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Deep Vein Thrombosis (DVT) is a common yet potentially fatal condition, often leading to critical complications like pulmonary embolism. DVT is commonly diagnosed using Ultrasound (US) imaging, which can be inconsistent due to its high dependence on the operator's skill. Robotic US Systems (RUSs) aim to improve diagnostic test consistency but face challenges with the complex scanning pattern needed for DVT assessment, where precise control over US probe pressure is crucial for indirectly detecting occlusions. This work introduces an imitation learning method, based on Kernelized Movement Primitives (KMP), to standardize DVT US exams by training an autonomous robotic controller using sonographer demonstrations. A new recording device design enhances demonstration ergonomics, integrating with US probes and enabling seamless force and position data recording. KMPs are used to capture scanning skills, linking scan trajectory and force, enabling generalization beyond the demonstrations. Our approach, evaluated on synthetic models and volunteers, shows that the KMP-based RUS can replicate an expert's force control and image quality in DVT US examination. It outperforms previous methods using manually defined force profiles, improving exam standardization and reducing reliance on specialized sonographers.

Positron Emission Tomography (PET) is a vital imaging modality widely used in clinical diagnosis and preclinical research but faces limitations in image resolution and signal-to-noise ratio due to inherent physical degradation factors. Current deep learning-based denoising methods face challenges in adapting to the variability of clinical settings, influenced by factors such as scanner types, tracer choices, dose levels, and acquisition times. In this work, we proposed a novel 3D ControlNet-based denoising method for whole-body PET imaging. We first pre-trained a 3D Denoising Diffusion Probabilistic Model (DDPM) using a large dataset of high-quality normal-dose PET images. Following this, we fine-tuned the model on a smaller set of paired low- and normal-dose PET images, integrating low-dose inputs through a 3D ControlNet architecture, thereby making the model adaptable to denoising tasks in diverse clinical settings. Experimental results based on clinical PET datasets show that the proposed framework outperformed other state-of-the-art PET image denoising methods both in visual quality and quantitative metrics. This plug-and-play approach allows large diffusion models to be fine-tuned and adapted to PET images from diverse acquisition protocols.

Automatic differential diagnosis (DDx) is an essential medical task that generates a list of potential diseases as differentials based on patient symptom descriptions. In practice, interpreting these differential diagnoses yields significant value but remains under-explored. Given the powerful capabilities of large language models (LLMs), we investigated using LLMs for interpretable DDx. Specifically, we curated the first DDx dataset with expert-derived interpretation on 570 clinical notes. Besides, we proposed Dual-Inf, a novel framework that enabled LLMs to conduct bidirectional inference (i.e., from symptoms to diagnoses and vice versa) for DDx interpretation. Both human and automated evaluation validated its efficacy in predicting and elucidating differentials across four base LLMs. In addition, Dual-Inf could reduce interpretation errors and hold promise for rare disease explanations. To the best of our knowledge, it is the first work that customizes LLMs for DDx explanation and comprehensively evaluates their interpretation performance. Overall, our study bridges a critical gap in DDx interpretation and enhances clinical decision-making.

Integrating data from different platforms, such as bulk and single-cell RNA sequencing, is crucial for improving the accuracy and interpretability of complex biological analyses like cell type deconvolution. However, this task is complicated by measurement and biological heterogeneity between target and reference datasets. For the problem of cell type deconvolution, existing methods often neglect the correlation and uncertainty in cell type proportion estimates, possibly leading to an additional concern of false positives in downstream comparisons across multiple individuals. We introduce MEAD, a comprehensive statistical framework that not only estimates cell type proportions but also provides asymptotically valid statistical inference on the estimates. One of our key contributions is the identifiability result, which rigorously establishes the conditions under which cell type proportions are identifiable despite arbitrary heterogeneity of measurement biases between platforms. MEAD also supports the comparison of cell type proportions across individuals after deconvolution, accounting for gene-gene correlations and biological variability. Through simulations and real-data analysis, MEAD demonstrates superior reliability for inferring cell type compositions in complex biological systems.

Pathological speech analysis has been of interest in the detection of certain diseases like depression and Alzheimer's disease and attracts much interest from researchers. However, previous pathological speech analysis models are commonly designed for a specific disease while overlooking the connection between diseases, which may constrain performance and lower training efficiency. Instead of fine-tuning deep models for different tasks, prompt tuning is a much more efficient training paradigm. We thus propose a unified pathological speech analysis system for as many as three diseases with the prompt tuning technique. This system uses prompt tuning to adjust only a small part of the parameters to detect different diseases from speeches of possible patients. Our system leverages a pre-trained spoken language model and demonstrates strong performance across multiple disorders while only fine-tuning a fraction of the parameters. This efficient training approach leads to faster convergence and improved F1 scores by allowing knowledge to be shared across tasks. Our experiments on Alzheimer's disease, Depression, and Parkinson's disease show competitive results, highlighting the effectiveness of our method in pathological speech analysis.

We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.

Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.

Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.

Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis, thereby allowing manual manipulation in predicting the final answer.

The amount of publicly available biomedical literature has been growing rapidly in recent years, yet question answering systems still struggle to exploit the full potential of this source of data. In a preliminary processing step, many question answering systems rely on retrieval models for identifying relevant documents and passages. This paper proposes a weighted cosine distance retrieval scheme based on neural network word embeddings. Our experiments are based on publicly available data and tasks from the BioASQ biomedical question answering challenge and demonstrate significant performance gains over a wide range of state-of-the-art models.