Kari

Frontiers in Molecular Biosciences  ·  10 Jan 2024

Computational Genomics

Paper

2023

BioMANIA: Simplifying bioinformatics data analysis through conversation

Z Dong, H Zhou, Y Jiang, V Zhong, YY Lu#

Cold Spring Harbor Laboratory  ·  01 Nov 2023

Large Language ModelBioinformatics

PreprintCodePosterDemo

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

A Kertesz-Farkas, FLA Acquaye, K Bimani, J Eng, WE Fondrie, CE Grant, MR Hoopmann, A Lin, YY Lu, RL Moritz, MJ MacCoss, WS Noble

Journal of Proteome Research  ·  04 Jan 2023

Computational ProteomicsMass Spectrometry

Paper

2022

Metric learning for comparing genomic data with triplet network

Z Ma*, YY Lu*#, Y Wang*, R Lin, Z Yang, F Zhang, Y Wang#

Briefings in Bioinformatics  ·  01 Sep 2022

Computational Genomics

PaperCode

Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning

AB Dincer, YY Lu, D Schweppe, S Oh, WS Noble

Journal of Proteome Research  ·  13 Jun 2022

Computational ProteomicsMass Spectrometry

PaperCode

Proteome-wide identification of amino acid substitutions deleterious for protein function

RA Rodriguez-Mias, KN Hess, BY Ruiz, IR Smith, AS Barente, SM Zimmerman, YY Lu, WS Noble, S Fields, J Villen

Cold Spring Harbor Laboratory  ·  09 Apr 2022

Computational ProteomicsMass Spectrometry

Preprint

2021

A wider field of view to predict expression

YY Lu, WS Noble

Nature Methods  ·  04 Oct 2021

Computational Genomics

Paper

DIAmeter: matching peptides to data-independent acquisition mass spectrometry data

YY Lu, J Bilmes, RA Rodriguez-Mias, J Villen, WS Noble

Bioinformatics  ·  25 Jul 2021

Computational ProteomicsMass Spectrometry

PaperCodeSlidesDatasets

ACE: Explaining cluster from an adversarial perspective

YY Lu, T Yu, G Bonora, WS Noble

Proceedings of International Conference on Machine Learning (ICML)  ·  18 Jul 2021

Interpretable Machine LearningComputational Genomics

PaperCodeSlidesDatasets

DANCE: Enhancing saliency maps using decoys

YY Lu*, W Guo*, X Xing, WS Noble

Proceedings of International Conference on Machine Learning (ICML)  ·  18 Jul 2021

Interpretable Machine Learning

PaperCodeSlides

CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase

YY Lu*, J Bai*, Y Wang, Y Wang, F Sun

Bioinformatics  ·  15 Jan 2021

Computational Genomics

PaperCode

2020

Ledidi: Designing genomic edits that induce functional activity

J Schreiber*, YY Lu*, William Stafford Noble

ICML Workshop on Computational Biology  ·  17 Jul 2020

Computational Genomics

PaperCodeSlidesTutorial

2019

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

DF Read, K Cook, YY Lu, KG Le Roch, WS Noble

PLOS Computational Biology  ·  11 Sep 2019

Computational Genomics

Paper

SolidBin: improving metagenome binning with semi-supervised normalized cut

Z Wang, Z Wang, YY Lu, F Sun, S Zhu

Bioinformatics  ·  12 Apr 2019

Computational Microbiomics

Paper

2018

DeepPINK: reproducible feature selection in deep neural networks

YY Lu*, Y Fan*, J Lv, WS Noble

Proceedings of International Conference on Neural Information Processing Systems (NeurIPS)  ·  03 Dec 2018

Error-controlled Machine LearningHypothesis Generation

PaperCodeSlidesDatasets

Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra

A Hu, YY Lu, J Bilmes, WS Noble

Journal of Proteome Research  ·  26 Oct 2018

Computational ProteomicsMass Spectrometry

PaperCode

Alignment-Free Sequence Analysis and Applications

J Ren, X Bai, YY Lu, K Tang, Y Wang, G Reinert, F Sun

Annual Review of Biomedical Data Science  ·  20 Jul 2018

Computational Genomics

Paper

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

K Tang, YY Lu, F Sun

Frontiers in Microbiology  ·  16 Apr 2018

Computational GenomicsComputational Microbiomics

Paper

2017

Big Data Analytics in Metagenomics: Integration, Representation, Management, and Visualization

YY Lu

Doctoral Thesis, University of Southern California  ·  01 Dec 2017

Computational GenomicsComputational Microbiomics

Thesis

Improving contig binning of metagenomic data using $$ {d}_2^S $$ oligonucleotide frequency dissimilarity

Y Wang, K Wang, YY Lu, F Sun

BMC Bioinformatics  ·  20 Sep 2017

Computational Microbiomics

Paper

Towards enhanced and interpretable clustering/classification in integrative genomics

YY Lu, J Lv, JA Fuhrman, F Sun

Nucleic Acids Research  ·  30 Aug 2017

Computational GenomicsMulti-omics Integration

PaperCode

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

J Ren, NA Ahlgren, YY Lu, JA Fuhrman, F Sun

Microbiome  ·  06 Jul 2017

Computational Microbiomics

Paper

CAFE: aCcelerated Alignment-FrEe sequence analysis

YY Lu, K Tang, J Ren, JA Fuhrman, MS Waterman, F Sun

Nucleic Acids Research  ·  03 May 2017

Computational Genomics

PaperCode

2016

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

NA Ahlgren, J Ren, YY Lu, JA Fuhrman, F Sun

Nucleic Acids Research  ·  28 Nov 2016

Computational GenomicsComputational Microbiomics

Paper

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

YY Lu, T Chen, JA Fuhrman, F Sun

Bioinformatics  ·  02 Jun 2016

Computational Microbiomics

PaperCode