Machine Learning for analysis of Multiple Sclerosis cross-tissue bulk and single-cell transcriptomics data

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.

Single-cell transcriptomics enables profiling of cellular states at unprecedented resolution, but its high dimensionality, sparsity, and technical batch effects pose significant challenges for representation learning. Existing single-cell foundation models typically encode each cell independently or only model cells from the same batch for denoising, thereby underutilizing the rich relational information across batches and cell types to model gene expression patterns. We argue that single-cell models can benefit from more informative cell-context modeling. By comparing consistency and variation across cells, models can capture fine-grained gene-gene dependencies associated with cell states, which are essential for learning high-quality representations. Inspired by the use of multiple sequence alignment (MSA) context in protein modeling, we propose CellMSA, a single-cell representation learning framework that introduces an MSA-inspired inductive bias into transcriptomic modeling. For each target cell, CellMSA retrieves relevant cells from different batches and biologically related cell types as context, and summarizes cross-cell patterns into a context-dependent gene-pair representation. This representation is then injected into a pair-aware target-cell encoder for fine-grained representation learning. We pretrain CellMSA on a large-scale human single-cell corpus of approximately 109 million cell observations, including 65.6 million primary observations. Experiments show that our framework consistently outperforms existing methods across multiple benchmarks. Code is available at the following repository: https://github.com/PharMolix/CellMSA.

Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models remain opaque to natural language. Here we introduce ELISA (Embedding-Linked Interactive Single-cell Agent), an interpretable framework that unifies scGPT expression embeddings with BioBERT-based semantic retrieval and LLM-mediated interpretation for interactive single-cell discovery. An automatic query classifier routes inputs to gene marker scoring, semantic matching, or reciprocal rank fusion pipelines depending on whether the query is a gene signature, natural language concept, or mixture of both. Integrated analytical modules perform pathway activity scoringacross 60+ gene sets, ligand-receptor interaction prediction using 280+ curated pairs, condition-aware comparative analysis, and cell-type proportion estimation all operating directly on embedded data without access to the original count matrix. Benchmarked across six diverse scRNA-seq datasets spanning inflammatory lung disease, pediatric and adult cancers, organoid models, healthy tissue, and neurodevelopment, ELISA significantly outperforms CellWhisperer, a classical lexical retriever (BM25), and a random baseline in cell type retrieval (combined permutation test, $p < 2\times10^{-5}$ for each), with particularly large gains on gene-signature queries (Cohen's $d = 5.98$ for MRR). ELISA replicates published biological findings (mean composite score 0.88), and generates candidate hypotheses through grounded LLM reasoning, bridging the gap between transcriptomic data exploration and biological discovery.