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Organic Solar Cells (OSCs) are a promising technology for sustainable energy production. However, the identification of molecules with desired OSC properties typically involves laborious experimental research. To accelerate progress in the field, it is crucial to develop machine learning models capable of accurately predicting the properties of OSC molecules. While graph representation learning has demonstrated success in molecular property prediction, it remains underexplored for OSC-specific tasks. Existing methods fail to capture the unique structural features of OSC molecules, particularly the intricate ring systems that critically influence OSC properties, leading to suboptimal performance. To fill the gap, we present RingFormer, a novel graph transformer framework specially designed to capture both atom and ring level structural patterns in OSC molecules. RingFormer constructs a hierarchical graph that integrates atomic and ring structures and employs a combination of local message passing and global attention mechanisms to generate expressive graph representations for accurate OSC property prediction. We evaluate RingFormer's effectiveness on five curated OSC molecule datasets through extensive experiments. The results demonstrate that RingFormer consistently outperforms existing methods, achieving a 22.77% relative improvement over the nearest competitor on the CEPDB dataset., Comment: 12 pages, 4 figures. This is the extended version of the paper accepted at AAAI 2025, which includes all technical appendices and additional experimental details

Attributed networks containing entity-specific information in node attributes are ubiquitous in modeling social networks, e-commerce, bioinformatics, etc. Their inherent network topology ranges from simple graphs to hypergraphs with high-order interactions and multiplex graphs with separate layers. An important graph mining task is node clustering, aiming to partition the nodes of an attributed network into k disjoint clusters such that intra-cluster nodes are closely connected and share similar attributes, while inter-cluster nodes are far apart and dissimilar. It is highly challenging to capture multi-hop connections via nodes or attributes for effective clustering on multiple types of attributed networks. In this paper, we first present AHCKA as an efficient approach to attributed hypergraph clustering (AHC). AHCKA includes a carefully-crafted K-nearest neighbor augmentation strategy for the optimized exploitation of attribute information on hypergraphs, a joint hypergraph random walk model to devise an effective AHC objective, and an efficient solver with speedup techniques for the objective optimization. The proposed techniques are extensible to various types of attributed networks, and thus, we develop ANCKA as a versatile attributed network clustering framework, capable of attributed graph clustering (AGC), attributed multiplex graph clustering (AMGC), and AHC. Moreover, we devise ANCKA with algorithmic designs tailored for GPU acceleration to boost efficiency. We have conducted extensive experiments to compare our methods with 19 competitors on 8 attributed hypergraphs, 16 competitors on 6 attributed graphs, and 16 competitors on 3 attributed multiplex graphs, all demonstrating the superb clustering quality and efficiency of our methods., Comment: 25 pages, 15 figures

Graph Neural Networks (GNNs) excel in machine learning tasks involving graphs, such as node classification, graph classification, and link prediction. However, explaining their decision-making process is challenging due to the complex transformations GNNs perform by aggregating relational information from graph topology. Existing methods for explaining GNNs face key limitations: (1) lack of flexibility in generating explanations at varying levels, (2) difficulty in identifying unique substructures relevant to class differentiation, and (3) little support to ensure the trustworthiness of explanations. To address these challenges, we introduce GNNAnatomy, a visual analytics system designed to generate and evaluate multi-level GNN explanations for graph classification tasks. GNNAnatomy uses graphlets, primitive graph substructures, to identify the most critical substructures in a graph class by analyzing the correlation between GNN predictions and graphlet frequencies. These correlations are presented interactively for user-selected group of graphs through our visual analytics system. To further validate top-ranked graphlets, we measure the change in classification confidence after removing each graphlet from the original graph. We demonstrate the effectiveness of GNNAnatomy through case studies on synthetic and real-world graph datasets from sociology and biology domains. Additionally, we compare GNNAnatomy with state-of-the-art explainable GNN methods to showcase its utility and versatility.

Communication among healthcare professionals (HCPs) is crucial for the quality of patient treatment. Surrounding each patient's treatment, communication among HCPs can be examined as temporal networks, constructed from Electronic Health Record (EHR) access logs. This paper introduces a visual analytics system designed to study the effectiveness and efficiency of temporal communication networks mediated by the EHR system. We present a method that associates network measures with patient survival outcomes and devises effectiveness metrics based on these associations. To analyze communication efficiency, we extract the latencies and frequencies of EHR accesses. Our visual analytics system is designed to assist in inspecting and understanding the composed communication effectiveness metrics and to enable the exploration of communication efficiency by encoding latencies and frequencies in an information flow diagram. We demonstrate and evaluate our system through multiple case studies and an expert review.

The inherent diversity of computation types within the deep neural network (DNN) models often requires a variety of specialized units in hardware processors, which limits computational efficiency, increasing both inference latency and power consumption, especially when the hardware processor needs to support and execute different neural networks. In this study, we introduce NeuralMatrix, which elastically transforms the computations of entire DNNs into linear matrix operations. This transformation allows seamless execution of various DNN models all with matrix operations and paves the way for running versatile DNN models with a single General Matrix Multiplication (GEMM) accelerator.Extensive experiments with both CNN and transformer-based models demonstrate the potential of NeuralMatrix to accurately and efficiently execute a wide range of DNN models, achieving 2.17-38.72 times computation efficiency (i.e., throughput per power) compared to CPUs, GPUs, and SoC platforms. This level of efficiency is usually only attainable with the accelerator designed for a specific neural network., Comment: 9 pages, 8figures, Submitted to The 39th Annual AAAI Conference on Artificial Intelligence

Vision transformer (ViT) expands the success of transformer models from sequential data to images. The model decomposes an image into many smaller patches and arranges them into a sequence. Multi-head self-attentions are then applied to the sequence to learn the attention between patches. Despite many successful interpretations of transformers on sequential data, little effort has been devoted to the interpretation of ViTs, and many questions remain unanswered. For example, among the numerous attention heads, which one is more important? How strong are individual patches attending to their spatial neighbors in different heads? What attention patterns have individual heads learned? In this work, we answer these questions through a visual analytics approach. Specifically, we first identify what heads are more important in ViTs by introducing multiple pruning-based metrics. Then, we profile the spatial distribution of attention strengths between patches inside individual heads, as well as the trend of attention strengths across attention layers. Third, using an autoencoder-based learning solution, we summarize all possible attention patterns that individual heads could learn. Examining the attention strengths and patterns of the important heads, we answer why they are important. Through concrete case studies with experienced deep learning experts on multiple ViTs, we validate the effectiveness of our solution that deepens the understanding of ViTs from head importance, head attention strength, and head attention pattern., Comment: Accepted by PacificVis 2023 and selected to be published in TVCG

Adversarial attacks on a convolutional neural network (CNN) -- injecting human-imperceptible perturbations into an input image -- could fool a high-performance CNN into making incorrect predictions. The success of adversarial attacks raises serious concerns about the robustness of CNNs, and prevents them from being used in safety-critical applications, such as medical diagnosis and autonomous driving. Our work introduces a visual analytics approach to understanding adversarial attacks by answering two questions: (1) which neurons are more vulnerable to attacks and (2) which image features do these vulnerable neurons capture during the prediction? For the first question, we introduce multiple perturbation-based measures to break down the attacking magnitude into individual CNN neurons and rank the neurons by their vulnerability levels. For the second, we identify image features (e.g., cat ears) that highly stimulate a user-selected neuron to augment and validate the neuron's responsibility. Furthermore, we support an interactive exploration of a large number of neurons by aiding with hierarchical clustering based on the neurons' roles in the prediction. To this end, a visual analytics system is designed to incorporate visual reasoning for interpreting adversarial attacks. We validate the effectiveness of our system through multiple case studies as well as feedback from domain experts., Comment: Accepted by the Special Issue on Human-Centered Explainable AI, ACM Transactions on Interactive Intelligent Systems

Purpose: Arterial spin labeling (ASL) perfusion imaging indicates direct and absolute measurement of cerebral blood flow (CBF). Arterial transit time (ATT) is a related physiological parameter reflecting the duration for the labeled spins to reach the brain region of interest. Multiple post-labeling delay (PLDs) can provide robust measures of both CBF and ATT, allowing for optimization of regional CBF modeling based on ATT. The prolonged acquisition time can potentially reduce the quality and accuracy of the CBF and ATT estimation. We proposed a novel network to significantly reduce the number of PLDs with higher signal-to-noise ratio (SNR). Method: CBF and ATT estimations were performed for one PLD and two PLDs sepa-rately. Each model was trained independently to learn the nonlinear transformation from perfusion weighted image (PWI) to CBF and ATT images. Results: Both one-PLD and two-PLD models outperformed the conventional method visually on CBF and two-PLD model showed more accurate structure on ATT estima-tion. The proposed method significantly reduces the number of PLDs from 6 to 2 on ATT and even to single PLD on CBF without sacrificing the SNR. Conclusion: It is feasible to generate CBF and ATT maps with reduced PLDs using deep learning with high quality.

A domain-theoretic framework is presented for validated robustness analysis of neural networks. First, global robustness of a general class of networks is analyzed. Then, using the fact that Edalat's domain-theoretic L-derivative coincides with Clarke's generalized gradient, the framework is extended for attack-agnostic local robustness analysis. The proposed framework is ideal for designing algorithms which are correct by construction. This claim is exemplified by developing a validated algorithm for estimation of Lipschitz constant of feedforward regressors. The completeness of the algorithm is proved over differentiable networks, and also over general position ReLU networks. Computability results are obtained within the framework of effectively given domains. Using the proposed domain model, differentiable and non-differentiable networks can be analyzed uniformly. The validated algorithm is implemented using arbitrary-precision interval arithmetic, and the results of some experiments are presented. The software implementation is truly validated, as it handles floating-point errors as well., Comment: 35 pages, 10 figures, 3 tables

Arterial spin labeling (ASL) perfusion MRI provides a non-invasive way to quantify cerebral blood flow (CBF) but it still suffers from a low signal-to-noise-ratio (SNR). Using deep machine learning (DL), several groups have shown encouraging denoising results. Interestingly, the improvement was obtained when the deep neural network was trained using noise-contaminated surrogate reference because of the lack of golden standard high quality ASL CBF images. More strikingly, the output of these DL ASL networks (ASLDN) showed even higher SNR than the surrogate reference. This phenomenon indicates a learning-from-noise capability of deep networks for ASL CBF image denoising, which can be further enhanced by network optimization. In this study, we proposed a new ASLDN to test whether similar or even better ASL CBF image quality can be achieved in the case of highly noisy training reference. Different experiments were performed to validate the learning-from-noise hypothesis. The results showed that the learning-from-noise strategy produced better output quality than ASLDN trained with relatively high SNR reference.

We propose a graph neural network (GNN) approach to the problem of predicting the stylistic compatibility of a set of furniture items from images. While most existing results are based on siamese networks which evaluate pairwise compatibility between items, the proposed GNN architecture exploits relational information among groups of items. We present two GNN models, both of which comprise a deep CNN that extracts a feature representation for each image, a gated recurrent unit (GRU) network that models interactions between the furniture items in a set, and an aggregation function that calculates the compatibility score. In the first model, a generalized contrastive loss function that promotes the generation of clustered embeddings for items belonging to the same furniture set is introduced. Also, in the first model, the edge function between nodes in the GRU and the aggregation function are fixed in order to limit model complexity and allow training on smaller datasets; in the second model, the edge function and aggregation function are learned directly from the data. We demonstrate state-of-the art accuracy for compatibility prediction and "fill in the blank" tasks on the Bonn and Singapore furniture datasets. We further introduce a new dataset, called the Target Furniture Collections dataset, which contains over 6000 furniture items that have been hand-curated by stylists to make up 1632 compatible sets. We also demonstrate superior prediction accuracy on this dataset., Comment: Accepted for publication at CVPR Workshops

There is a growing trend of applying machine learning methods to medical datasets in order to predict patients' future status. Although some of these methods achieve high performance, challenges still exist in comparing and evaluating different models through their interpretable information. Such analytics can help clinicians improve evidence-based medical decision making. In this work, we develop a visual analytics system that compares multiple models' prediction criteria and evaluates their consistency. With our system, users can generate knowledge on different models' inner criteria and how confidently we can rely on each model's prediction for a certain patient. Through a case study of a publicly available clinical dataset, we demonstrate the effectiveness of our visual analytics system to assist clinicians and researchers in comparing and quantitatively evaluating different machine learning methods., Comment: This is the author's version of the article that has been accepted to PacificVis 2020 Visualization Meets AI Workshop

Machine learning for data-driven diagnosis has been actively studied in medicine to provide better healthcare. Supporting analysis of a patient cohort similar to a patient under treatment is a key task for clinicians to make decisions with high confidence. However, such analysis is not straightforward due to the characteristics of medical records: high dimensionality, irregularity in time, and sparsity. To address this challenge, we introduce a method for similarity calculation of medical records. Our method employs event and sequence embeddings. While we use an autoencoder for the event embedding, we apply its variant with the self-attention mechanism for the sequence embedding. Moreover, in order to better handle the irregularity of data, we enhance the self-attention mechanism with consideration of different time intervals. We have developed a visual analytics system to support comparative studies of patient records. To make a comparison of sequences with different lengths easier, our system incorporates a sequence alignment method. Through its interactive interface, the user can quickly identify patients of interest and conveniently review both the temporal and multivariate aspects of the patient records. We demonstrate the effectiveness of our design and system with case studies using a real-world dataset from the neonatal intensive care unit of UC Davis., Comment: This is the author's version of the article that has been accepted in PacificVis 2020 Visualization Meets AI Workshop