William Hsu

Elisa Warner, Joonsang Lee, William Hsu et al.

Machine learning (ML) applications in medical artificial intelligence (AI) systems have shifted from traditional and statistical methods to increasing application of deep learning models. This survey navigates the current landscape of multimodal ML, focusing on its profound impact on medical image analysis and clinical decision support systems. Emphasizing challenges and innovations in addressing multimodal representation, fusion, translation, alignment, and co-learning, the paper explores the transformative potential of multimodal models for clinical predictions. It also highlights the need for principled assessments and practical implementation of such models, bringing attention to the dynamics between decision support systems and healthcare providers and personnel. Despite advancements, challenges such as data biases and the scarcity of "big data" in many biomedical domains persist. We conclude with a discussion on principled innovation and collaborative efforts to further the mission of seamless integration of multimodal ML models into biomedical practice.

Luoting Zhuang, Seyed Mohammad Hossein Tabatabaei, Ramin Salehi-Rad et al.

Machine learning models have utilized semantic features, deep features, or both to assess lung nodule malignancy. However, their reliance on manual annotation during inference, limited interpretability, and sensitivity to imaging variations hinder their application in real-world clinical settings. Thus, this research aims to integrate semantic features derived from radiologists' assessments of nodules, guiding the model to learn clinically relevant, robust, and explainable imaging features for predicting lung cancer. We obtained 938 low-dose CT scans from the National Lung Screening Trial (NLST) with 1,261 nodules and semantic features. Additionally, the Lung Image Database Consortium dataset contains 1,018 CT scans, with 2,625 lesions annotated for nodule characteristics. Three external datasets were obtained from UCLA Health, the LUNGx Challenge, and the Duke Lung Cancer Screening. We fine-tuned a pretrained Contrastive Language-Image Pretraining (CLIP) model with a parameter-efficient fine-tuning approach to align imaging and semantic text features and predict the one-year lung cancer diagnosis. Our model outperformed state-of-the-art (SOTA) models in the NLST test set with an AUROC of 0.901 and AUPRC of 0.776. It also showed robust results in external datasets. Using CLIP, we also obtained predictions on semantic features through zero-shot inference, such as nodule margin (AUROC: 0.807), nodule consistency (0.812), and pleural attachment (0.840). Our approach surpasses the SOTA models in predicting lung cancer across datasets collected from diverse clinical settings, providing explainable outputs, aiding clinicians in comprehending the underlying meaning of model predictions. This approach also prevents the model from learning shortcuts and generalizes across clinical settings. The code is available at https://github.com/luotingzhuang/CLIP_nodule.

Raja Farrukh Ali, Stephanie Milani, John Woods et al.

Reinforcement learning (RL) has recently shown promise in predicting Alzheimer's disease (AD) progression due to its unique ability to model domain knowledge. However, it is not clear which RL algorithms are well-suited for this task. Furthermore, these methods are not inherently explainable, limiting their applicability in real-world clinical scenarios. Our work addresses these two important questions. Using a causal, interpretable model of AD, we first compare the performance of four contemporary RL algorithms in predicting brain cognition over 10 years using only baseline (year 0) data. We then apply SHAP (SHapley Additive exPlanations) to explain the decisions made by each algorithm in the model. Our approach combines interpretability with explainability to provide insights into the key factors influencing AD progression, offering both global and individual, patient-level analysis. Our findings show that only one of the RL methods is able to satisfactorily model disease progression, but the post-hoc explanations indicate that all methods fail to properly capture the importance of amyloid accumulation, one of the pathological hallmarks of Alzheimer's disease. Our work aims to merge predictive accuracy with transparency, assisting clinicians and researchers in enhancing disease progression modeling for informed healthcare decisions. Code is available at https://github.com/rfali/xrlad.

Ruiwen Ding, Kha-Dinh Luong, Erika Rodriguez et al.

In computational pathology, extracting spatial features from gigapixel whole slide images (WSIs) is a fundamental task, but due to their large size, WSIs are typically segmented into smaller tiles. A critical aspect of this analysis is aggregating information from these tiles to make predictions at the WSI level. We introduce a model that combines a message-passing graph neural network (GNN) with a state space model (Mamba) to capture both local and global spatial relationships among the tiles in WSIs. The model's effectiveness was demonstrated in predicting progression-free survival among patients with early-stage lung adenocarcinomas (LUAD). We compared the model with other state-of-the-art methods for tile-level information aggregation in WSIs, including tile-level information summary statistics-based aggregation, multiple instance learning (MIL)-based aggregation, GNN-based aggregation, and GNN-transformer-based aggregation. Additional experiments showed the impact of different types of node features and different tile sampling strategies on the model performance. This work can be easily extended to any WSI-based analysis. Code: https://github.com/rina-ding/gat-mamba.

Tengyue Zhang, Ruiwen Ding, Luoting Zhuang et al.

Deep learning models in computational pathology often fail to generalize across cohorts and institutions due to domain shift. Existing approaches either fail to leverage unlabeled data from the target domain or rely on image-to-image translation, which can distort tissue structures and compromise model accuracy. In this work, we propose a semi-supervised domain adaptation (SSDA) framework that utilizes a latent diffusion model trained on unlabeled data from both the source and target domains to generate morphology-preserving and target-aware synthetic images. By conditioning the diffusion model on foundation model features, cohort identity, and tissue preparation method, we preserve tissue structure in the source domain while introducing target-domain appearance characteristics. The target-aware synthetic images, combined with real, labeled images from the source cohort, are subsequently used to train a downstream classifier, which is then tested on the target cohort. The effectiveness of the proposed SSDA framework is demonstrated on the task of lung adenocarcinoma prognostication. The proposed augmentation yielded substantially better performance on the held-out test set from the target cohort, without degrading source-cohort performance. The approach improved the weighted F1 score on the target-cohort held-out test set from 0.611 to 0.706 and the macro F1 score from 0.641 to 0.716. Our results demonstrate that target-aware diffusion-based synthetic data augmentation provides a promising and effective approach for improving domain generalization in computational pathology.

Syed Ahsan Masud Zaidi, Lior Shamir, William Hsu et al.

American football practice generates video at scale, yet the interaction of interest occupies only a brief window of each long, untrimmed clip. Reliable biomechanical analysis, therefore, depends on spatiotemporal localization that identifies both the interacting entities and the onset of contact. We study First Point of Contact (FPOC), defined as the first frame in which a player physically touches a tackle dummy, in unconstrained practice footage with camera motion, clutter, multiple similarly equipped athletes, and rapid pose changes around impact. We present GRAZE, a training-free pipeline for FPOC localization that requires no labeled tackle-contact examples. GRAZE uses Grounding DINO to discover candidate player-dummy interactions, refines them with motion-aware temporal reasoning, and uses SAM2 as an explicit pixel-level verifier of contact rather than relying on detection confidence alone. This separation between candidate discovery and contact confirmation makes the approach robust to cluttered scenes and unstable grounding near impact. On 738 tackle-practice videos, GRAZE produces valid outputs for 97.4% of clips and localizes FPOC within $\pm$ 10 frames on 77.5% of all clips and within $\pm$ 20 frames on 82.7% of all clips. These results show that frame-accurate contact onset localization in real-world practice footage is feasible without task-specific training.

Syed Ahsan Masud Zaidi, William Hsu, Scott Dietrich

Early identification of hazardous actions in contact sports enables timely intervention and improves player safety. We present a method for detecting risky tackles in American football practice videos and introduce a substantially expanded dataset for this task. Our work contains 733 single-athlete-dummy tackle clips, each temporally localized around first point contact and labeled with a strike zone component of the standardized Assessment for Tackling Technique (SATT-3), extending prior work that reported 178 annotated videos. Using a Vision transformer-based model with imbalance-aware training, we obtain risky recall of 0.67 and Risky F1 of 0.59 under crossvalidation. Relative to the previous baseline in a smaller subset (risky recall of 0.58; Risky F1 0.56 ), our approach improves risky recall by more than 8% points on a much larger dataset. These results indicate that the vision transformer-based video analysis, coupled with careful handling of class imbalance, can reliably detect rare but safety-critical tackling patterns, offering a practical pathway toward coach-centered injury prevention tools.

Luoting Zhuang, Stephen H. Park, Steven J. Skates et al.

Cancer evolves continuously over time through a complex interplay of genetic, epigenetic, microenvironmental, and phenotypic changes. This dynamic behavior drives uncontrolled cell growth, metastasis, immune evasion, and therapy resistance, posing challenges for effective monitoring and treatment. However, today's data-driven research in oncology has primarily focused on cross-sectional analysis using data from a single modality, limiting the ability to fully characterize and interpret the disease's dynamic heterogeneity. Advances in multiscale data collection and computational methods now enable the discovery of longitudinal multimodal biomarkers for precision oncology. Longitudinal data reveal patterns of disease progression and treatment response that are not evident from single-timepoint data, enabling timely abnormality detection and dynamic treatment adaptation. Multimodal data integration offers complementary information from diverse sources for more precise risk assessment and targeting of cancer therapy. In this review, we survey methods of longitudinal and multimodal modeling, highlighting their synergy in providing multifaceted insights for personalized care tailored to the unique characteristics of a patient's cancer. We summarize the current challenges and future directions of longitudinal multimodal analysis in advancing precision oncology.

Lasse Hansen, Wiebke Heyer, Christoph Großbröhmer et al.

Medical image registration is critical for clinical applications, and fair benchmarking of different methods is essential for monitoring ongoing progress. To date, the Learn2Reg 2020-2023 challenges have released several complementary datasets and established metrics for evaluations. However, these editions did not capture all aspects of the registration problem, particularly in terms of modality diversity and task complexity. To address these limitations, the 2024 edition introduces three new tasks, including large-scale multi-modal registration and unsupervised inter-subject brain registration, as well as the first microscopy-focused benchmark within Learn2Reg. The new datasets also inspired new method developments, including invertibility constraints, pyramid features, keypoints alignment and instance optimisation.

Noor Nakhaei, Chrysostomos Marasinou, Akinyinka Omigbodun et al.

Accurate characterization of suspicious microcalcifications is critical to determine whether these calcifications are associated with invasive disease. Our overarching objective is to enable the joint characterization of microcalcifications and surrounding breast tissue using mammography images and digital histopathology images. Towards this goal, we investigate a template matching-based approach that utilizes microcalcifications as landmarks to match radiographs taken of biopsy core specimens to groups of calcifications that are visible on mammography. Our approach achieved a high negative predictive value (0.98) but modest precision (0.66) and recall (0.58) in identifying the mammographic region where microcalcifications were taken during a core needle biopsy.

Ademola Okerinde, Sam Hoggatt, Divya Vani Lakkireddy et al.

In recent years, self-supervised learning has had significant success in applications involving computer vision and natural language processing. The type of pretext task is important to this boost in performance. One common pretext task is the measure of similarity and dissimilarity between pairs of images. In this scenario, the two images that make up the negative pair are visibly different to humans. However, in entomology, species are nearly indistinguishable and thus hard to differentiate. In this study, we explored the performance of a Siamese neural network using contrastive loss by learning to push apart embeddings of bumblebee species pair that are dissimilar, and pull together similar embeddings. Our experimental results show a 61% F1-score on zero-shot instances, a performance showing 11% improvement on samples of classes that share intersections with the training set.

Ademola Okerinde, Lior Shamir, William Hsu et al.

Class imbalance is an inherent problem in many machine learning classification tasks. This often leads to trained models that are unusable for any practical purpose. In this study we explore an unsupervised approach to address these imbalances by leveraging transfer learning from pre-trained image classification models to encoder-based Generative Adversarial Network (eGAN). To the best of our knowledge, this is the first work to tackle this problem using GAN without needing to augment with synthesized fake images. In the proposed approach we use the discriminator network to output a negative or positive score. We classify as minority, test samples with negative scores and as majority those with positive scores. Our approach eliminates epistemic uncertainty in model predictions, as the P(minority) + P(majority) need not sum up to 1. The impact of transfer learning and combinations of different pre-trained image classification models at the generator and discriminator is also explored. Best result of 0.69 F1-score was obtained on CIFAR-10 classification task with imbalance ratio of 1:2500. Our approach also provides a mechanism of thresholding the specificity or sensitivity of our machine learning system. Keywords: Class imbalance, Transfer Learning, GAN, nash equilibrium

Ademola Okerinde, Lior Shamir, William Hsu et al.

Ceramic insulators are important to electronic systems, designed and installed to protect humans from the danger of high voltage electric current. However, insulators are not immortal, and natural deterioration can gradually damage them. Therefore, the condition of insulators must be continually monitored, which is normally done using UAVs. UAVs collect many images of insulators, and these images are then analyzed to identify those that are damaged. Here we describe AdeNet as a deep neural network designed to identify damaged insulators, and test multiple approaches to automatic analysis of the condition of insulators. Several deep neural networks were tested, as were shallow learning methods. The best results (88.8\%) were achieved using AdeNet without transfer learning. AdeNet also reduced the false negative rate to $\sim$7\%. While the method cannot fully replace human inspection, its high throughput can reduce the amount of labor required to monitor lines for damaged insulators and provide early warning to replace damaged insulators.

Adedolapo Okanlawon, Huichen Yang, Avishek Bose et al.

We present a machine learning framework and a new test bed for data mining from the Slurm Workload Manager for high-performance computing (HPC) clusters. The focus was to find a method for selecting features to support decisions: helping users decide whether to resubmit failed jobs with boosted CPU and memory allocations or migrate them to a computing cloud. This task was cast as both supervised classification and regression learning, specifically, sequential problem solving suitable for reinforcement learning. Selecting relevant features can improve training accuracy, reduce training time, and produce a more comprehensible model, with an intelligent system that can explain predictions and inferences. We present a supervised learning model trained on a Simple Linux Utility for Resource Management (Slurm) data set of HPC jobs using three different techniques for selecting features: linear regression, lasso, and ridge regression. Our data set represented both HPC jobs that failed and those that succeeded, so our model was reliable, less likely to overfit, and generalizable. Our model achieved an R^2 of 95\% with 99\% accuracy. We identified five predictors for both CPU and memory properties.

Lei Luo, William Hsu, Shangxian Wang

Generative adversarial networks (GANs) have been successfully applied to transfer visual attributes in many domains, including that of human face images. This success is partly attributable to the facts that human faces have similar shapes and the positions of eyes, noses, and mouths are fixed among different people. Attribute transfer is more challenging when the source and target domain share different shapes. In this paper, we introduce a shape-aware GAN model that is able to preserve shape when transferring attributes, and propose its application to some real-world domains. Compared to other state-of-art GANs-based image-to-image translation models, the model we propose is able to generate more visually appealing results while maintaining the quality of results from transfer learning.

Leihao Wei, Yannan Lin, William Hsu

Computer-Aided-Diagnosis (CADx) systems assist radiologists with identifying and classifying potentially malignant pulmonary nodules on chest CT scans using morphology and texture-based (radiomic) features. However, radiomic features are sensitive to differences in acquisitions due to variations in dose levels and slice thickness. This study investigates the feasibility of generating a normalized scan from heterogeneous CT scans as input. We obtained projection data from 40 low-dose chest CT scans, simulating acquisitions at 10%, 25% and 50% dose and reconstructing the scans at 1.0mm and 2.0mm slice thickness. A 3D generative adversarial network (GAN) was used to simultaneously normalize reduced dose, thick slice (2.0mm) images to normal dose (100%), thinner slice (1.0mm) images. We evaluated the normalized image quality using peak signal-to-noise ratio (PSNR), structural similarity index (SSIM) and Learned Perceptual Image Patch Similarity (LPIPS). Our GAN improved perceptual similarity by 35%, compared to a baseline CNN method. Our analysis also shows that the GAN-based approach led to a significantly smaller error (p-value < 0.05) in nine studied radiomic features. These results indicated that GANs could be used to normalize heterogeneous CT images and reduce the variability in radiomic feature values.

Vahid Behzadan, William Hsu

This paper proposes a novel scheme for the watermarking of Deep Reinforcement Learning (DRL) policies. This scheme provides a mechanism for the integration of a unique identifier within the policy in the form of its response to a designated sequence of state transitions, while incurring minimal impact on the nominal performance of the policy. The applications of this watermarking scheme include detection of unauthorized replications of proprietary policies, as well as enabling the graceful interruption or termination of DRL activities by authorized entities. We demonstrate the feasibility of our proposal via experimental evaluation of watermarking a DQN policy trained in the Cartpole environment.

Vahid Behzadan, William Hsu

This paper investigates a class of attacks targeting the confidentiality aspect of security in Deep Reinforcement Learning (DRL) policies. Recent research have established the vulnerability of supervised machine learning models (e.g., classifiers) to model extraction attacks. Such attacks leverage the loosely-restricted ability of the attacker to iteratively query the model for labels, thereby allowing for the forging of a labeled dataset which can be used to train a replica of the original model. In this work, we demonstrate the feasibility of exploiting imitation learning techniques in launching model extraction attacks on DRL agents. Furthermore, we develop proof-of-concept attacks that leverage such techniques for black-box attacks against the integrity of DRL policies. We also present a discussion on potential solution concepts for mitigation techniques.

Vahid Behzadan, William Hsu

This paper investigates the effectiveness of adversarial training in enhancing the robustness of Deep Q-Network (DQN) policies to state-space perturbations. We first present a formal analysis of adversarial training in DQN agents and its performance with respect to the proportion of adversarial perturbations to nominal observations used for training. Next, we consider the sample-inefficiency of current adversarial training techniques, and propose a novel Adversarially-Guided Exploration (AGE) mechanism based on a modified hybrid of the $ε$-greedy algorithm and Boltzmann exploration. We verify the feasibility of this exploration mechanism through experimental evaluation of its performance in comparison with the traditional decaying $ε$-greedy and parameter-space noise exploration algorithms.

Vahid Behzadan, William Hsu

This paper investigates the resilience and robustness of Deep Reinforcement Learning (DRL) policies to adversarial perturbations in the state space. We first present an approach for the disentanglement of vulnerabilities caused by representation learning of DRL agents from those that stem from the sensitivity of the DRL policies to distributional shifts in state transitions. Building on this approach, we propose two RL-based techniques for quantitative benchmarking of adversarial resilience and robustness in DRL policies against perturbations of state transitions. We demonstrate the feasibility of our proposals through experimental evaluation of resilience and robustness in DQN, A2C, and PPO2 policies trained in the Cartpole environment.

Justin Wood, Nicholas J. Matiasz, Alcino J. Silva et al.

The biological literature is rich with sentences that describe causal relations. Methods that automatically extract such sentences can help biologists to synthesize the literature and even discover latent relations that had not been articulated explicitly. Current methods for extracting causal sentences are based on either machine learning or a predefined database of causal terms. Machine learning approaches require a large set of labeled training data and can be susceptible to noise. Methods based on predefined databases are limited by the quality of their curation and are unable to capture new concepts or mistakes in the input. We address these challenges by adapting and improving a method designed for a seemingly unrelated problem: finding alignments between genomic sequences. This paper presents a novel and outperforming method for extracting causal relations from text by aligning the part-of-speech representations of an input set with that of known causal sentences. Our experiments show that when applied to the task of finding causal sentences in biological literature, our method improves on the accuracy of other methods in a computationally efficient manner.

Meng Li, Shiwen Shen, Wen Gao et al.

Computed tomography (CT) is increasingly being used for cancer screening, such as early detection of lung cancer. However, CT studies have varying pixel spacing due to differences in acquisition parameters. Thick slice CTs have lower resolution, hindering tasks such as nodule characterization during computer-aided detection due to partial volume effect. In this study, we propose a novel 3D enhancement convolutional neural network (3DECNN) to improve the spatial resolution of CT studies that were acquired using lower resolution/slice thicknesses to higher resolutions. Using a subset of the LIDC dataset consisting of 20,672 CT slices from 100 scans, we simulated lower resolution/thick section scans then attempted to reconstruct the original images using our 3DECNN network. A significant improvement in PSNR (29.3087dB vs. 28.8769dB, p-value < 2.2e-16) and SSIM (0.8529dB vs. 0.8449dB, p-value < 2.2e-16) compared to other state-of-art deep learning methods is observed.

Dan Andresen, William Hsu, Huichen Yang et al.

We address the problem of predicting whether sufficient memory and CPU resources have been requested for jobs at submission time. For this purpose, we examine the task of training a supervised machine learning system to predict the outcome - whether the job will fail specifically due to insufficient resources - as a classification task. Sufficiently high accuracy, precision, and recall at this task facilitates more anticipatory decision support applications in the domain of HPC resource allocation. Our preliminary results using a new test bed show that the probability of failed jobs is associated with information freely available at job submission time and may thus be usable by a learning system for user modeling that gives personalized feedback to users.

Ahmed M. Alaa, Kyeong H. Moon, William Hsu et al.

Breast cancer screening policies attempt to achieve timely diagnosis by the regular screening of apparently healthy women. Various clinical decisions are needed to manage the screening process; those include: selecting the screening tests for a woman to take, interpreting the test outcomes, and deciding whether or not a woman should be referred to a diagnostic test. Such decisions are currently guided by clinical practice guidelines (CPGs), which represent a one-size-fits-all approach that are designed to work well on average for a population, without guaranteeing that it will work well uniformly over that population. Since the risks and benefits of screening are functions of each patients features, personalized screening policies that are tailored to the features of individuals are needed in order to ensure that the right tests are recommended to the right woman. In order to address this issue, we present ConfidentCare: a computer-aided clinical decision support system that learns a personalized screening policy from the electronic health record (EHR) data. ConfidentCare operates by recognizing clusters of similar patients, and learning the best screening policy to adopt for each cluster. A cluster of patients is a set of patients with similar features (e.g. age, breast density, family history, etc.), and the screening policy is a set of guidelines on what actions to recommend for a woman given her features and screening test scores. ConfidentCare algorithm ensures that the policy adopted for every cluster of patients satisfies a predefined accuracy requirement with a high level of confidence. We show that our algorithm outperforms the current CPGs in terms of cost-efficiency and false positive rates.

William Hsu, Mohammed Abduljabbar, Ryuichi Osuga et al.

The problem of spatiotemporal event visualization based on reports entails subtasks ranging from named entity recognition to relationship extraction and mapping of events. We present an approach to event extraction that is driven by data mining and visualization goals, particularly thematic mapping and trend analysis. This paper focuses on bridging the information extraction and visualization tasks and investigates topic modeling approaches. We develop a static, finite topic model and examine the potential benefits and feasibility of extending this to dynamic topic modeling with a large number of topics and continuous time. We describe an experimental test bed for event mapping that uses this end-to-end information retrieval system, and report preliminary results on a geoinformatics problem: tracking of methamphetamine lab seizure events across time and space.

Wesam Elshamy, Doina Caragea, William Hsu

We describe our language-independent unsupervised word sense induction system. This system only uses topic features to cluster different word senses in their global context topic space. Using unlabeled data, this system trains a latent Dirichlet allocation (LDA) topic model then uses it to infer the topics distribution of the test instances. By clustering these topics distributions in their topic space we cluster them into different senses. Our hypothesis is that closeness in topic space reflects similarity between different word senses. This system participated in SemEval-2 word sense induction and disambiguation task and achieved the second highest V-measure score among all other systems.