J. Andrew Zhang

Ming Y. Lu, Bowen Chen, Andrew Zhang et al.

Contrastive visual language pretraining has emerged as a powerful method for either training new language-aware image encoders or augmenting existing pretrained models with zero-shot visual recognition capabilities. However, existing works typically train on large datasets of image-text pairs and have been designed to perform downstream tasks involving only small to medium sized-images, neither of which are applicable to the emerging field of computational pathology where there are limited publicly available paired image-text datasets and each image can span up to 100,000 x 100,000 pixels. In this paper we present MI-Zero, a simple and intuitive framework for unleashing the zero-shot transfer capabilities of contrastively aligned image and text models on gigapixel histopathology whole slide images, enabling multiple downstream diagnostic tasks to be carried out by pretrained encoders without requiring any additional labels. MI-Zero reformulates zero-shot transfer under the framework of multiple instance learning to overcome the computational challenge of inference on extremely large images. We used over 550k pathology reports and other available in-domain text corpora to pre-train our text encoder. By effectively leveraging strong pre-trained encoders, our best model pretrained on over 33k histopathology image-caption pairs achieves an average median zero-shot accuracy of 70.2% across three different real-world cancer subtyping tasks. Our code is available at: https://github.com/mahmoodlab/MI-Zero.

Guillaume Jaume, Anurag Vaidya, Andrew Zhang et al.

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

Wayes Tushar, Jian Andrew Zhang, Chau Yuen et al.

This paper proposes an energy management scheme to maximize the use of solar energy in the smart grid. In this context, a shared facility controller (SFC) with a number of solar photovoltaic (PV) panels in a smart community is considered that has the capability to schedule the generated energy for consumption and trade to other entities. Particularly, a mechanism is designed for the SFC to decide on the energy surplus, if there is any, that it can use to charge its battery and sell to the households and the grid based on the offered prices. In this regard, a hierarchical energy management scheme is proposed with a view to reduce the total operational cost to the SFC. The concept of a virtual cost (VC) is introduced that aids the SFC to estimate its future operational cost based on some available current information. The energy management is conducted for three different cases and the optimal cost to the SFC is determined for each case via the theory of maxima and minima. A real-time algorithm is proposed to reach the optimal cost for all cases and some numerical examples are provided to demonstrate the beneficial properties of the proposed scheme.

Richard J. Chen, Tong Ding, Ming Y. Lu et al.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Ming Y. Lu, Bowen Chen, Drew F. K. Williamson et al.

The accelerated adoption of digital pathology and advances in deep learning have enabled the development of powerful models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain and the model's usage is limited by the specific task and disease for which it is trained. Additionally, most models in histopathology leverage only image data, a stark contrast to how humans teach each other and reason about histopathologic entities. We introduce CONtrastive learning from Captions for Histopathology (CONCH), a visual-language foundation model developed using diverse sources of histopathology images, biomedical text, and notably over 1.17 million image-caption pairs via task-agnostic pretraining. Evaluated on a suite of 13 diverse benchmarks, CONCH can be transferred to a wide range of downstream tasks involving either or both histopathology images and text, achieving state-of-the-art performance on histology image classification, segmentation, captioning, text-to-image and image-to-text retrieval. CONCH represents a substantial leap over concurrent visual-language pretrained systems for histopathology, with the potential to directly facilitate a wide array of machine learning-based workflows requiring minimal or no further supervised fine-tuning.

Andrew H. Song, Mane Williams, Drew F. K. Williamson et al.

Human tissue and its constituent cells form a microenvironment that is fundamentally three-dimensional (3D). However, the standard-of-care in pathologic diagnosis involves selecting a few two-dimensional (2D) sections for microscopic evaluation, risking sampling bias and misdiagnosis. Diverse methods for capturing 3D tissue morphologies have been developed, but they have yet had little translation to clinical practice; manual and computational evaluations of such large 3D data have so far been impractical and/or unable to provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting the value of capturing larger extents of heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.

Dianhao Zheng, Hongbin Zhang, J. Andrew Zhang et al.

This note investigates the stability of both linear and nonlinear switched systems with average dwell time. Two new analysis methods are proposed. Different from existing approaches, the proposed methods take into account the sequence in which the subsystems are switched. Depending on the predecessor or successor subsystems to be considered, sequence-based average preceding dwell time (SBAPDT) and sequence-based average subsequence dwell time (SBASDT) approaches are proposed and discussed for both continuous and discrete time systems. These proposed methods, when considering the switch sequence, have the potential to further reduce the conservativeness of the existing approaches. A comparative numerical example is also given to demonstrate the advantages of the proposed approaches.

Bryan Zhao, Andrew Zhang, Blake Watson et al.

Moderation of social media content is currently a highly manual task, yet there is too much content posted daily to do so effectively. With the advent of a number of multimodal models, there is the potential to reduce the amount of manual labor for this task. In this work, we aim to explore different models and determine what is most effective for the Hateful Memes Challenge, a challenge by Meta designed to further machine learning research in content moderation. Specifically, we explore the differences between early fusion and late fusion models in classifying multimodal memes containing text and images. We first implement a baseline using unimodal models for text and images separately using BERT and ResNet-152, respectively. The outputs from these unimodal models were then concatenated together to create a late fusion model. In terms of early fusion models, we implement ConcatBERT, VisualBERT, ViLT, CLIP, and BridgeTower. It was found that late fusion performed significantly worse than early fusion models, with the best performing model being CLIP which achieved an AUROC of 70.06. The code for this work is available at https://github.com/bzhao18/CS-7643-Project.

Andrew Zhang, Guillaume Jaume, Anurag Vaidya et al.

Advances in foundation modeling have reshaped computational pathology. However, the increasing number of available models and lack of standardized benchmarks make it increasingly complex to assess their strengths, limitations, and potential for further development. To address these challenges, we introduce a new suite of software tools for whole-slide image processing, foundation model benchmarking, and curated publicly available tasks. We anticipate that these resources will promote transparency, reproducibility, and continued progress in the field.

Xiaozhou You, Jian Zhang

Text-guided image generation aimed to generate desired images conditioned on given texts, while text-guided image manipulation refers to semantically edit parts of a given image based on specified texts. For these two similar tasks, the key point is to ensure image fidelity as well as semantic consistency. Many previous approaches require complex multi-stage generation and adversarial training, while struggling to provide a unified framework for both tasks. In this work, we propose TextCLIP, a unified framework for text-guided image generation and manipulation without adversarial training. The proposed method accepts input from images or random noise corresponding to these two different tasks, and under the condition of the specific texts, a carefully designed mapping network that exploits the powerful generative capabilities of StyleGAN and the text image representation capabilities of Contrastive Language-Image Pre-training (CLIP) generates images of up to $1024\times1024$ resolution that can currently be generated. Extensive experiments on the Multi-modal CelebA-HQ dataset have demonstrated that our proposed method outperforms existing state-of-the-art methods, both on text-guided generation tasks and manipulation tasks.

Zhongqin Wang, J. Andrew Zhang, Kai Wu et al.

Integrated Sensing and Communication (ISAC) is a key enabler for next-generation wireless systems. However, real-world deployment is often limited to low-cost, single-antenna transceivers. In such bistatic Single-Input Single-Output (SISO) setup, clock asynchrony introduces random phase offsets in Channel State Information (CSI), which cannot be mitigated using conventional multi-antenna methods. This work proposes WiDFS 3.0, a lightweight bistatic SISO sensing framework that enables accurate delay and Doppler estimation from distorted CSI by effectively suppressing Doppler mirroring ambiguity. It operates with only a single antenna at both the transmitter and receiver, making it suitable for low-complexity deployments. We propose a self-referencing cross-correlation (SRCC) method for SISO random phase removal and employ delay-domain beamforming to resolve Doppler ambiguity. The resulting unambiguous delay-Doppler-time features enable robust sensing with compact neural networks. Extensive experiments show that WiDFS 3.0 achieves accurate parameter estimation, with performance comparable to or even surpassing that of prior multi-antenna methods, especially in delay estimation. Validated under single- and multi-target scenarios, the extracted ambiguity-resolved features show strong sensing accuracy and generalization. For example, when deployed on the embedded-friendly MobileViT-XXS with only 1.3M parameters, WiDFS 3.0 consistently outperforms conventional features such as CSI amplitude, mirrored Doppler, and multi-receiver aggregated Doppler.

Zhongyue Zhang, Jiahua Rao, Jie Zhong et al.

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

Bai Yan, Qi Zhao, Jin Zhang et al.

Reconfigurable Intelligent Surface (RIS) is a revolutionizing approach to provide cost-effective yet energy-efficient communications. The transmit beamforming of the base station (BS) and discrete phase shifts of the RIS are jointly optimized to provide high quality of service. However, existing works ignore the high dependence between the large number of phase shifts and estimate them separately, consequently, easily getting trapped into local optima. To investigate the number and distribution of local optima, we conduct a fitness landscape analysis on the sum rate maximization problems. Two landscape features, the fitness distribution correlation and autocorrelation, are employed to investigate the ruggedness of landscape. The investigation results indicate that the landscape exhibits a rugged, multi-modal structure, i.e., has many local peaks, particularly in the cases with large-scale RISs. To handle the multi-modal landscape structure, we propose a novel niching genetic algorithm to solve the sum rate maximization problem. Particularly, a niching technique, nearest-better clustering, is incorporated to partition the population into several neighborhood species, thereby locating multiple local optima and enhance the global search ability. We also present a minimum species size to further improve the convergence speed. Simulation results demonstrate that our method achieves significant capacity gains compared to existing algorithms, particularly in the cases with large-scale RISs.

Bai Yan, Qi Zhao, Jin Zhang et al.

The source number identification is an essential step in direction-of-arrival (DOA) estimation. Existing methods may provide a wrong source number due to inferior statistical properties (in low SNR or limited snapshots) or modeling errors (caused by relaxing sparse penalties), especially in impulsive noise. To address this issue, we propose a novel idea of simultaneous source number identification and DOA estimation. We formulate a multiobjective off-grid DOA estimation model to realize this idea, by which the source number can be automatically identified together with DOA estimation. In particular, the source number is properly exploited by the $l_0$ norm of impinging signals without relaxations, guaranteeing accuracy. Furthermore, we design a multiobjective bilevel evolutionary algorithm to solve the proposed model. The source number identification and sparse recovery are simultaneously optimized at the on-grid (lower) level. A forward search strategy is developed to further refine the grid at the off-grid (upper) level. This strategy does not need linear approximations and can eliminate the off-grid gap with low computational complexity. Simulation results demonstrate the outperformance of our method in terms of source number and root mean square error.

Heather Jones, Siri Maley, Mohammadreza Mousaei et al.

Miles of contaminated pipe must be measured, foot by foot, as part of the decommissioning effort at deactivated gaseous diffusion enrichment facilities. The current method requires cutting away asbestos-lined thermal enclosures and performing repeated, elevated operations to manually measure pipe from the outside. The RadPiper robot, part of the Pipe Crawling Activity Measurement System (PCAMS) developed by Carnegie Mellon University and commissioned for use at the DOE Portsmouth Gaseous Diffusion Enrichment Facility, automatically measures U-235 in pipes from the inside. This improves certainty, increases safety, and greatly reduces measurement time. The heart of the RadPiper robot is a sodium iodide scintillation detector in an innovative disc-collimated assembly. By measuring from inside pipes, the robot significantly increases its count rate relative to external through-pipe measurements. The robot also provides imagery, models interior pipe geometry, and precisely measures distance in order to localize radiation measurements. Data collected by this system provides insight into pipe interiors that is simply not possible from exterior measurements, all while keeping operators safer. This paper describes the technical details of the PCAMS RadPiper robot. Key features for this robot include precision distance measurement, in-pipe obstacle detection, ability to transform for two pipe sizes, and robustness in autonomous operation. Test results demonstrating the robot's functionality are presented, including deployment tolerance tests, safeguarding tests, and localization tests. Integrated robot tests are also shown.

Tianbing Xu, Andrew Zhang, Liang Zhao

There are two halves to RL systems: experience collection time and policy learning time. For a large number of samples in rollouts, experience collection time is the major bottleneck. Thus, it is necessary to speed up the rollout generation time with multi-process architecture support. Our work, dubbed WALL-E, utilizes multiple rollout samplers running in parallel to rapidly generate experience. Due to our parallel samplers, we experience not only faster convergence times, but also higher average reward thresholds. For example, on the MuJoCo HalfCheetah-v2 task, with $N = 10$ parallel sampler processes, we are able to achieve much higher average return than those from using only a single process architecture.