Latent Patient Network Learning for Automatic Diagnosis

Recently, Graph Convolutional Networks (GCNs) has proven to be a powerful machine learning tool for Computer Aided Diagnosis (CADx) and disease prediction. A key component in these models is to build a population graph, where the graph adjacency matrix represents pair-wise patient similarities. Until now, the similarity metrics have been defined manually, usually based on meta-features like demographics or clinical scores. The definition of the metric, however, needs careful tuning, as GCNs are very sensitive to the graph structure. In this paper, we demonstrate for the first time in the CADx domain that it is possible to learn a single, optimal graph towards the GCN's downstream task of disease classification. To this end, we propose a novel, end-to-end trainable graph learning architecture for dynamic and localized graph pruning. Unlike commonly employed spectral GCN approaches, our GCN is spatial and inductive, and can thus infer previously unseen patients as well. We demonstrate significant classification improvements with our learned graph on two CADx problems in medicine. We further explain and visualize this result using an artificial dataset, underlining the importance of graph learning for more accurate and robust inference with GCNs in medical applications

Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions

Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research.Comment: Accepted by 2023 IMIA Yearbook of Medical Informatic

Multi-Target Prediction: A Unifying View on Problems and Methods

Multi-target prediction (MTP) is concerned with the simultaneous prediction of multiple target variables of diverse type. Due to its enormous application potential, it has developed into an active and rapidly expanding research field that combines several subfields of machine learning, including multivariate regression, multi-label classification, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. In this paper, we present a unifying view on MTP problems and methods. First, we formally discuss commonalities and differences between existing MTP problems. To this end, we introduce a general framework that covers the above subfields as special cases. As a second contribution, we provide a structured overview of MTP methods. This is accomplished by identifying a number of key properties, which distinguish such methods and determine their suitability for different types of problems. Finally, we also discuss a few challenges for future research

Recent Progress in Transformer-based Medical Image Analysis

The transformer is primarily used in the field of natural language processing. Recently, it has been adopted and shows promise in the computer vision (CV) field. Medical image analysis (MIA), as a critical branch of CV, also greatly benefits from this state-of-the-art technique. In this review, we first recap the core component of the transformer, the attention mechanism, and the detailed structures of the transformer. After that, we depict the recent progress of the transformer in the field of MIA. We organize the applications in a sequence of different tasks, including classification, segmentation, captioning, registration, detection, enhancement, localization, and synthesis. The mainstream classification and segmentation tasks are further divided into eleven medical image modalities. A large number of experiments studied in this review illustrate that the transformer-based method outperforms existing methods through comparisons with multiple evaluation metrics. Finally, we discuss the open challenges and future opportunities in this field. This task-modality review with the latest contents, detailed information, and comprehensive comparison may greatly benefit the broad MIA community.Comment: Computers in Biology and Medicine Accepte

Data-Driven Representation Learning in Multimodal Feature Fusion

abstract: Modern machine learning systems leverage data and features from multiple modalities to gain more predictive power. In most scenarios, the modalities are vastly different and the acquired data are heterogeneous in nature. Consequently, building highly effective fusion algorithms is at the core to achieve improved model robustness and inferencing performance. This dissertation focuses on the representation learning approaches as the fusion strategy. Specifically, the objective is to learn the shared latent representation which jointly exploit the structural information encoded in all modalities, such that a straightforward learning model can be adopted to obtain the prediction. We first consider sensor fusion, a typical multimodal fusion problem critical to building a pervasive computing platform. A systematic fusion technique is described to support both multiple sensors and descriptors for activity recognition. Targeted to learn the optimal combination of kernels, Multiple Kernel Learning (MKL) algorithms have been successfully applied to numerous fusion problems in computer vision etc. Utilizing the MKL formulation, next we describe an auto-context algorithm for learning image context via the fusion with low-level descriptors. Furthermore, a principled fusion algorithm using deep learning to optimize kernel machines is developed. By bridging deep architectures with kernel optimization, this approach leverages the benefits of both paradigms and is applied to a wide variety of fusion problems. In many real-world applications, the modalities exhibit highly specific data structures, such as time sequences and graphs, and consequently, special design of the learning architecture is needed. In order to improve the temporal modeling for multivariate sequences, we developed two architectures centered around attention models. A novel clinical time series analysis model is proposed for several critical problems in healthcare. Another model coupled with triplet ranking loss as metric learning framework is described to better solve speaker diarization. Compared to state-of-the-art recurrent networks, these attention-based multivariate analysis tools achieve improved performance while having a lower computational complexity. Finally, in order to perform community detection on multilayer graphs, a fusion algorithm is described to derive node embedding from word embedding techniques and also exploit the complementary relational information contained in each layer of the graph.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201