Weihan Li

Ruizhi Wang, Weihan Li, Zunlei Feng et al.

Real-time, high-fidelity monocular depth estimation from remote sensing imagery is crucial for numerous applications, yet existing methods face a stark trade-off between accuracy and efficiency. Although using Vision Transformer (ViT) backbones for dense prediction is fast, they often exhibit poor perceptual quality. Conversely, diffusion models offer high fidelity but at a prohibitive computational cost. To overcome these limitations, we propose Depth Detail Diffusion for Remote Sensing Monocular Depth Estimation ($D^3$-RSMDE), an efficient framework designed to achieve an optimal balance between speed and quality. Our framework first leverages a ViT-based module to rapidly generate a high-quality preliminary depth map construction, which serves as a structural prior, effectively replacing the time-consuming initial structure generation stage of diffusion models. Based on this prior, we propose a Progressive Linear Blending Refinement (PLBR) strategy, which uses a lightweight U-Net to refine the details in only a few iterations. The entire refinement step operates efficiently in a compact latent space supported by a Variational Autoencoder (VAE). Extensive experiments demonstrate that $D^3$-RSMDE achieves a notable 11.85% reduction in the Learned Perceptual Image Patch Similarity (LPIPS) perceptual metric over leading models like Marigold, while also achieving over a 40x speedup in inference and maintaining VRAM usage comparable to lightweight ViT models.

Chengrui Li, Yule Wang, Weihan Li et al.

Maximizing the log-likelihood is a crucial aspect of learning latent variable models, and variational inference (VI) stands as the commonly adopted method. However, VI can encounter challenges in achieving a high log-likelihood when dealing with complicated posterior distributions. In response to this limitation, we introduce a novel variational importance sampling (VIS) approach that directly estimates and maximizes the log-likelihood. VIS leverages the optimal proposal distribution, achieved by minimizing the forward $χ^2$ divergence, to enhance log-likelihood estimation. We apply VIS to various popular latent variable models, including mixture models, variational auto-encoders, and partially observable generalized linear models. Results demonstrate that our approach consistently outperforms state-of-the-art baselines, both in terms of log-likelihood and model parameter estimation.

Jingyang Ke, Weihan Li, Amartya Pradhan et al.

Understanding freely moving animal behavior is central to neuroscience, where pose estimation and behavioral understanding form the foundation for linking neural activity to natural actions. Yet both tasks still depend heavily on human annotation or unstable unsupervised pipelines, limiting scalability and reproducibility. We present BehaviorVLM, a unified vision-language framework for pose estimation and behavioral understanding that requires no task-specific finetuning and minimal human labeling by guiding pretrained Vision-Language Models (VLMs) through detailed, explicit, and verifiable reasoning steps. For pose estimation, we leverage quantum-dot-grounded behavioral data and propose a multi-stage pipeline that integrates temporal, spatial, and cross-view reasoning. This design greatly reduces human annotation effort, exposes low-confidence labels through geometric checks such as reprojection error, and produces labels that can later be filtered, corrected, or used to fine-tune downstream pose models. For behavioral understanding, we propose a pipeline that integrates deep embedded clustering for over-segmented behavior discovery, VLM-based per-clip video captioning, and LLM-based reasoning to merge and semantically label behavioral segments. The behavioral pipeline can operate directly from visual information and does not require keypoints to segment behavior. Together, these components enable scalable, interpretable, and label-light analysis of multi-animal behavior.

Yule Wang, Chengrui Li, Weihan Li et al.

Understanding the neural basis of behavior is a fundamental goal in neuroscience. Current research in large-scale neuro-behavioral data analysis often relies on decoding models, which quantify behavioral information in neural data but lack details on behavior encoding. This raises an intriguing scientific question: ``how can we enable in-depth exploration of neural representations in behavioral tasks, revealing interpretable neural dynamics associated with behaviors''. However, addressing this issue is challenging due to the varied behavioral encoding across different brain regions and mixed selectivity at the population level. To tackle this limitation, our approach, named ``BeNeDiff'', first identifies a fine-grained and disentangled neural subspace using a behavior-informed latent variable model. It then employs state-of-the-art generative diffusion models to synthesize behavior videos that interpret the neural dynamics of each latent factor. We validate the method on multi-session datasets containing widefield calcium imaging recordings across the dorsal cortex. Through guiding the diffusion model to activate individual latent factors, we verify that the neural dynamics of latent factors in the disentangled neural subspace provide interpretable quantifications of the behaviors of interest. At the same time, the neural subspace in BeNeDiff demonstrates high disentanglement and neural reconstruction quality.

Weihan Li, Chengrui Li, Yule Wang et al.

Studying the complex interactions between different brain regions is crucial in neuroscience. Various statistical methods have explored the latent communication across multiple brain regions. Two main categories are the Gaussian Process (GP) and Linear Dynamical System (LDS), each with unique strengths. The GP-based approach effectively discovers latent variables with frequency bands and communication directions. Conversely, the LDS-based approach is computationally efficient but lacks powerful expressiveness in latent representation. In this study, we merge both methodologies by creating an LDS mirroring a multi-output GP, termed Multi-Region Markovian Gaussian Process (MRM-GP). Our work establishes a connection between an LDS and a multi-output GP that explicitly models frequencies and phase delays within the latent space of neural recordings. Consequently, the model achieves a linear inference cost over time points and provides an interpretable low-dimensional representation, revealing communication directions across brain regions and separating oscillatory communications into different frequency bands.

Chengrui Li, Yunmiao Wang, Yule Wang et al.

A fully disentangled variational auto-encoder (VAE) aims to identify disentangled latent components from observations. However, enforcing full independence between all latent components may be too strict for certain datasets. In some cases, multiple factors may be entangled together in a non-separable manner, or a single independent semantic meaning could be represented by multiple latent components within a higher-dimensional manifold. To address such scenarios with greater flexibility, we develop the Partially Disentangled VAE (PDisVAE), which generalizes the total correlation (TC) term in fully disentangled VAEs to a partial correlation (PC) term. This framework can handle group-wise independence and can naturally reduce to either the standard VAE or the fully disentangled VAE. Validation through three synthetic experiments demonstrates the correctness and practicality of PDisVAE. When applied to real-world datasets, PDisVAE discovers valuable information that is difficult to find using fully disentangled VAEs, implying its versatility and effectiveness.

Tianshi Zheng, Weihan Li, Jiaxin Bai et al.

Retrieval-Augmented Generation (RAG) systems show remarkable potential as question answering tools in the K-12 Education domain, where knowledge is typically queried within the restricted scope of authoritative textbooks. However, discrepancies between these textbooks and the parametric knowledge inherent in Large Language Models (LLMs) can undermine the effectiveness of RAG systems. To systematically investigate RAG system robustness against such knowledge discrepancies, we introduce KnowShiftQA. This novel question answering dataset simulates these discrepancies by applying deliberate hypothetical knowledge updates to both answers and source documents, reflecting how textbook knowledge can shift. KnowShiftQA comprises 3,005 questions across five subjects, designed with a comprehensive question typology focusing on context utilization and knowledge integration. Our extensive experiments on retrieval and question answering performance reveal that most RAG systems suffer a substantial performance drop when faced with these knowledge discrepancies. Furthermore, questions requiring the integration of contextual (textbook) knowledge with parametric (LLM) knowledge pose a significant challenge to current LLMs.

Chengrui Li, Weihan Li, Yule Wang et al.

The partially observable generalized linear model (POGLM) is a powerful tool for understanding neural connectivity under the assumption of existing hidden neurons. With spike trains only recorded from visible neurons, existing works use variational inference to learn POGLM meanwhile presenting the difficulty of learning this latent variable model. There are two main issues: (1) the sampled Poisson hidden spike count hinders the use of the pathwise gradient estimator in VI; and (2) the existing design of the variational model is neither expressive nor time-efficient, which further affects the performance. For (1), we propose a new differentiable POGLM, which enables the pathwise gradient estimator, better than the score function gradient estimator used in existing works. For (2), we propose the forward-backward message-passing sampling scheme for the variational model. Comprehensive experiments show that our differentiable POGLMs with our forward-backward message passing produce a better performance on one synthetic and two real-world datasets. Furthermore, our new method yields more interpretable parameters, underscoring its significance in neuroscience.

Chengrui Li, Yunmiao Wang, Yule Wang et al.

Low-rank recurrent neural networks (lrRNNs) are a class of models that uncover low-dimensional latent dynamics underlying neural population activity. Although their functional connectivity is low-rank, it lacks disentanglement interpretations, making it difficult to assign distinct computational roles to different latent dimensions. To address this, we propose the Disentangled Recurrent Neural Network (DisRNN), a generative lrRNN framework that assumes group-wise independence among latent dynamics while allowing flexible within-group entanglement. These independent latent groups allow latent dynamics to evolve separately, but are internally rich for complex computation. We reformulate the lrRNN under a variational autoencoder (VAE) framework, enabling us to introduce a partial correlation penalty that encourages disentanglement between groups of latent dimensions. Experiments on synthetic, monkey M1, and mouse voltage imaging data show that DisRNN consistently improves the disentanglement and interpretability of learned neural latent trajectories in low-dimensional space and low-rank connectivity over baseline lrRNNs that do not encourage partial disentanglement.

Yule Wang, Joseph Yu, Chengrui Li et al.

Understanding how neural populations in higher visual areas encode object-centered visual information remains a central challenge in computational neuroscience. Prior works have investigated representational alignment between artificial neural networks and the visual cortex. Nevertheless, these findings are indirect and offer limited insights to the structure of neural populations themselves. Similarly, decoding-based methods have quantified semantic features from neural populations but have not uncovered their underlying organizations. This leaves open a scientific question: "how feature-specific visual information is distributed across neural populations in higher visual areas, and whether it is organized into structured, semantically meaningful subspaces." To tackle this problem, we present MIG-Vis, a method that leverages the generative power of diffusion models to visualize and validate the visual-semantic attributes encoded in neural latent subspaces. Our method first uses a variational autoencoder to infer a group-wise disentangled neural latent subspace from neural populations. Subsequently, we propose a mutual information (MI)-guided diffusion synthesis procedure to visualize the specific visual-semantic features encoded by each latent group. We validate MIG-Vis on multi-session neural spiking datasets from the inferior temporal (IT) cortex of two macaques. The synthesized results demonstrate that our method identifies neural latent groups with clear semantic selectivity to diverse visual features, including object pose, inter-category transformations, and intra-class content. These findings provide direct, interpretable evidence of structured semantic representation in the higher visual cortex and advance our understanding of its encoding principles.

Amir Ali Panahi, Daniel Luder, Billy Wu et al.

Reliable digital twins of lithium-ion batteries must achieve high physical fidelity with sub-millisecond speed. In this work, we benchmark three operator-learning surrogates for the Single Particle Model (SPM): Deep Operator Networks (DeepONets), Fourier Neural Operators (FNOs) and a newly proposed parameter-embedded Fourier Neural Operator (PE-FNO), which conditions each spectral layer on particle radius and solid-phase diffusivity. Models are trained on simulated trajectories spanning four current families (constant, triangular, pulse-train, and Gaussian-random-field) and a full range of State-of-Charge (SOC) (0 % to 100 %). DeepONet accurately replicates constant-current behaviour but struggles with more dynamic loads. The basic FNO maintains mesh invariance and keeps concentration errors below 1 %, with voltage mean-absolute errors under 1.7 mV across all load types. Introducing parameter embedding marginally increases error, but enables generalisation to varying radii and diffusivities. PE-FNO executes approximately 200 times faster than a 16-thread SPM solver. Consequently, PE-FNO's capabilities in inverse tasks are explored in a parameter estimation task with Bayesian optimisation, recovering anode and cathode diffusivities with 1.14 % and 8.4 % mean absolute percentage error, respectively, and 0.5918 percentage points higher error in comparison with classical methods. These results pave the way for neural operators to meet the accuracy, speed and parametric flexibility demands of real-time battery management, design-of-experiments and large-scale inference. PE-FNO outperforms conventional neural surrogates, offering a practical path towards high-speed and high-fidelity electrochemical digital twins.

Shengxuming Zhang, Weihan Li, Tianhong Gao et al.

Pathological diagnosis is vital for determining disease characteristics, guiding treatment, and assessing prognosis, relying heavily on detailed, multi-scale analysis of high-resolution whole slide images (WSI). However, existing large vision-language models (LVLMs) are limited by input resolution constraints, hindering their efficiency and accuracy in pathology image analysis. To overcome these issues, we propose two innovative strategies: the mixed task-guided feature enhancement, which directs feature extraction toward lesion-related details across scales, and the prompt-guided detail feature completion, which integrates coarse- and fine-grained features from WSI based on specific prompts without compromising inference speed. Leveraging a comprehensive dataset of 490K samples from diverse pathology tasks, we trained the pathology-specialized LVLM, OmniPath. Extensive experiments demonstrate that this model significantly outperforms existing methods in diagnostic accuracy and efficiency, providing an interactive, clinically aligned approach for auxiliary diagnosis in a wide range of pathology applications.

Weihan Li, Yule Wang, Chengrui Li et al.

Understanding and constructing brain communications that capture dynamic communications across multiple regions is fundamental to modern system neuroscience, yet current methods struggle to find time-varying region-level communications or scale to large neural datasets with long recording durations. We present a novel framework using Markovian Gaussian Processes to learn brain communications with time-varying temporal delays from multi-region neural recordings, named Adaptive Delay Model (ADM). Our method combines Gaussian Processes with State Space Models and employs parallel scan inference algorithms, enabling efficient scaling to large datasets while identifying concurrent communication patterns that evolve over time. This time-varying approach captures how brain region interactions shift dynamically during cognitive processes. Validated on synthetic and multi-region neural recordings datasets, our approach discovers both the directionality and temporal dynamics of neural communication. This work advances our understanding of distributed neural computation and provides a scalable tool for analyzing dynamic brain networks.