AI Medical Compendium

Widespread use of invalid statistical tests in biomedical machine learning

bioRxiv May 20, 2026

Machine learning is accelerating biomedical research. Cross-validation is widely used to compare predictive performance -- not only to benchmark algorithms, but also to inform scientific applications, such as ranking biomarkers. However, prediction p... read more

bioinformatics

A Unified Form of Batch Harmonization Equation for Normative Modeling: A Location Scale Framework

bioRxiv May 20, 2026

Normative modeling quantifies individual deviation from population norms by estimating the conditional mean and variance of brain-derived measures as functions of clinically relevant parameters such as age. The rapid growth of multi-center consortia ... read more

bioengineering

Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation

bioRxiv May 20, 2026

Despite the fundamental role of spatial context in driving tumor progression, most current computational models for virtual perturbation have largely overlooked its importance. Here, we introduce TMEformer, a tumor microenvironment-aware deep learnin... read more

bioinformatics

Energetic gradients emerge in developing motor-microtubule structures

bioRxiv May 20, 2026

Living matter produces a variety of beautiful spatiotemporal structures and patterns that are not enduringly present in their nonliving counterparts. These ordered, non-equilibrium steady states are often sustained through the consumption of energy. ... read more

biophysics

CharacTERT: A machine learning tool for classifying hTERT missense variants

bioRxiv May 20, 2026

Missense mutations in TERT, the gene encoding the human telomerase catalytic subunit hTERT, are associated with Telomere Biology Disorders (TBDs). Experimentally elucidating the effects of all possible missense variants would be time-consuming and te... read more

bioinformatics

Domain-adversarial learning predicts clinically actionable drug combination synergy in leukemia patients using bulk transcriptomics data

bioRxiv May 20, 2026

Deep learning has gained popularity in drug combination synergy prediction; however, DL models require large training datasets from cell line pharmacogenomic screens that poorly capture the heterogeneity in transcriptomic features and phenotypic resp... read more

cancer biology

From 3D Time-of-Flight Angiography to Accelerated 4D Arterial Spin Labeling Angiography: A Fast Few-Shot Transfer Learning Approach

bioRxiv May 20, 2026

Purpose: To develop a data-efficient deep learning framework for rapid reconstruction of highly accelerated 4D arterial spin labeling (ASL) magnetic resonance angiography (MRA) with robust generalization using extremely limited acquired data, address... read more

neuroscience

Counterfactual Explanations for Graph Neural Networks in Patient Outcome Prediction

bioRxiv May 20, 2026

Counterfactual Explanation (CE) algorithms have been successfully applied to uncover the main factors driving computational diagnostic and prognostic predictions on tabular medical data.Recently, a new Network Medicine paradigm has been introduced fo... read more

bioinformatics

GeoEPred: A Multimodal Structure-Aware Geometric Deep Learning Framework for Gram-Negative Bacterial Secreted Effector Prediction with Sequence Semantics

bioRxiv May 20, 2026

Accurate prediction of effector proteins secreted by Gram-negative bacteria is important for elucidating bacterial pathogenic mechanisms and developing precise anti-infective strategies. Although existing methods have benefited from the strong sequen... read more

genomics

Prediction of Transcription Factor DNA Binding Affinity with High-Throughput Kd Measurements and Deep Learning

bioRxiv May 20, 2026

Transcription factors (TFs) regulate gene expression through specific interactions with genomic DNA. While TF binding motifs from public databases describe sequence preferences, quantifying genome-wide affinity (Kd) is highly desirable for a more acc... read more

biophysics

Artificial Intelligence Medical Compendium

Widespread use of invalid statistical tests in biomedical machine learning

A Unified Form of Batch Harmonization Equation for Normative Modeling: A Location Scale Framework

Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation

Energetic gradients emerge in developing motor-microtubule structures

CharacTERT: A machine learning tool for classifying hTERT missense variants

Domain-adversarial learning predicts clinically actionable drug combination synergy in leukemia patients using bulk transcriptomics data

From 3D Time-of-Flight Angiography to Accelerated 4D Arterial Spin Labeling Angiography: A Fast Few-Shot Transfer Learning Approach

Counterfactual Explanations for Graph Neural Networks in Patient Outcome Prediction

GeoEPred: A Multimodal Structure-Aware Geometric Deep Learning Framework for Gram-Negative Bacterial Secreted Effector Prediction with Sequence Semantics

Prediction of Transcription Factor DNA Binding Affinity with High-Throughput Kd Measurements and Deep Learning

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