arXiv subjects

Hongpeng Zhou

Publications and source records attributed to Hongpeng Zhou.

13 recordsLinked to original sources

arXiv2026

CellWorld: From Gene-Level Reconstruction to Latent Cell Prediction in Spatial Transcriptomics Foundation Models

This paper shows that latent-space predictive pretraining can provide a scalable route to foundation models for spatial transcriptomics. Existing spatial transcriptomics foundation models primarily reconstruct masked gene identities or expression values, potentially encouraging the reproduction of assay-specific technical variation and limiting representation transferability. To avoid directly reconstructing such variation, we shift the prediction target from observed gene measurements to latent cell representations and introduce CellWorld, which predicts the latent representations of masked cells from visible spatial context and a limited partial-expression hint. We pretrain four CellWorld variants, spanning 5.74M to 94.56M trainable parameters, on a corpus of 46 million human cells. Our controlled scaling experiments show that performance improves with model capacity, particularly on spatial tasks, while spatial transfer depends more on sufficient optimization and broad biological source diversity than on cell count alone. Across four held-out datasets, even CellWorld-Small, with 5.74M trainable parameters, outperforms every baseline on all 11 linear-probe benchmarks and all seven fine-tuned spatial benchmarks. Most notably, a frozen CellWorld-Large pretrained on only 5\% of the corpus with broad biological source coverage outperforms every fully fine-tuned baseline across all seven spatial benchmarks. Code is available at https://github.com/UoM-HealthAI/CellWorld.

cs.AI↗

arXiv2026

PMMC: Prospective Multimodal Memory Compilation for Long-Term LVLM Agents

Long-term memory is essential for LVLM agents to maintain consistency and integrate information across extended multimodal interactions. Existing agent memory systems, however, often reduce visual experiences into textual summaries or rely on static retrieve-then-reason pipelines, which are inefficient at query time and brittle when questions require image-text binding, temporal updates, or visual details. We propose Prospective Multimodal Memory Compilation, a framework that shifts part of the memory reasoning process from query time to memory consolidation time. Given accumulated multimodal interactions, a Questioner predicts future question candidates, a Planner compiles question-conditioned multimodal memory programs, and a Doubter verifies whether the planned evidence path can support the predicted answer. The verified question-program pairs form a structured question bank for efficient query-time routing and evidence retrieval. Experiments on multimodal long-term memory benchmarks show that our method improves answer quality and visual evidence recall while reducing query-time token and latency costs. Extensive ablations analyze the effects of self-feedback, dynamic planning, raw-image access, and question bank coverage.

cs.AI↗

arXiv2026

TrajWiki: Source-Grounded Memory Trajectories for Long-Horizon Dialogue Agents

Large language model agents have shown strong capabilities in generating coherent and contextually appropriate responses, yet robust long-horizon dialogue remains limited by the lack of external memory that is traceable, updatable, and diagnostically transparent. Existing memory-augmented agents often store memories as isolated records or overwritable states, making it difficult to preserve how information originates, evolves, conflicts, or becomes obsolete over time. We propose TrajWiki, a trajectory-based memory framework for long-horizon conversational agents. Instead of treating memory as static entries, TrajWiki represents each memory as a source-grounded evolution trajectory, maintained through immutable episodic snapshots and claim-level operations such as ADD, REVISE, and DEPRECATE. To reduce fragmentation and retrieval cost, TrajWiki further introduces Memory Wiki, a persistent intermediate layer that incrementally compiles dialogue history into structured and interlinked wiki pages capturing salient entities, events, quantities, topics, and conflicts. At inference time, queries are routed hierarchically from relevant wiki pages to linked memory trajectories, then to corresponding snapshots and source messages for evidence-grounded answer synthesis. Experiments on LoCoMo and MedMT show that TrajWiki improves long-horizon dialogue performance across both open-source and closed-source LLM backbones, while providing greater interpretability and diagnostic visibility into memory evolution, retrieval failures, and answer generation.

cs.AI↗

arXiv2026

Seeing What Is Actually There: PriVE-Bench and PriVE-Tools for Counterfactual Evaluation of Agentic Visual Evidence in VLMs

Vision-language models (VLMs) often answer visual questions using learned language and category priors rather than grounding their predictions in the image itself. Counterfactual images provide a natural diagnostic setting for this failure mode: when visible evidence contradicts what is usually true, a grounded model should answer from the pixels, while a prior-following model will produce a canonical but visually incorrect response. However, existing counterfactual benchmarks mainly ask whether such prior-following behavior exists. In this paper, we ask a further question motivated by the rise of tool-augmented and agentic vision systems: can additional visual evidence views help VLMs reason against their priors? We introduce PriVE-Bench, a Prior-vs-Visual Evidence Benchmark that uses paired original and counterfactual images to distinguish visually grounded answers from prior-consistent errors. We further introduce PriVE-Tools, a controlled agentic-vision-inspired extension that evaluates whether tool-derived visual evidence -- including bounding boxes, crops, zoom panels, and contours -- improves grounding under the same counterfactual conflicts. Across open- and closed-source VLMs, we compare raw, paired-image, and tool-conditioned inputs using accuracy, prior-following error rate, and other-response rate. Our results show that visual evidence tools can help in some settings, especially when models can use localized evidence effectively, but they are not a universal remedy: several models continue to follow language and category priors even when relevant visual evidence is explicitly provided.

cs.CV↗

arXiv2026

Computational Lesions in Multilingual Language Models Separate Shared and Language-specific Brain Alignment

How the brain supports language across different languages is a basic question in neuroscience and a useful test for multilingual artificial intelligence. Neuroimaging has identified language-responsive brain regions across languages, but it cannot by itself show whether the underlying processing is shared or language-specific. Here we use six multilingual large language models (LLMs) as controllable systems and create targeted ``computational lesions'' by zeroing small parameter sets that are important across languages or especially important for one language. We then compare intact and lesioned models in predicting functional magnetic resonance imaging (fMRI) responses during 100 minutes of naturalistic story listening in native English, Chinese and French (112 participants). Lesioning a compact shared core reduces whole-brain encoding correlation by 60.32% relative to intact models, whereas language-specific lesions preserve cross-language separation in embedding space but selectively weaken brain predictivity for the matched native language. These results support a shared backbone with embedded specializations and provide a causal framework for studying multilingual brain-model alignment.

cs.CL↗

arXiv2026

Multimodal Spatial Omics: From Data Acquisition to Computational Integration

Recent developments in spatial omics technologies have enabled the generation of high dimensional molecular data, such as transcriptomes, proteomes, and epigenomes, within their spatial tissue context, either through coprofiling on the same slice or through serial tissue sections. These datasets, which are often complemented by images, have given rise to multimodal frameworks that capture both the cellular and architectural complexity of tissues across multiple molecular layers. Integration in such multimodal data poses significant computational challenges due to differences in scale, resolution, and data modality. In this review, we present a comprehensive overview of computational methods developed to integrate multimodal spatial omics and imaging datasets. We highlight key algorithmic principles underlying these methods, ranging from probabilistic to the latest deep learning approaches.

q-bio.QM↗

arXiv2025

Improved Extended Kalman Filter-Based Disturbance Observers for Exoskeletons

The nominal performance of mechanical systems is often degraded by unknown disturbances. A two-degree-of-freedom control structure can decouple nominal performance from disturbance rejection. However, perfect disturbance rejection is unattainable when the disturbance dynamic is unknown. In this work, we reveal an inherent trade-off in disturbance estimation subject to tracking speed and tracking uncertainty. Then, we propose two novel methods to enhance disturbance estimation: an interacting multiple model extended Kalman filter-based disturbance observer and a multi-kernel correntropy extended Kalman filter-based disturbance observer. Experiments on an exoskeleton verify that the proposed two methods improve the tracking accuracy $36.3\%$ and $16.2\%$ in hip joint error, and $46.3\%$ and $24.4\%$ in knee joint error, respectively, compared to the extended Kalman filter-based disturbance observer, in a time-varying interaction force scenario, demonstrating the superiority of the proposed method.

cs.RO↗

arXiv2025

Rethinking RoPE: A Mathematical Blueprint for N-dimensional Positional Embedding

Rotary Position Embedding (RoPE) is widely adopted in large language models (LLMs) due to its efficient encoding of relative positions with strong extrapolation capabilities. However, while its application in higher-dimensional input domains, such as 2D images, have been explored in several attempts, a unified theoretical framework is still lacking. To address this, we propose a systematic mathematical framework for RoPE grounded in Lie group and Lie algebra theory. We derive the necessary and sufficient conditions for any valid $N$-dimensional RoPE based on two core properties of RoPE - relativity and reversibility. We demonstrate that RoPE can be characterized as a basis of a maximal abelian subalgebra (MASA) in the special orthogonal Lie algebra, and that the commonly used axis-aligned block-diagonal RoPE, where each input axis is encoded by an independent 2x2 rotation block, corresponds to the maximal toral subalgebra. Furthermore, we reduce spatial inter-dimensional interactions to a change of basis, resolved by learning an orthogonal transformation. Our experiment results suggest that inter-dimensional interactions should be balanced with local structure preservation. Overall, our framework unifies and explains existing RoPE designs while enabling principled extensions to higher-dimensional modalities and tasks.

cs.LG↗

arXiv2025

Does Acceleration Cause Hidden Instability in Vision Language Models? Uncovering Instance-Level Divergence Through a Large-Scale Empirical Study

Vision-Language Models (VLMs) are powerful yet computationally intensive for widespread practical deployments. To address such challenge without costly re-training, post-training acceleration techniques like quantization and token reduction are extensively explored. However, current acceleration evaluations primarily target minimal overall performance degradation, overlooking a crucial question: does the accelerated model still give the same answers to the same questions as it did before acceleration? This is vital for stability-centered industrial applications where consistently correct answers for specific, known situations are paramount, such as in AI-based disease diagnosis. We systematically investigate this for accelerated VLMs, testing four leading models (LLaVA-1.5, LLaVA-Next, Qwen2-VL, Qwen2.5-VL) with eight acceleration methods on ten multi-modal benchmarks. Our findings are stark: despite minimal aggregate performance drops, accelerated models changed original answers up to 20% of the time. Critically, up to 6.5% of these changes converted correct answers to incorrect. Input perturbations magnified these inconsistencies, and the trend is confirmed by case studies with the medical VLM LLaVA-Med. This research reveals a significant oversight in VLM acceleration, stressing an urgent need for instance-level stability checks to ensure trustworthy real-world deployment.

cs.CV↗

arXiv2022

Sparse Bayesian Deep Learning for Dynamic System Identification

This paper proposes a sparse Bayesian treatment of deep neural networks (DNNs) for system identification. Although DNNs show impressive approximation ability in various fields, several challenges still exist for system identification problems. First, DNNs are known to be too complex that they can easily overfit the training data. Second, the selection of the input regressors for system identification is nontrivial. Third, uncertainty quantification of the model parameters and predictions are necessary. The proposed Bayesian approach offers a principled way to alleviate the above challenges by marginal likelihood/model evidence approximation and structured group sparsity-inducing priors construction. The identification algorithm is derived as an iterative regularised optimisation procedure that can be solved as efficiently as training typical DNNs. Remarkably, an efficient and recursive Hessian calculation method for each layer of DNNs is developed, turning the intractable training/optimisation process into a tractable one. Furthermore, a practical calculation approach based on the Monte-Carlo integration method is derived to quantify the uncertainty of the parameters and predictions. The effectiveness of the proposed Bayesian approach is demonstrated on several linear and nonlinear system identification benchmarks by achieving good and competitive simulation accuracy. The code to reproduce the experimental results is open-sourced and available online.

eess.SY↗

arXiv2022

Bayesian Learning to Discover Mathematical Operations in Governing Equations of Dynamic Systems

Discovering governing equations from data is critical for diverse scientific disciplines as they can provide insights into the underlying phenomenon of dynamic systems. This work presents a new representation for governing equations by designing the Mathematical Operation Network (MathONet) with a deep neural network-like hierarchical structure. Specifically, the MathONet is stacked by several layers of unary operations (e.g., sin, cos, log) and binary operations (e.g., +,-), respectively. An initialized MathONet is typically regarded as a super-graph with a redundant structure, a sub-graph of which can yield the governing equation. We develop a sparse group Bayesian learning algorithm to extract the sub-graph by employing structurally constructed priors over the redundant mathematical operations. By demonstrating the chaotic Lorenz system, Lotka-Volterra system, and Kolmogorov-Petrovsky-Piskunov system, the proposed method can discover the ordinary differential equations (ODEs) and partial differential equations (PDEs) from the observations given limited mathematical operations, without any prior knowledge on possible expressions of the ODEs and PDEs.

cs.LG↗

arXiv2019

A Sparse Bayesian Deep Learning Approach for Identification of Cascaded Tanks Benchmark

Nonlinear system identification is important with a wide range of applications. The typical approaches for nonlinear system identification include Volterra series models, nonlinear autoregressive with exogenous inputs models, block-structured models, state-space models and neural network models. Among them, neural networks (NN) is an important black-box method thanks to its universal approximation capability and less dependency on prior information. However, there are several challenges associated with NN. The first one lies in the design of a proper neural network structure. A relatively simple network cannot approximate the feature of the system, while a complex model may lead to overfitting. The second lies in the availability of data for some nonlinear systems. For some systems, it is difficult to collect enough data to train a neural network. This raises the challenge that how to train a neural network for system identification with a small dataset. In addition, if the uncertainty of the NN parameter could be obtained, it would be also beneficial for further analysis. In this paper, we propose a sparse Bayesian deep learning approach to address the above problems. Specifically, the Bayesian method can reinforce the regularization on neural networks by introducing introduced sparsity-inducing priors. The Bayesian method can also compute the uncertainty of the NN parameter. An efficient iterative re-weighted algorithm is presented in this paper. We also test the capacity of our method to identify the system on various ratios of the original dataset. The one-step-ahead prediction experiment on Cascaded Tank System shows the effectiveness of our method. Furthermore, we test our algorithm with more challenging simulation experiment on this benchmark, which also outperforms other methods.

eess.SY↗

arXiv2019

BayesNAS: A Bayesian Approach for Neural Architecture Search

One-Shot Neural Architecture Search (NAS) is a promising method to significantly reduce search time without any separate training. It can be treated as a Network Compression problem on the architecture parameters from an over-parameterized network. However, there are two issues associated with most one-shot NAS methods. First, dependencies between a node and its predecessors and successors are often disregarded which result in improper treatment over zero operations. Second, architecture parameters pruning based on their magnitude is questionable. In this paper, we employ the classic Bayesian learning approach to alleviate these two issues by modeling architecture parameters using hierarchical automatic relevance determination (HARD) priors. Unlike other NAS methods, we train the over-parameterized network for only one epoch then update the architecture. Impressively, this enabled us to find the architecture on CIFAR-10 within only 0.2 GPU days using a single GPU. Competitive performance can be also achieved by transferring to ImageNet. As a byproduct, our approach can be applied directly to compress convolutional neural networks by enforcing structural sparsity which achieves extremely sparse networks without accuracy deterioration.

cs.LG↗