2026-08-07 04:00 UTCOriginal source2 min readUpdated: 2026-08-07 08:34 UTC

MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification

arXiv:2608.05196v1 Announce Type: new Abstract: Multiple sclerosis (MS) is diagnosed through clinical assessment, magnetic resonance imaging, laboratory evidence when appropriate, and exclusion of better explanations. Blood RNA expression data may contain disease associated immune signal, but a blood RNA classifier cannot be treated as a replacement for clinical diagnosis. This paper presents MS-MLB (Multiple Sclerosis Machine Learning Benchmark), a reproducible open benchmark for machine learning based MS research classification from whole blood RNA expression data. MS-MLB uses the public GSE17048 cohort, converts it into an MS versus healthy control task, and evaluates multiple algorithms under a shared, leakage controlled pipeline that a researcher can rerun without reconfiguring the evaluation. The evaluation includes nested cross-validation, an untouched stratified holdout set, bootstrap confidence intervals, ROC and precision recall analysis, calibration measurement, and an exploratory MS Research Score. In the final benchmark summary, Gradient Boosting ranked first by MS Research Score on the holdout set, with an MS Research Score of 93.83, AUC-ROC of 0.989, sensitivity of 0.950, specificity of 0.778, $F_{1}$ score of 0.927, and Brier score of 0.050. Prior studies have applied machine learning to MS blood transcriptomic data, including PBMC stage classification and whole blood diagnostic signature modeling. The contribution here is different and narrower. To our knowledge, MS-MLB is the first open benchmark focused on MS versus healthy control classification from GSE17048 whole blood RNA expression data with a documented external model submission pathway built into the framework. The score is intended for research comparison only and has not been clinically validated. The benchmark is accessible here: https://github.com/duckyquang/MS-MLB.

SourcearXiv Machine LearningAuthor: Adam Simson, Ankush Dutta, Quang Bui

-->

[Submitted on 4 Aug 2026]

Title:MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification

View a PDF of the paper titled MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification, by Adam Simson and 2 other authors

View PDF HTML (experimental)

Abstract:Multiple sclerosis (MS) is diagnosed through clinical assessment, magnetic resonance imaging, laboratory evidence when appropriate, and exclusion of better explanations. Blood RNA expression data may contain disease associated immune signal, but a blood RNA classifier cannot be treated as a replacement for clinical diagnosis. This paper presents MS-MLB (Multiple Sclerosis Machine Learning Benchmark), a reproducible open benchmark for machine learning based MS research classification from whole blood RNA expression data. MS-MLB uses the public GSE17048 cohort, converts it into an MS versus healthy control task, and evaluates multiple algorithms under a shared, leakage controlled pipeline that a researcher can rerun without reconfiguring the evaluation. The evaluation includes nested cross-validation, an untouched stratified holdout set, bootstrap confidence intervals, ROC and precision recall analysis, calibration measurement, and an exploratory MS Research Score. In the final benchmark summary, Gradient Boosting ranked first by MS Research Score on the holdout set, with an MS Research Score of 93.83, AUC-ROC of 0.989, sensitivity of 0.950, specificity of 0.778, $F_{1}$ score of 0.927, and Brier score of 0.050. Prior studies have applied machine learning to MS blood transcriptomic data, including PBMC stage classification and whole blood diagnostic signature modeling. The contribution here is different and narrower. To our knowledge, MS-MLB is the first open benchmark focused on MS versus healthy control classification from GSE17048 whole blood RNA expression data with a documented external model submission pathway built into the framework. The score is intended for research comparison only and has not been clinically validated. The benchmark is accessible here: this https URL.

Subjects:

Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)

Cite as: arXiv:2608.05196 [cs.LG]

(or arXiv:2608.05196v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2608.05196

arXiv-issued DOI via DataCite

Submission history

From: Quang Bui [view email] [v1] Tue, 4 Aug 2026 11:20:36 UTC (959 KB)

Full-text links:

Access Paper:

View a PDF of the paper titled MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification, by Adam Simson and 2 other authors

View PDF

HTML (experimental)

TeX Source

view license

Current browse context:

cs.LG

new | recent | 2026-08

Change to browse by:

cs q-bio q-bio.QM

References & Citations

NASA ADS

Google Scholar

Semantic Scholar

Data provided by:

Bibliographic Tools

Bibliographic and Citation Tools

Bibliographic Explorer Toggle

Bibliographic Explorer (What is the Explorer?)

Connected Papers Toggle

Connected Papers (What is Connected Papers?)

Litmaps Toggle

Litmaps (What is Litmaps?)

scite.ai Toggle

scite Smart Citations (What are Smart Citations?)

Code, Data, Media

Code, Data and Media Associated with this Article

alphaXiv Toggle

alphaXiv (What is alphaXiv?)

Links to Code Toggle

CatalyzeX Code Finder for Papers (What is CatalyzeX?)

DagsHub Toggle

DagsHub (What is DagsHub?)

GotitPub Toggle

Gotit.pub (What is GotitPub?)

Huggingface Toggle

Hugging Face (What is Huggingface?)

ScienceCast Toggle

ScienceCast (What is ScienceCast?)

Demos

Replicate Toggle

Replicate (What is Replicate?)

Spaces Toggle

Hugging Face Spaces (What is Spaces?)

Spaces Toggle

TXYZ.AI (What is TXYZ.AI?)