arXiv subjects

Zongbo Han

Publications and source records attributed to Zongbo Han.

At least 19 recordsLinked to original sources

arXiv2026

FAR-DPO: Feasibility-Aware and Robust Direct Preference Optimization for Cyclic Peptide Design

Cyclic peptides are emerging as promising molecular scaffolds in drug discovery due to their high binding affinity and structural stability. However, extending generative models from linear to cyclic peptide design remains challenging, as cyclization sharply restricts the feasible design space through coupled geometric and biophysical constraints. Moreover, limited training data has led existing approaches to rely largely on zero-shot generation or post hoc filtering, resulting in low yields of feasible designs and limited control over multi-objective trade-offs. To address these limitations, we propose FAR-DPO (Feasibility-Aware and Robust Direct Preference Optimization), an architecture-agnostic framework that steers generative models toward structurally and biophysically feasible cyclic peptide designs, particularly for challenging targets. FAR-DPO integrates feasibility-aware preference construction with difficulty-aware group-robust optimization. Specifically, it constructs within-target preference pairs through feasibility-gated multi-objective dominance and adaptively reweights predefined difficulty groups according to their current preference losses. On the CPSea LNR benchmark, under a fixed generation budget, FAR-DPO increases overall success rate from 46.89% to 57.79% on PepGLAD and from 47.96% to 49.57% on PepFlow. These gains also extend to the hardest target quartile and are accompanied by more favorable best-per-target binding scores. Together, these results demonstrate FAR-DPO's effectiveness in improving feasibility and target-wise robustness.

cs.LG↗

arXiv2026

Towards World Models in Biomedical Research

A central goal of biomedicine is to understand, predict and ultimately control the dynamic mechanisms by which biological systems respond to perturbations, disease progression and therapeutic intervention. Although foundation models and large language models have accelerated biomedical data interpretation, most current systems remain focused on static pattern recognition rather than prospective simulation of biological futures. Here we propose biomedical world models as a paradigm for AI-driven discovery. These models learn latent representations of molecular, cellular, tissue and clinical states, together with intervention-conditioned dynamics that allow future trajectories to be simulated before actions are taken. We discuss how biomedical world models could function as data engines, environment simulators and scientific planning substrates across applications including virtual cells, organoids, virtual patients and surgical simulation. We outline the data infrastructure, evaluation benchmarks, safety constraints and governance frameworks required. Biomedical world models may provide a foundation for simulation-guided, closed-loop and experimentally actionable biomedical discovery.

cs.AI↗

arXiv2025

MULTIBENCH++: A Unified and Comprehensive Multimodal Fusion Benchmarking Across Specialized Domains

Although multimodal fusion has made significant progress, its advancement is severely hindered by the lack of adequate evaluation benchmarks. Current fusion methods are typically evaluated on a small selection of public datasets, a limited scope that inadequately represents the complexity and diversity of real-world scenarios, potentially leading to biased evaluations. This issue presents a twofold challenge. On one hand, models may overfit to the biases of specific datasets, hindering their generalization to broader practical applications. On the other hand, the absence of a unified evaluation standard makes fair and objective comparisons between different fusion methods difficult. Consequently, a truly universal and high-performance fusion model has yet to emerge. To address these challenges, we have developed a large-scale, domain-adaptive benchmark for multimodal evaluation. This benchmark integrates over 30 datasets, encompassing 15 modalities and 20 predictive tasks across key application domains. To complement this, we have also developed an open-source, unified, and automated evaluation pipeline that includes standardized implementations of state-of-the-art models and diverse fusion paradigms. Leveraging this platform, we have conducted large-scale experiments, successfully establishing new performance baselines across multiple tasks. This work provides the academic community with a crucial platform for rigorous and reproducible assessment of multimodal models, aiming to propel the field of multimodal artificial intelligence to new heights.

cs.LG↗

arXiv2025

Retrieval-Augmented Prompt for OOD Detection

Out-of-Distribution (OOD) detection is crucial for the reliable deployment of machine learning models in-the-wild, enabling accurate identification of test samples that differ from the training data distribution. Existing methods rely on auxiliary outlier samples or in-distribution (ID) data to generate outlier information for training, but due to limited outliers and their mismatch with real test OOD samples, they often fail to provide sufficient semantic supervision, leading to suboptimal performance. To address this, we propose a novel OOD detection method called Retrieval-Augmented Prompt (RAP). RAP augments a pre-trained vision-language model's prompts by retrieving external knowledge, offering enhanced semantic supervision for OOD detection. During training, RAP retrieves descriptive words for outliers based on joint similarity with external textual knowledge and uses them to augment the model's OOD prompts. During testing, RAP dynamically updates OOD prompts in real-time based on the encountered OOD samples, enabling the model to rapidly adapt to the test environment. Our extensive experiments demonstrate that RAP achieves state-of-the-art performance on large-scale OOD detection benchmarks. For example, in 1-shot OOD detection on the ImageNet-1k dataset, RAP reduces the average FPR95 by 7.05% and improves the AUROC by 1.71% compared to previous methods. Additionally, comprehensive ablation studies validate the effectiveness of each module and the underlying motivations of our approach.

cs.CV↗

arXiv2025

Helping CLIP See Both the Forest and the Trees: A Decomposition and Description Approach

Vision-Language Models (VLMs) like CLIP achieve cross-modal semantic alignment through contrastive learning, exhibiting robust zero-shot generalization. Traditional prompt engineering, however, predominantly relies on coarse-grained category labels, neglecting fine-grained local semantics. Existing approaches assume that VLMs inherently recognize localized visual details and attempt to enhance classification by augmenting text prompts with attribute descriptors generated by large language models. However, our systematic experiments reveal critical limitations: CLIP's strong bias toward global image patterns hinders its ability to process localized visual descriptors. To address this fundamental constraint, we propose a simple, effective, and plug-and-play solution that enables CLIP to ``See Both the Forest and the Trees." Specifically, we employ stochastic multi-crop augmentation to activate CLIP's latent capacity for localized feature analysis. By cropping only partial regions, the approach effectively constrains the model's receptive field and recalibrates its attention mechanism, thereby mitigating its inherent bias. We evaluate the proposed method under zero-shot, few-shot, and test-time adaptation settings, and extensive experiments demonstrate that D&D achieves promising performance.

cs.CV↗

arXiv2025

MedSG-Bench: A Benchmark for Medical Image Sequences Grounding

Visual grounding is essential for precise perception and reasoning in multimodal large language models (MLLMs), especially in medical imaging domains. While existing medical visual grounding benchmarks primarily focus on single-image scenarios, real-world clinical applications often involve sequential images, where accurate lesion localization across different modalities and temporal tracking of disease progression (e.g., pre- vs. post-treatment comparison) require fine-grained cross-image semantic alignment and context-aware reasoning. To remedy the underrepresentation of image sequences in existing medical visual grounding benchmarks, we propose MedSG-Bench, the first benchmark tailored for Medical Image Sequences Grounding. It comprises eight VQA-style tasks, formulated into two paradigms of the grounding tasks, including 1) Image Difference Grounding, which focuses on detecting change regions across images, and 2) Image Consistency Grounding, which emphasizes detection of consistent or shared semantics across sequential images. MedSG-Bench covers 76 public datasets, 10 medical imaging modalities, and a wide spectrum of anatomical structures and diseases, totaling 9,630 question-answer pairs. We benchmark both general-purpose MLLMs (e.g., Qwen2.5-VL) and medical-domain specialized MLLMs (e.g., HuatuoGPT-vision), observing that even the advanced models exhibit substantial limitations in medical sequential grounding tasks. To advance this field, we construct MedSG-188K, a large-scale instruction-tuning dataset tailored for sequential visual grounding, and further develop MedSeq-Grounder, an MLLM designed to facilitate future research on fine-grained understanding across medical sequential images. The benchmark, dataset, and model are available at https://huggingface.co/MedSG-Bench

cs.CV↗

arXiv2025

Computational Reasoning of Large Language Models

With the rapid development and widespread application of Large Language Models (LLMs), multidimensional evaluation has become increasingly critical. However, current evaluations are often domain-specific and overly complex, limiting their effectiveness as cross-domain proxies for core capabilities. To address these limitations and enable a unified and simple evaluation framework, an ideal proxy task should target a basic capability that generalizes across tasks and is independent of domain-specific knowledge. Turing machine provides a powerful theoretical lens by reducing complex processes to basic, domain-agnostic computational operations. This perspective offers a principled framework for evaluating basic computational abilities essential to a wide range of tasks. Motivated by this abstraction, we introduce \textbf{Turing Machine Bench}, a benchmark designed to assess the ability of LLMs to \textbf{strictly follow rules} and \textbf{accurately manage internal states} for multi-step, referred to as \textbf{computational reasoning}. TMBench incorporates four key features: self-contained and knowledge-agnostic reasoning, a minimalistic multi-step structure, controllable difficulty, and a solid theoretical foundation based on Turing machine. Empirical results demonstrate that TMBench serves as an effective proxy for evaluating computational reasoning on representative LLMs. It produces clear step-wise accuracy curves, revealing LLMs' ability to execute multi-step reasoning processes. By analyzing performance trends across TMBench and established reasoning benchmarks, we find strong correlations with real-world tasks, bridging real-task evaluation with basic ability assessment. These findings suggest that TMBench holds potential as a cross-domain dimension for evaluating reasoning in LLMs. Code and data are available at \href{https://github.com/HaitaoWuTJU/Turing-Machine-Bench}{Repo}.

cs.CL↗

arXiv2024

Out-Of-Distribution Detection with Diversification (Provably)

Out-of-distribution (OOD) detection is crucial for ensuring reliable deployment of machine learning models. Recent advancements focus on utilizing easily accessible auxiliary outliers (e.g., data from the web or other datasets) in training. However, we experimentally reveal that these methods still struggle to generalize their detection capabilities to unknown OOD data, due to the limited diversity of the auxiliary outliers collected. Therefore, we thoroughly examine this problem from the generalization perspective and demonstrate that a more diverse set of auxiliary outliers is essential for enhancing the detection capabilities. However, in practice, it is difficult and costly to collect sufficiently diverse auxiliary outlier data. Therefore, we propose a simple yet practical approach with a theoretical guarantee, termed Diversity-induced Mixup for OOD detection (diverseMix), which enhances the diversity of auxiliary outlier set for training in an efficient way. Extensive experiments show that diverseMix achieves superior performance on commonly used and recent challenging large-scale benchmarks, which further confirm the importance of the diversity of auxiliary outliers.

cs.LG↗

arXiv2024

DOTA: Distributional Test-Time Adaptation of Vision-Language Models

Vision-language foundation models (VLMs), such as CLIP, exhibit remarkable performance across a wide range of tasks. However, deploying these models can be unreliable when significant distribution gaps exist between training and test data, while fine-tuning for diverse scenarios is often costly. Cache-based test-time adapters offer an efficient alternative by storing representative test samples to guide subsequent classifications. Yet, these methods typically employ naive cache management with limited capacity, leading to severe catastrophic forgetting when samples are inevitably dropped during updates. In this paper, we propose DOTA (DistributiOnal Test-time Adaptation), a simple yet effective method addressing this limitation. Crucially, instead of merely memorizing individual test samples, DOTA continuously estimates the underlying distribution of the test data stream. Test-time posterior probabilities are then computed using these dynamically estimated distributions via Bayes' theorem for adaptation. This distribution-centric approach enables the model to continually learn and adapt to the deployment environment. Extensive experiments validate that DOTA significantly mitigates forgetting and achieves state-of-the-art performance compared to existing methods.

cs.LG↗

arXiv2024

Confidence-aware multi-modality learning for eye disease screening

Multi-modal ophthalmic image classification plays a key role in diagnosing eye diseases, as it integrates information from different sources to complement their respective performances. However, recent improvements have mainly focused on accuracy, often neglecting the importance of confidence and robustness in predictions for diverse modalities. In this study, we propose a novel multi-modality evidential fusion pipeline for eye disease screening. It provides a measure of confidence for each modality and elegantly integrates the multi-modality information using a multi-distribution fusion perspective. Specifically, our method first utilizes normal inverse gamma prior distributions over pre-trained models to learn both aleatoric and epistemic uncertainty for uni-modality. Then, the normal inverse gamma distribution is analyzed as the Student's t distribution. Furthermore, within a confidence-aware fusion framework, we propose a mixture of Student's t distributions to effectively integrate different modalities, imparting the model with heavy-tailed properties and enhancing its robustness and reliability. More importantly, the confidence-aware multi-modality ranking regularization term induces the model to more reasonably rank the noisy single-modal and fused-modal confidence, leading to improved reliability and accuracy. Experimental results on both public and internal datasets demonstrate that our model excels in robustness, particularly in challenging scenarios involving Gaussian noise and modality missing conditions. Moreover, our model exhibits strong generalization capabilities to out-of-distribution data, underscoring its potential as a promising solution for multimodal eye disease screening.

eess.IV↗

arXiv2024

Skip \n: A Simple Method to Reduce Hallucination in Large Vision-Language Models

Recent advancements in large vision-language models (LVLMs) have demonstrated impressive capability in visual information understanding with human language. Despite these advances, LVLMs still face challenges with multimodal hallucination, such as generating text descriptions of objects that are not present in the visual information. However, the underlying fundamental reasons of multimodal hallucinations remain poorly explored. In this paper, we propose a new perspective, suggesting that the inherent biases in LVLMs might be a key factor in hallucinations. Specifically, we systematically identify a semantic shift bias related to paragraph breaks (\n\n), where the content before and after '\n\n' in the training data frequently exhibit significant semantic changes. This pattern leads the model to infer that the contents following '\n\n' should be obviously different from the preceding contents with less hallucinatory descriptions, thereby increasing the probability of hallucinatory descriptions subsequent to the '\n\n'. We have validated this hypothesis on multiple publicly available LVLMs. Besides, we find that deliberately inserting '\n\n' at the generated description can induce more hallucinations. A simple method is proposed to effectively mitigate the hallucination of LVLMs by skipping the output of '\n'.

cs.CV↗

arXiv2024

Hallucination of Multimodal Large Language Models: A Survey

This survey presents a comprehensive analysis of the phenomenon of hallucination in multimodal large language models (MLLMs), also known as Large Vision-Language Models (LVLMs), which have demonstrated significant advancements and remarkable abilities in multimodal tasks. Despite these promising developments, MLLMs often generate outputs that are inconsistent with the visual content, a challenge known as hallucination, which poses substantial obstacles to their practical deployment and raises concerns regarding their reliability in real-world applications. This problem has attracted increasing attention, prompting efforts to detect and mitigate such inaccuracies. We review recent advances in identifying, evaluating, and mitigating these hallucinations, offering a detailed overview of the underlying causes, evaluation benchmarks, metrics, and strategies developed to address this issue. Additionally, we analyze the current challenges and limitations, formulating open questions that delineate potential pathways for future research. By drawing the granular classification and landscapes of hallucination causes, evaluation benchmarks, and mitigation methods, this survey aims to deepen the understanding of hallucinations in MLLMs and inspire further advancements in the field. Through our thorough and in-depth review, we contribute to the ongoing dialogue on enhancing the robustness and reliability of MLLMs, providing valuable insights and resources for researchers and practitioners alike. Resources are available at: https://github.com/showlab/Awesome-MLLM-Hallucination.

cs.CV↗

arXiv2024

Multimodal Fusion on Low-quality Data: A Comprehensive Survey

Multimodal fusion focuses on integrating information from multiple modalities with the goal of more accurate prediction, which has achieved remarkable progress in a wide range of scenarios, including autonomous driving and medical diagnosis. However, the reliability of multimodal fusion remains largely unexplored especially under low-quality data settings. This paper surveys the common challenges and recent advances of multimodal fusion in the wild and presents them in a comprehensive taxonomy. From a data-centric view, we identify four main challenges that are faced by multimodal fusion on low-quality data, namely (1) noisy multimodal data that are contaminated with heterogeneous noises, (2) incomplete multimodal data that some modalities are missing, (3) imbalanced multimodal data that the qualities or properties of different modalities are significantly different and (4) quality-varying multimodal data that the quality of each modality dynamically changes with respect to different samples. This new taxonomy will enable researchers to understand the state of the field and identify several potential directions. We also provide discussion for the open problems in this field together with interesting future research directions.

cs.LG↗

arXiv2024

ID-like Prompt Learning for Few-Shot Out-of-Distribution Detection

Out-of-distribution (OOD) detection methods often exploit auxiliary outliers to train model identifying OOD samples, especially discovering challenging outliers from auxiliary outliers dataset to improve OOD detection. However, they may still face limitations in effectively distinguishing between the most challenging OOD samples that are much like in-distribution (ID) data, i.e., \idlike samples. To this end, we propose a novel OOD detection framework that discovers \idlike outliers using CLIP \cite{DBLP:conf/icml/RadfordKHRGASAM21} from the vicinity space of the ID samples, thus helping to identify these most challenging OOD samples. Then a prompt learning framework is proposed that utilizes the identified \idlike outliers to further leverage the capabilities of CLIP for OOD detection. Benefiting from the powerful CLIP, we only need a small number of ID samples to learn the prompts of the model without exposing other auxiliary outlier datasets. By focusing on the most challenging \idlike OOD samples and elegantly exploiting the capabilities of CLIP, our method achieves superior few-shot learning performance on various real-world image datasets (e.g., in 4-shot OOD detection on the ImageNet-1k dataset, our method reduces the average FPR95 by 12.16\% and improves the average AUROC by 2.76\%, compared to state-of-the-art methods). Code is available at https://github.com/ycfate/ID-like.

cs.CV↗

arXiv2024

Selective Learning: Towards Robust Calibration with Dynamic Regularization

Miscalibration in deep learning refers to there is a discrepancy between the predicted confidence and performance. This problem usually arises due to the overfitting problem, which is characterized by learning everything presented in the training set, resulting in overconfident predictions during testing. Existing methods typically address overfitting and mitigate the miscalibration by adding a maximum-entropy regularizer to the objective function. The objective can be understood as seeking a model that fits the ground-truth labels by increasing the confidence while also maximizing the entropy of predicted probabilities by decreasing the confidence. However, previous methods lack clear guidance on confidence adjustment, leading to conflicting objectives (increasing but also decreasing confidence). Therefore, we introduce a method called Dynamic Regularization (DReg), which aims to learn what should be learned during training thereby circumventing the confidence adjusting trade-off. At a high level, DReg aims to obtain a more reliable model capable of acknowledging what it knows and does not know. Specifically, DReg effectively fits the labels for in-distribution samples (samples that should be learned) while applying regularization dynamically to samples beyond model capabilities (e.g., outliers), thereby obtaining a robust calibrated model especially on the samples beyond model capabilities. Both theoretical and empirical analyses sufficiently demonstrate the superiority of DReg compared with previous methods.

cs.LG↗

arXiv2023

Semantic Equivariant Mixup

Mixup is a well-established data augmentation technique, which can extend the training distribution and regularize the neural networks by creating ''mixed'' samples based on the label-equivariance assumption, i.e., a proportional mixup of the input data results in the corresponding labels being mixed in the same proportion. However, previous mixup variants may fail to exploit the label-independent information in mixed samples during training, which usually contains richer semantic information. To further release the power of mixup, we first improve the previous label-equivariance assumption by the semantic-equivariance assumption, which states that the proportional mixup of the input data should lead to the corresponding representation being mixed in the same proportion. Then a generic mixup regularization at the representation level is proposed, which can further regularize the model with the semantic information in mixed samples. At a high level, the proposed semantic equivariant mixup (sem) encourages the structure of the input data to be preserved in the representation space, i.e., the change of input will result in the obtained representation information changing in the same way. Different from previous mixup variants, which tend to over-focus on the label-related information, the proposed method aims to preserve richer semantic information in the input with semantic-equivariance assumption, thereby improving the robustness of the model against distribution shifts. We conduct extensive empirical studies and qualitative analyzes to demonstrate the effectiveness of our proposed method. The code of the manuscript is in the supplement.

cs.CV↗

arXiv2023

Exploring and Exploiting Uncertainty for Incomplete Multi-View Classification

Classifying incomplete multi-view data is inevitable since arbitrary view missing widely exists in real-world applications. Although great progress has been achieved, existing incomplete multi-view methods are still difficult to obtain a trustworthy prediction due to the relatively high uncertainty nature of missing views. First, the missing view is of high uncertainty, and thus it is not reasonable to provide a single deterministic imputation. Second, the quality of the imputed data itself is of high uncertainty. To explore and exploit the uncertainty, we propose an Uncertainty-induced Incomplete Multi-View Data Classification (UIMC) model to classify the incomplete multi-view data under a stable and reliable framework. We construct a distribution and sample multiple times to characterize the uncertainty of missing views, and adaptively utilize them according to the sampling quality. Accordingly, the proposed method realizes more perceivable imputation and controllable fusion. Specifically, we model each missing data with a distribution conditioning on the available views and thus introducing uncertainty. Then an evidence-based fusion strategy is employed to guarantee the trustworthy integration of the imputed views. Extensive experiments are conducted on multiple benchmark data sets and our method establishes a state-of-the-art performance in terms of both performance and trustworthiness.

cs.LG↗

arXiv2023

Reweighted Mixup for Subpopulation Shift

Subpopulation shift exists widely in many real-world applications, which refers to the training and test distributions that contain the same subpopulation groups but with different subpopulation proportions. Ignoring subpopulation shifts may lead to significant performance degradation and fairness concerns. Importance reweighting is a classical and effective way to handle the subpopulation shift. However, recent studies have recognized that most of these approaches fail to improve the performance especially when applied to over-parameterized neural networks which are capable of fitting any training samples. In this work, we propose a simple yet practical framework, called reweighted mixup (RMIX), to mitigate the overfitting issue in over-parameterized models by conducting importance weighting on the ''mixed'' samples. Benefiting from leveraging reweighting in mixup, RMIX allows the model to explore the vicinal space of minority samples more, thereby obtaining more robust model against subpopulation shift. When the subpopulation memberships are unknown, the training-trajectories-based uncertainty estimation is equipped in the proposed RMIX to flexibly characterize the subpopulation distribution. We also provide insightful theoretical analysis to verify that RMIX achieves better generalization bounds over prior works. Further, we conduct extensive empirical studies across a wide range of tasks to validate the effectiveness of the proposed method.

cs.LG↗