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The recent focus on microbes in human medicine highlights their potential role in the genetic framework of diseases. To decode the complex interactions among genes, microbes, and diseases, computational predictions of gene-microbe-disease (GMD) associations are crucial. Existing methods primarily address gene-disease and microbe-disease associations, but the more intricate triple-wise GMD associations remain less explored. In this paper, we propose a Heterogeneous Causal Metapath Graph Neural Network (HCMGNN) to predict GMD associations. HCMGNN constructs a heterogeneous graph linking genes, microbes, and diseases through their pairwise associations, and utilizes six predefined causal metapaths to extract directed causal subgraphs, which facilitate the multi-view analysis of causal relations among three entity types. Within each subgraph, we employ a causal semantic sharing message passing network for node representation learning, coupled with an attentive fusion method to integrate these representations for predicting GMD associations. Our extensive experiments show that HCMGNN effectively predicts GMD associations and addresses association sparsity issue by enhancing the graph's semantics and structure.

Whole slide images are the foundation of digital pathology for the diagnosis and treatment of carcinomas. Writing pathology reports is laborious and error-prone for inexperienced pathologists. To reduce the workload and improve clinical automation, we investigate how to generate pathology reports given whole slide images. On the data end, we curated the largest WSI-text dataset (PathText). In specific, we collected nearly 10000 high-quality WSI-text pairs for visual-language models by recognizing and cleaning pathology reports which narrate diagnostic slides in TCGA. On the model end, we propose the multiple instance generative model (MI-Gen) which can produce pathology reports for gigapixel WSIs. We benchmark our model on the largest subset of TCGA-PathoText. Experimental results show our model can generate pathology reports which contain multiple clinical clues and achieve competitive performance on certain slide-level tasks. We observe that simple semantic extraction from the pathology reports can achieve the best performance (0.838 of F1 score) on BRCA subtyping surpassing previous state-of-the-art approaches. Our collected dataset and related code are available.

Integrating prior knowledge of neurophysiology into neural network architecture enhances the performance of emotion decoding. While numerous techniques emphasize learning spatial and short-term temporal patterns, there has been limited emphasis on capturing the vital long-term contextual information associated with emotional cognitive processes. In order to address this discrepancy, we introduce a novel transformer model called emotion transformer (EmT). EmT is designed to excel in both generalized cross-subject EEG emotion classification and regression tasks. In EmT, EEG signals are transformed into a temporal graph format, creating a sequence of EEG feature graphs using a temporal graph construction module (TGC). A novel residual multi-view pyramid GCN module (RMPG) is then proposed to learn dynamic graph representations for each EEG feature graph within the series, and the learned representations of each graph are fused into one token. Furthermore, we design a temporal contextual transformer module (TCT) with two types of token mixers to learn the temporal contextual information. Finally, the task-specific output module (TSO) generates the desired outputs. Experiments on four publicly available datasets show that EmT achieves higher results than the baseline methods for both EEG emotion classification and regression tasks. The code is available at //github.com/yi-ding-cs/EmT.

Traditional diagnosis of chronic diseases involves in-person consultations with physicians to identify the disease. However, there is a lack of research focused on predicting and developing application systems using clinical notes and blood test values. We collected five years of Electronic Health Records (EHRs) from Taiwan's hospital database between 2017 and 2021 as an AI database. Furthermore, we developed an EHR-based chronic disease prediction platform utilizing Large Language Multimodal Models (LLMMs), successfully integrating with frontend web and mobile applications for prediction. This prediction platform can also connect to the hospital's backend database, providing physicians with real-time risk assessment diagnostics. The demonstration link can be found at //www.youtube.com/watch?v=oqmL9DEDFgA.

Interactive photorealistic rendering of 3D anatomy is used in medical education to explain the structure of the human body. It is currently restricted to frontal teaching scenarios, where even with a powerful GPU and high-speed access to a large storage device where the data set is hosted, interactive demonstrations can hardly be achieved. We present the use of novel view synthesis via compressed 3D Gaussian Splatting (3DGS) to overcome this restriction, and to even enable students to perform cinematic anatomy on lightweight and mobile devices. Our proposed pipeline first finds a set of camera poses that captures all potentially seen structures in the data. High-quality images are then generated with path tracing and converted into a compact 3DGS representation, consuming < 70 MB even for data sets of multiple GBs. This allows for real-time photorealistic novel view synthesis that recovers structures up to the voxel resolution and is almost indistinguishable from the path-traced images

Depression, a prevalent mental health disorder impacting millions globally, demands reliable assessment systems. Unlike previous studies that focus solely on either detecting depression or predicting its severity, our work identifies individual symptoms of depression while also predicting its severity using speech input. We leverage self-supervised learning (SSL)-based speech models to better utilize the small-sized datasets that are frequently encountered in this task. Our study demonstrates notable performance improvements by utilizing SSL embeddings compared to conventional speech features. We compare various types of SSL pretrained models to elucidate the type of speech information (semantic, speaker, or prosodic) that contributes the most in identifying different symptoms. Additionally, we evaluate the impact of combining multiple SSL embeddings on performance. Furthermore, we show the significance of multi-task learning for identifying depressive symptoms effectively.

Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.

Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.

Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.

Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.