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The ability of graph neural networks (GNNs) to count homomorphisms has recently been proposed as a practical and fine-grained measure of their expressive power. Although several existing works have investigated the homomorphism counting power of certain GNN families, a simple and unified framework for analyzing the problem is absent. In this paper, we first propose \emph{generalized folklore Weisfeiler-Leman (GFWL)} algorithms as a flexible design basis for expressive GNNs, and then provide a theoretical framework to algorithmically determine the homomorphism counting power of an arbitrary class of GNN within the GFWL design space. As the considered design space is large enough to accommodate almost all known powerful GNNs, our result greatly extends all existing works, and may find its application in the automation of GNN model design.

Smart medical devices are an integral component of the healthcare Internet of Things (IoT), providing patients with various healthcare services through an IoT-based application. Ensuring the dependability of such applications through system and integration-level testing mandates the physical integration of numerous medical devices, which is costly and impractical. In this context, digital twins of medical devices play an essential role in facilitating testing automation. Testing with digital twins without accounting for uncertain environmental factors of medical devices leaves many functionalities of IoT-based healthcare applications untested. In addition, digital twins operating without environmental factors remain out of sync and uncalibrated with their corresponding devices functioning in the real environment. To deal with these challenges, in this paper, we propose a model-based approach (EnvDT) for modeling and simulating the environment of medical devices' digital twins under uncertainties. We empirically evaluate the EnvDT using three medicine dispensers, Karie, Medido, and Pilly connected to a real-world IoT-based healthcare application. Our evaluation targets analyzing the coverage of environment models and the diversity of uncertain scenarios generated for digital twins. Results show that EnvDT achieves approximately 61% coverage of environment models and generates diverse uncertain scenarios (with a near-maximum diversity value of 0.62) during multiple environmental simulations.

It is widely recognised that semiparametric efficient estimation can be hard to achieve in practice: estimators that are in theory efficient may require unattainable levels of accuracy for the estimation of complex nuisance functions. As a consequence, estimators deployed on real datasets are often chosen in a somewhat ad hoc fashion, and may suffer high variance. We study this gap between theory and practice in the context of a broad collection of semiparametric regression models that includes the generalised partially linear model. We advocate using estimators that are robust in the sense that they enjoy $\sqrt{n}$-consistent uniformly over a sufficiently rich class of distributions characterised by certain conditional expectations being estimable by user-chosen machine learning methods. We show that even asking for locally uniform estimation within such a class narrows down possible estimators to those parametrised by certain weight functions. Conversely, we show that such estimators do provide the desired uniform consistency and introduce a novel random forest-based procedure for estimating the optimal weights. We prove that the resulting estimator recovers a notion of $\textbf{ro}$bust $\textbf{s}$emiparametric $\textbf{e}$fficiency (ROSE) and provides a practical alternative to semiparametric efficient estimators. We demonstrate the effectiveness of our ROSE random forest estimator in a variety of semiparametric settings on simulated and real-world data.

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce ProVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 9,500 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that ProVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research.

Predicting future disease progression risk from medical images is challenging due to patient heterogeneity, and subtle or unknown imaging biomarkers. Moreover, deep learning (DL) methods for survival analysis are susceptible to image domain shifts across scanners. We tackle these issues in the task of predicting late dry Age-related Macular Degeneration (dAMD) onset from retinal OCT scans. We propose a novel DL method for survival prediction to jointly predict from the current scan a risk score, inversely related to time-to-conversion, and the probability of conversion within a time interval $t$. It uses a family of parallel hyperplanes generated by parameterizing the bias term as a function of $t$. In addition, we develop unsupervised losses based on intra-subject image pairs to ensure that risk scores increase over time and that future conversion predictions are consistent with AMD stage prediction using actual scans of future visits. Such losses enable data-efficient fine-tuning of the trained model on new unlabeled datasets acquired with a different scanner. Extensive evaluation on two large datasets acquired with different scanners resulted in a mean AUROCs of 0.82 for Dataset-1 and 0.83 for Dataset-2, across prediction intervals of 6,12 and 24 months.

Endovascular interventions are a life-saving treatment for many diseases, yet suffer from drawbacks such as radiation exposure and potential scarcity of proficient physicians. Robotic assistance during these interventions could be a promising support towards these problems. Research focusing on autonomous endovascular interventions utilizing artificial intelligence-based methodologies is gaining popularity. However, variability in assessment environments hinders the ability to compare and contrast the efficacy of different approaches, primarily due to each study employing a unique evaluation framework. In this study, we present deep reinforcement learning-based autonomous endovascular device navigation on three distinct digital benchmark interventions: BasicWireNav, ArchVariety, and DualDeviceNav. The benchmark interventions were implemented with our modular simulation framework stEVE (simulated EndoVascular Environment). Autonomous controllers were trained solely in simulation and evaluated in simulation and on physical test benches with camera and fluoroscopy feedback. Autonomous control for BasicWireNav and ArchVariety reached high success rates and was successfully transferred from the simulated training environment to the physical test benches, while autonomous control for DualDeviceNav reached a moderate success rate. The experiments demonstrate the feasibility of stEVE and its potential for transferring controllers trained in simulation to real-world scenarios. Nevertheless, they also reveal areas that offer opportunities for future research. This study demonstrates the transferability of autonomous controllers from simulation to the real world in endovascular navigation and lowers the entry barriers and increases the comparability of research on endovascular assistance systems by providing open-source training scripts, benchmarks and the stEVE framework.

Automatic medical image segmentation technology has the potential to expedite pathological diagnoses, thereby enhancing the efficiency of patient care. However, medical images often have complex textures and structures, and the models often face the problem of reduced image resolution and information loss due to downsampling. To address this issue, we propose HC-Mamba, a new medical image segmentation model based on the modern state space model Mamba. Specifically, we introduce the technique of dilated convolution in the HC-Mamba model to capture a more extensive range of contextual information without increasing the computational cost by extending the perceptual field of the convolution kernel. In addition, the HC-Mamba model employs depthwise separable convolutions, significantly reducing the number of parameters and the computational power of the model. By combining dilated convolution and depthwise separable convolutions, HC-Mamba is able to process large-scale medical image data at a much lower computational cost while maintaining a high level of performance. We conduct comprehensive experiments on segmentation tasks including organ segmentation and skin lesion, and conduct extensive experiments on Synapse, ISIC17 and ISIC18 to demonstrate the potential of the HC-Mamba model in medical image segmentation. The experimental results show that HC-Mamba exhibits competitive performance on all these datasets, thereby proving its effectiveness and usefulness in medical image segmentation.

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.

Knowledge graph embedding, which aims to represent entities and relations as low dimensional vectors (or matrices, tensors, etc.), has been shown to be a powerful technique for predicting missing links in knowledge graphs. Existing knowledge graph embedding models mainly focus on modeling relation patterns such as symmetry/antisymmetry, inversion, and composition. However, many existing approaches fail to model semantic hierarchies, which are common in real-world applications. To address this challenge, we propose a novel knowledge graph embedding model---namely, Hierarchy-Aware Knowledge Graph Embedding (HAKE)---which maps entities into the polar coordinate system. HAKE is inspired by the fact that concentric circles in the polar coordinate system can naturally reflect the hierarchy. Specifically, the radial coordinate aims to model entities at different levels of the hierarchy, and entities with smaller radii are expected to be at higher levels; the angular coordinate aims to distinguish entities at the same level of the hierarchy, and these entities are expected to have roughly the same radii but different angles. Experiments demonstrate that HAKE can effectively model the semantic hierarchies in knowledge graphs, and significantly outperforms existing state-of-the-art methods on benchmark datasets for the link prediction task.

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.