Predicting Genetic Mutation from Whole Slide Images via Biomedical-Linguistic Knowledge Enhanced Multi-label Classification

Predicting genetic mutations from whole slide images is indispensable for cancer diagnosis. However, existing work training multiple binary classification models faces two challenges: (a) Training multiple binary classifiers is inefficient and would inevitably lead to a class imbalance problem. (b) The biological relationships among genes are overlooked, which limits the prediction performance. To tackle these challenges, we innovatively design a Biological-knowledge enhanced PathGenomic multi-label Transformer to improve genetic mutation prediction performances. BPGT first establishes a novel gene encoder that constructs gene priors by two carefully designed modules: (a) A gene graph whose node features are the genes' linguistic descriptions and the cancer phenotype, with edges modeled by genes' pathway associations and mutation consistencies. (b) A knowledge association module that fuses linguistic and biomedical knowledge into gene priors by transformer-based graph representation learning, capturing the intrinsic relationships between different genes' mutations. BPGT then designs a label decoder that finally performs genetic mutation prediction by two tailored modules: (a) A modality fusion module that firstly fuses the gene priors with critical regions in WSIs and obtains gene-wise mutation logits. (b) A comparative multi-label loss that emphasizes the inherent comparisons among mutation status to enhance the discrimination capabilities. Sufficient experiments on The Cancer Genome Atlas benchmark demonstrate that BPGT outperforms the state-of-the-art.

Electromagnetic Source Imaging via a Data-Synthesis-Based Denoising Autoencoder

Electromagnetic source imaging (ESI) is a highly ill-posed inverse problem. To find a unique solution, traditional ESI methods impose a variety of priors that may not reflect the actual source properties. Such limitations of traditional ESI methods hinder their further applications. Inspired by deep learning approaches, a novel data-synthesized spatio-temporal denoising autoencoder method (DST-DAE) method was proposed to solve the ESI inverse problem. Unlike the traditional methods, we utilize a neural network to directly seek generalized mapping from the measured E/MEG signals to the cortical sources. A novel data synthesis strategy is employed by introducing the prior information of sources to the generated large-scale samples using the forward model of ESI. All the generated data are used to drive the neural network to automatically learn inverse mapping. To achieve better estimation performance, a denoising autoencoder (DAE) architecture with spatio-temporal feature extraction blocks is designed. Compared with the traditional methods, we show (1) that the novel deep learning approach provides an effective and easy-to-apply way to solve the ESI problem, that (2) compared to traditional methods, DST-DAE with the data synthesis strategy can better consider the characteristics of real sources than the mathematical formulation of prior assumptions, and that (3) the specifically designed architecture of DAE can not only provide a better estimation of source signals but also be robust to noise pollution. Extensive numerical experiments show that the proposed method is superior to the traditional knowledge-driven ESI methods.