Beidi Zhao

Gexin Huang, Yanting Yang, Myeongkyun Kang et al.

Vision-language models (VLMs) excel on visual question answering and multimodal reasoning benchmarks. Yet their capability on ultra-resolution images - where critical evidence is tiny, subtle, spatially distant, or distributed - remains unclear. Existing evaluations largely report final-answer accuracy, offering limited insight into whether models acquire and integrate the necessary visual evidence. We introduce UltraVR, a diagnostic benchmark for evidence-grounded visual reasoning over ultra-resolution images. UltraVR spans four high-value scenarios: CCTV surveillance, remote sensing (RS), whole-slide image (WSI) pathology, and industrial anomaly detection (AD). These domains pose complementary challenges: fine-grained object grounding in crowded CCTV scenes, long-range spatial comparison in RS, multi-scale evidence navigation in WSI, and subtle irregularity detection in repetitive industrial layouts. Beyond standard QA triples, each instance includes a structured ground-truth chain of thought with step-level questions, intermediate answers, and reasoning labels. These labels decompose reasoning into evidence grounding, local perception, quantification, evidence integration, and decision inference, enabling process-level diagnosis over black-box scoring. Using UltraVR, we evaluate frontier VLMs and show that current models remain far from reliable on ultra-resolution reasoning. Importantly, the structured annotations allow us to localize failures across the visual-to-decision pipeline: errors concentrate in evidence grounding and local perception, while downstream inference often recovers when intermediate visual facts are supplied. These findings demonstrate UltraVR as a diagnostic testbed for measuring not only whether VLMs answer correctly, but where their ultra-resolution reasoning process breaks.

Beidi Zhao, Boxin Du, Zhe Xu et al.

Graph Neural Networks (GNNs) have achieved tremendous success in a variety of real-world applications by relying on the fixed graph data as input. However, the initial input graph might not be optimal in terms of specific downstream tasks, because of information scarcity, noise, adversarial attacks, or discrepancies between the distribution in graph topology, features, and groundtruth labels. In this paper, we propose a bi-level optimization approach for learning the optimal graph structure via directly learning the Personalized PageRank propagation matrix as well as the downstream semi-supervised node classification simultaneously. We also explore a low-rank approximation model for further reducing the time complexity. Empirical evaluations show the superior efficacy and robustness of the proposed model over all baseline methods.

Beidi Zhao, Wenlong Deng, Xinting Liao et al.

While Retrieval-Augmented Generation (RAG) is one of the dominant paradigms for enhancing Large Vision-Language Models (LVLMs) on knowledge-based VQA tasks, recent work attributes RAG failures to insufficient attention towards the retrieved context, proposing to reduce the attention allocated to image tokens. In this work, we identify a distinct failure mode that previous study overlooked: Attention Distraction (AD). When the retrieved context is sufficient (highly relevant or including the correct answer), the retrieved text suppresses the visual attention globally, and the attention on image tokens shifts away from question-relevant regions. This leads to failures on questions the model could originally answer correctly without the retrieved text. To mitigate this issue, we propose MAD-RAG, a training-free intervention that decouples visual grounding from context integration through a dual-question formulation, combined with attention mixing to preserve image-conditioned evidence. Extensive experiments on OK-VQA, E-VQA, and InfoSeek demonstrate that MAD-RAG consistently outperforms existing baselines across different model families, yielding absolute gains of up to 4.76%, 9.20%, and 6.18% over the vanilla RAG baseline. Notably, MAD-RAG rectifies up to 74.68% of failure cases with negligible computational overhead.

Ruinan Jin, Beidi Zhao, Myeongkyun Kang et al.

Self-verification, re-invoking the same vision language model (VLM) in a fresh context to check its own generated answer, is increasingly used as a default safety layer for medical visual question answering (VQA). We argue that this practice is fundamentally unreliable. We introduce [METHOD NAME], a diagnostic framework for mapping the reliability boundary of medical VLM self-verification by decomposing verifier behavior into discrimination capability and agreement bias. Because the verifier and answer generator are capacity-coupled, the verifier can overly agree with the generator, creating a verification mirage: a regime with both high verifier error and high agreement bias, driven by false acceptance of incorrect answers. Evaluating six open-weight VLMs across five medical VQA datasets and seven medical tasks, we find that this boundary is strongly task-conditioned. Knowledge-intensive clinical tasks fall deepest into the mirage, simpler tasks are more resistant, and perceptual tasks lie in between. Verification also fails to provide an independent safety signal: logistic mixed-effects analysis shows that verifier error and agreement bias become more likely when the generator is wrong, while saliency analyses show that verifiers under-attend to image evidence relative to generators, a phenomenon we call the lazy verifier. Cross-verification reduces but does not eliminate the mirage. Moreover, when verification is reused in multi-turn actor-verifier loops, most initially wrong answers become locked in by false verification. Since our experiments use clean benchmarks, the observed reliability boundary likely underestimates failures in real clinical deployment.

Beidi Zhao, Wenlong Deng, Zi Han et al.

In computational pathology, multiple instance learning (MIL) is widely used to circumvent the computational impasse in giga-pixel whole slide image (WSI) analysis. It usually consists of two stages: patch-level feature extraction and slide-level aggregation. Recently, pretrained models or self-supervised learning have been used to extract patch features, but they suffer from low effectiveness or inefficiency due to overlooking the task-specific supervision provided by slide labels. Here we propose a weakly-supervised Label-Efficient WSI Screening method, dubbed LESS, for cytological WSI analysis with only slide-level labels, which can be effectively applied to small datasets. First, we suggest using variational positive-unlabeled (VPU) learning to uncover hidden labels of both benign and malignant patches. We provide appropriate supervision by using slide-level labels to improve the learning of patch-level features. Next, we take into account the sparse and random arrangement of cells in cytological WSIs. To address this, we propose a strategy to crop patches at multiple scales and utilize a cross-attention vision transformer (CrossViT) to combine information from different scales for WSI classification. The combination of our two steps achieves task-alignment, improving effectiveness and efficiency. We validate the proposed label-efficient method on a urine cytology WSI dataset encompassing 130 samples (13,000 patches) and FNAC 2019 dataset with 212 samples (21,200 patches). The experiment shows that the proposed LESS reaches 84.79%, 85.43%, 91.79% and 78.30% on a urine cytology WSI dataset, and 96.88%, 96.86%, 98.95%, 97.06% on FNAC 2019 dataset in terms of accuracy, AUC, sensitivity and specificity. It outperforms state-of-the-art MIL methods on pathology WSIs and realizes automatic cytological WSI cancer screening.

Beidi Zhao, SangMook Kim, Hao Chen et al.

Multiple Instance Learning (MIL) has advanced WSI analysis but struggles with the complexity and heterogeneity of WSIs. Existing MIL methods face challenges in aggregating diverse patch information into robust WSI representations. While ViTs and clustering-based approaches show promise, they are computationally intensive and fail to capture task-specific and slide-specific variability. To address these limitations, we propose PTCMIL, a novel Prompt Token Clustering-based ViT for MIL aggregation. By introducing learnable prompt tokens into the ViT backbone, PTCMIL unifies clustering and prediction tasks in an end-to-end manner. It dynamically aligns clustering with downstream tasks, using projection-based clustering tailored to each WSI, reducing complexity while preserving patch heterogeneity. Through token merging and prototype-based pooling, PTCMIL efficiently captures task-relevant patterns. Extensive experiments on eight datasets demonstrate its superior performance in classification and survival analysis tasks, outperforming state-of-the-art methods. Systematic ablation studies confirm its robustness and strong interpretability. The code is released at https://github.com/ubc-tea/PTCMIL.

Yanting Yang, Beidi Zhao, Zhuohao Ni et al.

Neuroscientific research has revealed that the complex brain network can be organized into distinct functional communities, each characterized by a cohesive group of regions of interest (ROIs) with strong interconnections. These communities play a crucial role in comprehending the functional organization of the brain and its implications for neurological conditions, including Autism Spectrum Disorder (ASD) and biological differences, such as in gender. Traditional models have been constrained by the necessity of predefined community clusters, limiting their flexibility and adaptability in deciphering the brain's functional organization. Furthermore, these models were restricted by a fixed number of communities, hindering their ability to accurately represent the brain's dynamic nature. In this study, we present a token clustering brain transformer-based model ($\texttt{TC-BrainTF}$) for joint community clustering and classification. Our approach proposes a novel token clustering (TC) module based on the transformer architecture, which utilizes learnable prompt tokens with orthogonal loss where each ROI embedding is projected onto the prompt embedding space, effectively clustering ROIs into communities and reducing the dimensions of the node representation via merging with communities. Our results demonstrate that our learnable community-aware model $\texttt{TC-BrainTF}$ offers improved accuracy in identifying ASD and classifying genders through rigorous testing on ABIDE and HCP datasets. Additionally, the qualitative analysis on $\texttt{TC-BrainTF}$ has demonstrated the effectiveness of the designed TC module and its relevance to neuroscience interpretations.

Gexin Huang, Anqi Li, Yusheng Tan et al.

Pathology foundation models (FMs) have become central to computational histopathology, offering strong transfer performance across a wide range of diagnostic and prognostic tasks. The rapid proliferation of pathology foundation models creates a model-selection bottleneck: no single model is uniformly best, yet exhaustively adapting and validating many candidates for each downstream endpoint is prohibitively expensive. We address this challenge with a lightweight and novel model fusion strategy, LogitProd, which treats independently trained FM-based predictors as fixed experts and learns sample-adaptive fusion weights over their slide-level outputs. The fusion operates purely on logits, requiring no encoder retraining and no feature-space alignment across heterogeneous backbones. We further provide a theoretical analysis showing that the optimal weighted product fusion is guaranteed to perform at least as well as the best individual expert under the training objective. We systematically evaluate LogitProd on \textbf{22} benchmarks spanning WSI-level classification, tile-level classification, gene mutation prediction, and discrete-time survival modeling. LogitProd ranks first on 20/22 tasks and improves the average performance across all tasks by ~3% over the strongest single expert. LogitProd enables practitioners to upgrade heterogeneous FM-based pipelines in a plug-and-play manner, achieving multi-expert gains with $\sim$12$\times$ lower training cost than feature-fusion alternatives.

Wenlong Deng, Blair Chen, Beidi Zhao et al.

Mitigating biases in machine learning models has become an increasing concern in Natural Language Processing (NLP), particularly in developing fair text embeddings, which are crucial yet challenging for real-world applications like search engines. In response, this paper proposes a novel method for learning fair text embeddings. First, we define a novel content-conditional equal distance (CCED) fairness for text embeddings, ensuring content-conditional independence between sensitive attributes and text embeddings. Building on CCED, we introduce a content-conditional debiasing (CCD) loss to ensure that embeddings of texts with different sensitive attributes but identical content maintain the same distance from the embedding of their corresponding neutral text. Additionally, we tackle the issue of insufficient training data by using Large Language Models (LLMs) with instructions to fairly augment texts into different sensitive groups. Our extensive evaluations show that our approach effectively enhances fairness while maintaining the utility of embeddings. Furthermore, our augmented dataset, combined with the CCED metric, serves as an new benchmark for evaluating fairness.

Beidi Zhao, Shuai Li, Yanbo Gao et al.

Smartphone sensors based human activity recognition is attracting increasing interests nowadays with the popularization of smartphones. With the high sampling rates of smartphone sensors, it is a highly long-range temporal recognition problem, especially with the large intra-class distances such as the smartphones carried at different locations such as in the bag or on the body, and the small inter-class distances such as taking train or subway. To address this problem, we propose a new framework of combining short-term spatial/frequency feature extraction and a long-term Independently Recurrent Neural Network (IndRNN) for activity recognition. Considering the periodic characteristics of the sensor data, short-term temporal features are first extracted in the spatial and frequency domains. Then the IndRNN, which is able to capture long-term patterns, is used to further obtain the long-term features for classification. In view of the large differences when the smartphone is carried at different locations, a group based location recognition is first developed to pinpoint the location of the smartphone. The Sussex-Huawei Locomotion (SHL) dataset from the SHL Challenge is used for evaluation. An earlier version of the proposed method has won the second place award in the SHL Challenge 2020 (the first place if not considering multiple models fusion approach). The proposed method is further improved in this paper and achieves 80.72$\%$ accuracy, better than the existing methods using a single model.