ToxLens: A Reproducible Graph-Learning Framework for Leakage-Aware, Uncertainty-Calibrated Molecular Toxicity Prediction

Molecular toxicity prediction is increasingly used to prioritise compounds before experimental testing, but conventional benchmark performance can overstate practical utility when structurally related molecules occur across training and test folds. We introduce ToxLens, a reproducible multi-task graph-learning framework for 11 toxicity endpoints spanning Ames mutagenicity, acute oral toxicity, hERG inhibition, and Tox21 nuclear-receptor and stress-response assays. The workflow combines conservative chemical curation, sphere-exclusion filtering, a leakage-aware UMAP-HDBSCAN split, parallel graph and global-feature encoders joined by late concatenation, temperature-scaled Monte Carlo dropout with conformal-style prediction sets, applicability-domain analysis, and SHAP-guided toxicophore discovery with occlusion controls. On the leakage-controlled test fold, a five-seed soft-voting ensemble achieved a Matthews correlation coefficient score of 0.44, an area under the receiver operating characteristic curve score of 0.83, and an area under the precision-recall curve score of 0.58. It exceeded four ECFP4-based shallow baselines on all 11 endpoints under the same split and validation-based threshold-selection protocol. Controlled ablations showed that the global pathway was important, whereas late concatenation outperformed the tested gated and feature-wise linear modulation fusion variants. Conformal-style prediction sets revealed substantial endpoint-specific variation in set efficiency, and discrimination and calibration improved with similarity to the training domain. Retraining on fixed published Tox21 Challenge and TDA folds produced competitive, but not uniformly state-of-the-art, performance. SHAP-guided occlusion and consensus subgraph mining yielded model-derived structural hypotheses, 44 of which contained at least one occurrence that passed the predefined counterfactual criteria.

M-LINKX: Multiview Graph Learning for Brain Cognitive Disease Detection

Electroencephalogram (EEG) is a non-invasive and relatively low-cost procedure that measures brain electricity for the detection of cognitive diseases. EEG-based classification of dementia-related conditions, including Alzheimer's disease (AD), mild cognitive impairment (MCI), and frontotemporal dementia (FTD), remains challenging because EEG signals are noisy, non-stationary, and vary across subjects. Segment-based learning provides a practical way to model long EEG recordings by converting them into fixed-length inputs. For each segment, discriminative information may be explored by using signals within each channel (i.e. electrode), as well as interactions between EEG channels. In this paper, we propose M-LINKX, a multi-view graph learning framework for EEG-based dementia classification. For each segment, we extract channel-level node features and construct multiple functional-connectivity (FC) graph views, where each view is defined by a specific combination of connectivity metric, frequency band, and topology filter, respectively. Instead of relying on message passing over the constructed graphs, M-LINKX follows a simple design in modeling node features and adjacency-based connectivity representations. The graph-view representations are fused using global trainable view weights, and subject-level prediction is obtained by averaging segment-level probabilities. Experiments on two three-class EEG datasets with different diagnostic groups, CAUEEG (HC/MCI/Dementia) and AHEAP (HC/AD/FTD), show that M-LINKX achieves the best subject-level performance under the main experimental settings. Our study suggests that multi-view functional connectivity can improve EEG-based dementia classification when integrated with an appropriate graph-learning architecture. Code and data are available at https://github.com/anphantt/MLINKX.

LLM as Clinical Graph Structure Refiner: Enhancing Representation Learning in EEG Seizure Diagnosis

Electroencephalogram (EEG) signals are vital for automated seizure detection, but their inherent noise makes robust representation learning challenging. Existing graph construction methods, whether correlation-based or learning-based, often generate redundant or irrelevant edges due to the noisy nature of EEG data. This significantly impairs the quality of graph representation and limits downstream task performance. Motivated by the remarkable reasoning and contextual understanding capabilities of large language models (LLMs), we explore the idea of using LLMs as graph edge refiners. Specifically, we propose a two-stage framework: we first verify that LLM-based edge refinement can effectively identify and remove redundant connections, leading to significant improvements in seizure detection accuracy and more meaningful graph structures. Building on this insight, we further develop a robust solution where the initial graph is constructed using a Transformer-based edge predictor and multilayer perceptron, assigning probability scores to potential edges and applying a threshold to determine their existence. The LLM then acts as an edge set refiner, making informed decisions based on both textual and statistical features of node pairs to validate the remaining connections. Extensive experiments on TUSZ dataset demonstrate that our LLM-refined graph learning framework not only enhances task performance but also yields cleaner and more interpretable graph representations.

CMGL: Confidence-guided Multi-omics Graph Learning for Cancer Subtype Classification

Motivation: Multi-omics integration can improve cancer subtyping, but modality informativeness and noise vary across cancer types and patients. Existing graph-based methods optimize modality weights jointly with the classification objective and therefore lack independent reliability estimates, so low-quality omics distort patient similarity graphs and amplify noise through message passing. Results: We propose CMGL, a two-stage framework that estimates per-sample modality reliability through evidential deep learning and uses the frozen confidence scores to guide cross-omics fusion and graph construction. On four MLOmics cancer-subtype tasks and the 32-class pan-cancer task, CMGL consistently improves over the strongest baseline, surpassing it by 4.03% in average accuracy on the four single-cancer tasks. Its representations recover the PAM50 intrinsic subtypes of breast invasive carcinoma (BRCA), and the BRCA-trained model transfers without fine-tuning to kidney renal clear cell carcinoma (KIRC), stratifying patients into prognostically distinct groups.