LC
Lorin Crawford
bioinformaticsgeneticsgenomicsGenome-Wide Association Studystat.MEstat.MLcs.LGModels, GeneticSingle-Cell Analysisstat.AP
On Valency
published · living versionsW_e3f7vbsb·v1 · currentpublished
Attribution-based diagnostics for single-cell foundation models
with Farnoush Rezaei Jafari, Tristan Lazard, Kenza Bouzid, Shruthi Bannur +4
1 version
Preprints & journals
75 papers in the corpus · 2015–2026Multimodal alignment improves generalizability of genomic biomarker prediction in computational pathology.42710490 · Redekop, Ekaterina, Zimmermann, Eric, Amini, Ava P et al.2026 · 0 citationsCell reports methods. 2026;6(10):101578
Structural causal influence captures the forces of social inequality in models of infectious disease.42613058 · Surasinghe, Sudam, Manivannan, Swathi Nachiar, Scarpino, Samuel V et al.2026 · 0 citationsBiology letters. 2026;22(8)
Protein language models and the long tail of functional diversity10.64898/2026.08.14.744703v1 · Vinod, R., Char, S., Amini, A. P. et al.2026 · 0 citationsbioRxiv
JASPR: Joint Spatial Representation learning of histology and spatial genomics for improved virtual genomic screening and clinical prognostication2606.28395v1 · Marija Pizurica, Eric Zimmermann, Neil Tenenholtz et al.2026 · 0 citationsarXiv
MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays2605.15383v1 · Emre Hayir, Lorin Crawford, Alex X. Lu2026 · 0 citationsarXiv
A biologically annotated neural network for proteomic discovery in Parkinsons disease10.64898/2026.04.29.26351681v1 · Vijayaraghavan, A., Crawford, L., Krishnakant, S. et al.2026 · 0 citationsmedRxiv
Tackling the complexity of cancer with generative models.41997123 · Conard, Ashley Mae, Hughes, Madeline, Hall, James et al.2026 · 5 citationsCell. 2026;189(8):2218-2231
Evolutionary conditioning enables guided generation of functionally diverse enhancers10.64898/2026.04.13.718170v1 · Duncan, A. G., Consens, M. E., Crawford, L. et al.2026 · 0 citationsbioRxiv
Beyond alignment: synergistic integration is required for multimodal cell foundation models10.64898/2026.02.23.707420v2 · Richter, T., Zimmermann, E., Hall, J. et al.2026 · 0 citationsbioRxiv
Trainable subnetworks reveal insights into structure knowledge organization in protein language models.41662462 · Vinod, Ria, Amini, Ava P, Crawford, Lorin et al.2026 · 3 citationsPLoS computational biology. 2026;22(2):e1013925
Predicting evolutionary rate as a pretraining task improves genome language model representations10.64898/2026.02.02.703275v1 · Consens, M. E., Yang, K. K., Hall, J. et al.2026 · 0 citationsbioRxiv
Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss.41617882 · Cultrera di Montesano, Sebastiano, D'Ascenzo, Davide, Raghavan, Srivatsan et al.2026 · 1 citationNature computational science. 2026;6(3):243-249
Characterizing clinical toxicity in cancer combination therapies.41537239 · Wong, Alexandra M, Meier-Scherling, Cecile P G, Crawford, Lorin2026 · 1 citationBioinformatics (Oxford, England). 2026;42(2)
ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage.41260926 · Liu, Xiran, Crawford, Lorin, Ramachandran, Sohini2025 · 1 citationGenome research. 2025;35(12):2691-2700
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance.41278946 · DenAdel, Alan, Hughes, Madeline, Thoutam, Akshaya et al.2026 · 21 citationsbioRxiv : the preprint server for biology. 2025
Adaptive resampling for improved machine learning in imbalanced single-cell datasets.41279118 · Navidi, Zeinab, Thoutam, Akshaya, Hughes, Madeline et al.2025 · 1 citationbioRxiv : the preprint server for biology. 2025
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.38405697 · Nwizu, Chibuikem, Hughes, Madeline, Ramseier, Michelle L et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics2508.01490v2 · Rushin H. Gindra, Giovanni Palla, Mathias Nguyen et al.2025 · 3 citationsarXiv
Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies.40738108 · Stamp, Julian, Smith, Samuel Pattillo, Weinreich, Daniel et al.2025 · 0 citationsAmerican journal of human genetics. 2025;112(9):2198-2212
Epistasis in cardiac traits.40473954 · Stamp, Julian, Crawford, Lorin2025 · 0 citationsNature cardiovascular research. 2025;4(6):655-656
Hierarchical cross-entropy loss improves atlas-scale single-cell annotation models10.1101/2025.04.23.650210v1 · Cultrera di Montesano, S., D'Ascenzo, D., Raghavan, S. et al.2025 · 3 citationsbioRxiv
Zero-shot evaluation reveals limitations of single-cell foundation models.40251685 · Kedzierska, Kasia Z, Crawford, Lorin, Amini, Ava P et al.2025 · 107 citationsGenome biology. 2025;26(1):101
Artificial variables help to avoid over-clustering in single-cell RNA sequencing.40081375 · DenAdel, Alan, Ramseier, Michelle L, Navia, Andrew W et al.2025 · 6 citationsAmerican journal of human genetics. 2025;112(4):940-951
Incorporation of Epstein-Barr viral variation implicates significance of Latent Membrane Protein 1 in survival prediction and prognostic subgrouping in Burkitt lymphoma.40047459 · Kim, Isaac E, Oduor, Cliff, Stamp, Julian et al.2025 · 2 citationsInternational journal of cancer. 2025;156(11):2188-2199
Consequences of training data composition for deep learning models in single-cell biology.40060416 · Nadig, Ajay, Thoutam, Akshaya, Hughes, Madeline et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
ML-MAGES: A machine learning framework for multivariate genetic association analyses with genes and effect size shrinkage.39990474 · Liu, Xiran, Crawford, Lorin, Ramachandran, Sohini2025 · 0 citationsbioRxiv : the preprint server for biology. 2025
Rethinking cancer drug synergy prediction: a call for standardization in machine learning applications10.1101/2024.12.24.630216v1 · Wong, A. M., Crawford, L.2024 · 0 citationsbioRxiv
BetaExplainer: A Probabilistic Method to Explain Graph Neural Networks2412.11964v1 · Whitney Sloneker, Shalin Patel, Michael Wang et al.2024 · 1 citationarXiv
Scalable, compressed phenotypic screening using pooled perturbations.39375446 · Liu, Nuo, Kattan, Walaa E, Mead, Benjamin E et al.2025 · 21 citationsNature biotechnology. 2025;43(8):1324-1336
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections.39288189 · Li, Ke, Chaguza, Chrispin, Stamp, Julian et al.2024 · 4 citationsPLoS computational biology. 2024;20(9):e1012469
Structural causal influence (SCI) captures the forces of social inequality in models of disease dynamics2409.09096v2 · Sudam Surasinghe, Swathi Nachiar Manivannan, Samuel V. Scarpino et al.2024 · 3 citationsarXiv
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks.39080561 · Xie, Helen, Crawford, Lorin, Conard, Ashley Mae2024 · 2 citationsBMC bioinformatics. 2024;25(1):249
Discovering non-additive heritability using additive GWAS summary statistics.38913556 · Pattillo Smith, Samuel, Darnell, Gregory, Udwin, Dana et al.2024 · 14 citationseLife. 2024;13
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease.38915726 · Winter, Peter S, Ramseier, Michelle L, Navia, Andrew W et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2024
Incorporation of Epstein-Barr viral variation implicates significance of LMP1 in survival prediction and prognostic subgrouping in Burkitt lymphoma10.1101/2024.05.03.592343v1 · Kim, I. E., Oduor, C., Stamp, J. et al.2024 · 0 citationsbioRxiv
Generative modeling of biological shapes and images using a probabilistic α-shape sampler.38260340 · Winn-Nuñez, Emily T, Witt, Hadley, Bhaskar, Dhananjay et al.2024 · 1 citationbioRxiv : the preprint server for biology. 2024
Assessing the limits of zero-shot foundation models in single-cell biology10.1101/2023.10.16.561085v2 · Kedzierska, K. Z., Crawford, L., Amini, A. P. et al.2023 · 61 citationsbioRxiv
Statistical Inference on Grayscale Images via the Euler-Radon Transform2308.14249v1 · Kun Meng, Mattie Ji, Jinyu Wang et al.2023 · 0 citationsarXiv
Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies.37243672 · Stamp, Julian, DenAdel, Alan, Weinreich, Daniel et al.2023 · 13 citationsG3 (Bethesda, Md.). 2023;13(8)
Should I Stop or Should I Go: Early Stopping with Heterogeneous Populations2306.11839v3 · Hammaad Adam, Fan Yin, Huibin (Mary) Hu et al.2023 · 2 citationsarXiv
Deep self-supervised learning for biosynthetic gene cluster detection and product classification.37220151 · Rios-Martinez, Carolina, Bhattacharya, Nicholas, Amini, Ava P et al.2023 · 47 citationsPLoS computational biology. 2023;19(5):e1011162
A Simple Approach for Local and Global Variable Importance in Nonlinear Regression Models2302.02024v2 · Emily T. Winn-Nunez, Maryclare Griffin, Lorin Crawford2023 · 4 citationsarXiv
Uncertainty quantification in variable selection for genetic fine-mapping using bayesian neural networks.35769876 · Cheng, Wei, Ramachandran, Sohini, Crawford, Lorin2025 · 4 citationsiScience. 2022;25(7):104553
A topological data analytic approach for discovering biophysical signatures in protein dynamics.35500014 · Tang, Wai Shing, da Silva, Gabriel Monteiro, Kirveslahti, Henry et al.2022 · 21 citationsPLoS computational biology. 2022;18(5):e1010045
Randomness of Shapes and Statistical Inference on Shapes via the Smooth Euler Characteristic Transform2204.12699v5 · Kun Meng, Jinyu Wang, Lorin Crawford et al.2022 · 6 citationsJournal of the American Statistical Association, 2024
Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries.35349783 · Smith, Samuel Pattillo, Shahamatdar, Sahar, Cheng, Wei et al.2022 · 19 citationsAmerican journal of human genetics. 2022;109(5):871-884
Randomized gates eliminate bias in sort-seq assays10.1101/2022.02.17.480881v1 · Trippe, B. L., Huang, B., DeBenedictis, E. A. et al.2022 · 11 citationsbioRxiv
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.34890551 · Raghavan, Srivatsan, Winter, Peter S, Navia, Andrew W et al.2022 · 586 citationsCell. 2021;184(25):6119-6137.e26
Misuse of the term 'trans-ethnic' in genomics research.34741159 · Kamariza, Mireille, Crawford, Lorin, Jones, David et al.2021 · 9 citationsNature genetics. 2021;53(11):1520-1521
Multi-scale inference of genetic trait architecture using biologically annotated neural networks.34411094 · Demetci, Pinar, Cheng, Wei, Darnell, Gregory et al.2021 · 34 citationsPLoS genetics. 2021;17(8):e1009754
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