Meta-Analysis of Datasets
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Bias in Filter Feature Selection Evaluation: A Meta-Analysis of Datasets, Baselines, and Experimental Design Choices
arXiv:2606.07068v1 Announce Type: new Abstract: Background: Since 1990 many feature selection methods have been proposed across heterogeneous applications. To validate the usefulness of a new method, it needs to be compared against at least one baseline method from the existing literature on a feature selection task using at least one dataset. Recent developments in tabular Deep Learning (DL) and data valuation in Machine Learning (ML) suggest that the evaluation of new methods, algorithms,...
Integrative genomics reveals shared and stress-specific adaptive pathways underlying acidic soil-associated metal toxicity in rice
Soil acidity-associated toxicities of aluminum (Al), cadmium (Cd), and manganese (Mn) severely constrain rice productivity in upland ecosystems. To investigate the genomic basis of adaptation to acidic soil-related metal stress, we conducted an integrated meta-QTL (M-QTL) and functional genomics analysis in rice. Meta-analysis of 681 QTLs and MTAs from 53 QTL mapping and GWAS studies identified 79 robust M-QTLs, including ten overlapping regions associated with Al-, Cd-, and Mn-responsive...
PAG-Agent: a biologist-oriented research assistant for context-aware pathway-level analysis and interpretation
Pathway analysis is a critical step for translating gene-level omics results into biological mechanisms, yet existing workflows often leave researchers with long lists of statistically significant pathways that are difficult to interpret, validate, and connect to experimental context. We developed PAG-Agent, a biologist-oriented virtual research assistant that integrates pathway-level statistical analysis, context-aware biological interpretation, literature-supported reasoning, and...
A prognostic human brain network for diffuse midline glioma
Abstract Diffuse midline gliomas (DMGs) are near-universally lethal tumours of the childhood central nervous system1,2. In animal models, DMGs form brain-wide integrated networks through neuron-to-glioma synapses3,4,5,6 and glioma-to-glioma gap junctional coupling3. This extensive connectivity robustly promotes the growth and invasion of DMG3,4,5,6,7,8,9 and other glial malignancies10,11,12 through paracrine mechanisms and direct neuron-to-glioma synapses.
Mutation-dependent responses to sleep and exercise in clonal haematopoiesis
Abstract Clonal haematopoiesis (CH) activates inflammation and increases the risk of atherosclerosis1,2. Whether lifestyle alters CH clone expansion or the phenotypic programming of CH mutant cells, thereby affecting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, Trp53 and Dnmt3a, we demonstrate mutation-dependent responses to sleep and exercise in CH and show that mutant cells are uniquely sensitive to lifestyle.