arXiv subjects

Jingbo Zhou

Publications and source records attributed to Jingbo Zhou.

At least 37 records · Page 2Linked to original sources

arXiv2026

Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control

The discovery of novel proteins relies on sensitive protein identification, for which de novo peptide sequencing (DNPS) from mass spectra is a crucial approach. While deep learning has advanced DNPS, existing models inadequately enforce the fundamental mass consistency constraint, that a predicted peptide's mass must match the experimental measured precursor mass. Previous DNPS methods often treat this critical information as a simple input feature or use it in post-processing, leading to numerous implausible predictions that do not adhere to this fundamental physical property. To address this limitation, we introduce DiffuNovo, a novel regressor-guided diffusion model for de novo peptide sequencing that provides explicit peptide-level mass control. Our approach integrates the mass constraint at two critical stages: during training, a novel peptide-level mass loss guides model optimization, while at inference, regressor-based guidance from gradient-based updates in the latent space steers the generation to compel the predicted peptide adheres to the mass constraint. Comprehensive evaluations on established benchmarks demonstrate that DiffuNovo surpasses state-of-the-art methods in DNPS accuracy. Additionally, as the first DNPS model to employ a diffusion model as its core backbone, DiffuNovo leverages the powerful controllability of diffusion architecture and achieves a significant reduction in mass error, thereby producing much more physically plausible peptides. These innovations represent a substantial advancement toward robust and broadly applicable DNPS. The source code is available in the supplementary material.

q-bio.QM↗

arXiv2026

ChartAnchor: Chart Grounding with Structural-Semantic Fidelity

Recent advances in multimodal large language models (MLLMs) highlight the need for benchmarks that rigorously evaluate structured chart comprehension. Chart grounding refers to the bidirectional alignment between a chart's visual appearance and its structured semantics. This task requires models to produce a symbolic specification that faithfully captures the chart's visual and structural intent, while also recovering the underlying tabular data with precise values and relationships. Chart grounding directly reflects a model's capabilities in numerical reasoning, multimodal alignment, and structural reconstruction, and has several important real-world applications. Existing benchmarks, constrained by narrow chart diversity, isolated tasks, and incomplete evaluation frameworks, fail to holistically assess grounding. To address this, we propose ChartAnchor, a comprehensive benchmark of 8k+ chart-table-code triples spanning 30 chart types drawn from diverse real-world and augmented sources. ChartAnchor introduces two complementary tasks: chart-to-code generation and controlled chart-to-table reconstruction, enabling cross-validation of visual and numerical fidelity. A multi-level evaluation framework integrates semantic validation, stylistic analysis, and perceptual metrics to assess both structural and content-level correctness. Extensive experiments on MLLMs reveal critical limitations in numerical precision and code synthesis, emphasizing the need for structured reasoning beyond surface-level perception. By unifying symbolic and data-driven grounding, ChartAnchor establishes a rigorous foundation for chart grounding, offering meaningful insights for advancing MLLMs in scientific, financial, and industrial domains.

cs.AI↗

arXiv2026

Unrewarded Exploration in Large Language Models Reveals Latent Learning from Psychology

Latent learning, classically theorized by Tolman, shows that biological agents (e.g., rats) can acquire internal representations of their environment without rewards, enabling rapid adaptation once rewards are introduced. In contrast, from a cognitive science perspective, reward learning remains overly dependent on external feedback, limiting flexibility and generalization. Although recent advances in the reasoning capabilities of large language models (LLMs), such as OpenAI-o1 and DeepSeek-R1, mark a significant breakthrough, these models still rely primarily on reward-centric reinforcement learning paradigms. Whether and how the well-established phenomenon of latent learning in psychology can inform or emerge within LLMs' training remains largely unexplored. In this work, we present novel findings from our experiments that LLMs also exhibit the latent learning dynamics. During an initial phase of unrewarded exploration, LLMs display modest performance improvements, as this phase allows LLMs to organize task-relevant knowledge without being constrained by reward-driven biases, and performance is further enhanced once rewards are introduced. LLMs post-trained under this two-stage exploration regime ultimately achieve higher competence than those post-trained with reward-based reinforcement learning throughout. Beyond these empirical observations, we also provide theoretical analyses for our experiments explaining why unrewarded exploration yields performance gains, offering a mechanistic account of these dynamics. Specifically, we conducted extensive experiments across multiple model families and diverse task domains to establish the existence of the latent learning dynamics in LLMs.

cs.LG↗

arXiv2026

OmegaUse: Building a General-Purpose GUI Agent for Autonomous Task Execution

Graphical User Interface (GUI) agents show great potential for enabling foundation models to complete real-world tasks, revolutionizing human-computer interaction and improving human productivity. In this report, we present OmegaUse, a general-purpose GUI agent model for autonomous task execution on both mobile and desktop platforms, supporting computer-use and phone-use scenarios. Building an effective GUI agent model relies on two factors: (1) high-quality data and (2) effective training methods. To address these, we introduce a carefully engineered data-construction pipeline and a decoupled training paradigm. For data construction, we leverage rigorously curated open-source datasets and introduce a novel automated synthesis framework that integrates bottom-up autonomous exploration with top-down taxonomy-guided generation to create high-fidelity synthetic data. For training, to better leverage these data, we adopt a two-stage strategy: Supervised Fine-Tuning (SFT) to establish fundamental interaction syntax, followed by Group Relative Policy Optimization (GRPO) to improve spatial grounding and sequential planning. To balance computational efficiency with agentic reasoning capacity, OmegaUse is built on a Mixture-of-Experts (MoE) backbone. To evaluate cross-terminal capabilities in an offline setting, we introduce OS-Nav, a benchmark suite spanning multiple operating systems: ChiM-Nav, targeting Chinese Android mobile environments, and Ubu-Nav, focusing on routine desktop interactions on Ubuntu. Extensive experiments show that OmegaUse is highly competitive across established GUI benchmarks, achieving a state-of-the-art (SOTA) score of 96.3% on ScreenSpot-V2 and a leading 79.1% step success rate on AndroidControl. OmegaUse also performs strongly on OS-Nav, reaching 74.24% step success on ChiM-Nav and 55.9% average success on Ubu-Nav.

cs.AI↗

arXiv2025

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

q-bio.GN↗

arXiv2025

PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

cs.LG↗

arXiv2025

DeepV: A Model-Agnostic Retrieval-Augmented Framework for Verilog Code Generation with a High-Quality Knowledge Base

As large language models (LLMs) continue to be integrated into modern technology, there has been an increased push towards code generation applications, which also naturally extends to hardware design automation. LLM-based solutions for register transfer level (RTL) code generation for intellectual property (IP) designs have grown, especially with fine-tuned LLMs, prompt engineering, and agentic approaches becoming popular in literature. However, a gap has been exposed in these techniques, as they fail to integrate novel IPs into the model's knowledge base, subsequently resulting in poorly generated code. Additionally, as general-purpose LLMs continue to improve, fine-tuned methods on older models will not be able to compete to produce more accurate and efficient designs. Although some retrieval augmented generation (RAG) techniques exist to mitigate challenges presented in fine-tuning approaches, works tend to leverage low-quality codebases, incorporate computationally expensive fine-tuning in the frameworks, or do not use RAG directly in the RTL generation step. In this work, we introduce DeepV: a model-agnostic RAG framework to generate RTL designs by enhancing context through a large, high-quality dataset without any RTL-specific training. Our framework benefits the latest commercial LLM, OpenAI's GPT-5, with a near 17% increase in performance on the VerilogEval benchmark. We host DeepV for use by the community in a Hugging Face (HF) Space: https://huggingface.co/spaces/FICS-LLM/DeepV.

cs.AR↗

arXiv2025

SVAgent: AI Agent for Hardware Security Verification Assertion

Verification using SystemVerilog assertions (SVA) is one of the most popular methods for detecting circuit design vulnerabilities. However, with the globalization of integrated circuit design and the continuous upgrading of security requirements, the SVA development model has exposed major limitations. It is not only inefficient in development, but also unable to effectively deal with the increasing number of security vulnerabilities in modern complex integrated circuits. In response to these challenges, this paper proposes an innovative SVA automatic generation framework SVAgent. SVAgent introduces a requirement decomposition mechanism to transform the original complex requirements into a structured, gradually solvable fine-grained problem-solving chain. Experiments have shown that SVAgent can effectively suppress the influence of hallucinations and random answers, and the key evaluation indicators such as the accuracy and consistency of the SVA are significantly better than existing frameworks. More importantly, we successfully integrated SVAgent into the most mainstream integrated circuit vulnerability assessment framework and verified its practicality and reliability in a real engineering design environment.

cs.CR↗

arXiv2025

Efficient Federated Learning with Heterogeneous Data and Adaptive Dropout

Federated Learning (FL) is a promising distributed machine learning approach that enables collaborative training of a global model using multiple edge devices. The data distributed among the edge devices is highly heterogeneous. Thus, FL faces the challenge of data distribution and heterogeneity, where non-Independent and Identically Distributed (non-IID) data across edge devices may yield in significant accuracy drop. Furthermore, the limited computation and communication capabilities of edge devices increase the likelihood of stragglers, thus leading to slow model convergence. In this paper, we propose the FedDHAD FL framework, which comes with two novel methods: Dynamic Heterogeneous model aggregation (FedDH) and Adaptive Dropout (FedAD). FedDH dynamically adjusts the weights of each local model within the model aggregation process based on the non-IID degree of heterogeneous data to deal with the statistical data heterogeneity. FedAD performs neuron-adaptive operations in response to heterogeneous devices to improve accuracy while achieving superb efficiency. The combination of these two methods makes FedDHAD significantly outperform state-of-the-art solutions in terms of accuracy (up to 6.7% higher), efficiency (up to 2.02 times faster), and computation cost (up to 15.0% smaller).

cs.DC↗

arXiv2025

SV-LLM: An Agentic Approach for SoC Security Verification using Large Language Models

Ensuring the security of complex system-on-chips (SoCs) designs is a critical imperative, yet traditional verification techniques struggle to keep pace due to significant challenges in automation, scalability, comprehensiveness, and adaptability. The advent of large language models (LLMs), with their remarkable capabilities in natural language understanding, code generation, and advanced reasoning, presents a new paradigm for tackling these issues. Moving beyond monolithic models, an agentic approach allows for the creation of multi-agent systems where specialized LLMs collaborate to solve complex problems more effectively. Recognizing this opportunity, we introduce SV-LLM, a novel multi-agent assistant system designed to automate and enhance SoC security verification. By integrating specialized agents for tasks like verification question answering, security asset identification, threat modeling, test plan and property generation, vulnerability detection, and simulation-based bug validation, SV-LLM streamlines the workflow. To optimize their performance in these diverse tasks, agents leverage different learning paradigms, such as in-context learning, fine-tuning, and retrieval-augmented generation (RAG). The system aims to reduce manual intervention, improve accuracy, and accelerate security analysis, supporting proactive identification and mitigation of risks early in the design cycle. We demonstrate its potential to transform hardware security practices through illustrative case studies and experiments that showcase its applicability and efficacy.

cs.CR↗

arXiv2025

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.

q-bio.QM↗

arXiv2025

SDWPF: A Dataset for Spatial Dynamic Wind Power Forecasting Challenge at KDD Cup 2022

The variability of wind power supply can present substantial challenges to incorporating wind power into a grid system. Thus, Wind Power Forecasting (WPF) has been widely recognized as one of the most critical issues in wind power integration and operation. There has been an explosion of studies on wind power forecasting problems in the past decades. Nevertheless, how to well handle the WPF problem is still challenging, since high prediction accuracy is always demanded to ensure grid stability and security of supply. We present a unique Spatial Dynamic Wind Power Forecasting dataset: SDWPF, which includes the spatial distribution of wind turbines, as well as the dynamic context factors. Whereas, most of the existing datasets have only a small number of wind turbines without knowing the locations and context information of wind turbines at a fine-grained time scale. By contrast, SDWPF provides the wind power data of 134 wind turbines from a wind farm over half a year with their relative positions and internal statuses. We use this dataset to launch the Baidu KDD Cup 2022 to examine the limit of current WPF solutions. The dataset is released at https://aistudio.baidu.com/aistudio/competition/detail/152/0/datasets.

cs.LG↗

arXiv2025

ImageScope: Unifying Language-Guided Image Retrieval via Large Multimodal Model Collective Reasoning

With the proliferation of images in online content, language-guided image retrieval (LGIR) has emerged as a research hotspot over the past decade, encompassing a variety of subtasks with diverse input forms. While the development of large multimodal models (LMMs) has significantly facilitated these tasks, existing approaches often address them in isolation, requiring the construction of separate systems for each task. This not only increases system complexity and maintenance costs, but also exacerbates challenges stemming from language ambiguity and complex image content, making it difficult for retrieval systems to provide accurate and reliable results. To this end, we propose ImageScope, a training-free, three-stage framework that leverages collective reasoning to unify LGIR tasks. The key insight behind the unification lies in the compositional nature of language, which transforms diverse LGIR tasks into a generalized text-to-image retrieval process, along with the reasoning of LMMs serving as a universal verification to refine the results. To be specific, in the first stage, we improve the robustness of the framework by synthesizing search intents across varying levels of semantic granularity using chain-of-thought (CoT) reasoning. In the second and third stages, we then reflect on retrieval results by verifying predicate propositions locally, and performing pairwise evaluations globally. Experiments conducted on six LGIR datasets demonstrate that ImageScope outperforms competitive baselines. Comprehensive evaluations and ablation studies further confirm the effectiveness of our design.

cs.IR↗

arXiv2025

TimeFound: A Foundation Model for Time Series Forecasting

We present TimeFound, an encoder-decoder transformer-based time series foundation model for out-of-the-box zero-shot forecasting. To handle time series data from various domains, TimeFound employs a multi-resolution patching strategy to capture complex temporal patterns at multiple scales. We pre-train our model with two sizes (200M and 710M parameters) on a large time-series corpus comprising both real-world and synthetic datasets. Over a collection of unseen datasets across diverse domains and forecasting horizons, our empirical evaluations suggest that TimeFound can achieve superior or competitive zero-shot forecasting performance, compared to state-of-the-art time series foundation models.

cs.LG↗

arXiv2025

NodeReg: Mitigating the Imbalance and Distribution Shift Effects in Semi-Supervised Node Classification via Norm Consistency

Aggregating information from neighboring nodes benefits graph neural networks (GNNs) in semi-supervised node classification tasks. Nevertheless, this mechanism also renders nodes susceptible to the influence of their neighbors. For instance, this will occur when the neighboring nodes are imbalanced or the neighboring nodes contain noise, which can even affect the GNN's ability to generalize out of distribution. We find that ensuring the consistency of the norm for node representations can significantly reduce the impact of these two issues on GNNs. To this end, we propose a regularized optimization method called NodeReg that enforces the consistency of node representation norms. This method is simple but effective and satisfies Lipschitz continuity, thus facilitating stable optimization and significantly improving semi-supervised node classification performance under the above two scenarios. To illustrate, in the imbalance scenario, when training a GCN with an imbalance ratio of 0.1, NodeReg outperforms the most competitive baselines by 1.4%-25.9% in F1 score across five public datasets. Similarly, in the distribution shift scenario, NodeReg outperforms the most competitive baseline by 1.4%-3.1% in accuracy.

cs.LG↗

arXiv2025

CHAT: Beyond Contrastive Graph Transformer for Link Prediction in Heterogeneous Networks

Link prediction in heterogeneous networks is crucial for understanding the intricacies of network structures and forecasting their future developments. Traditional methodologies often face significant obstacles, including over-smoothing-wherein the excessive aggregation of node features leads to the loss of critical structural details-and a dependency on human-defined meta-paths, which necessitate extensive domain knowledge and can be inherently restrictive. These limitations hinder the effective prediction and analysis of complex heterogeneous networks. In response to these challenges, we propose the Contrastive Heterogeneous grAph Transformer (CHAT). CHAT introduces a novel sampling-based graph transformer technique that selectively retains nodes of interest, thereby obviating the need for predefined meta-paths. The method employs an innovative connection-aware transformer to encode node sequences and their interconnections with high fidelity, guided by a dual-faceted loss function specifically designed for heterogeneous network link prediction. Additionally, CHAT incorporates an ensemble link predictor that synthesizes multiple samplings to achieve enhanced prediction accuracy. We conducted comprehensive evaluations of CHAT using three distinct drug-target interaction (DTI) datasets. The empirical results underscore CHAT's superior performance, outperforming both general-task approaches and models specialized in DTI prediction. These findings substantiate the efficacy of CHAT in addressing the complex problem of link prediction in heterogeneous networks.

cs.CE↗

arXiv2024

Improving Retrieval Augmented Language Model with Self-Reasoning

The Retrieval-Augmented Language Model (RALM) has shown remarkable performance on knowledge-intensive tasks by incorporating external knowledge during inference, which mitigates the factual hallucinations inherited in large language models (LLMs). Despite these advancements, challenges persist in the implementation of RALMs, particularly concerning their reliability and traceability. To be specific, the irrelevant document retrieval may result in unhelpful response generation or even deteriorate the performance of LLMs, while the lack of proper citations in generated outputs complicates efforts to verify the trustworthiness of the models. To this end, we propose a novel self-reasoning framework aimed at improving the reliability and traceability of RALMs, whose core idea is to leverage reasoning trajectories generated by the LLM itself. The framework involves constructing self-reason trajectories with three processes: a relevance-aware process, an evidence-aware selective process, and a trajectory analysis process. We have evaluated our framework across four public datasets (two short-form QA datasets, one long-form QA dataset, and one fact verification dataset) to demonstrate the superiority of our method, which can outperform existing state-of-the-art models and can achieve comparable performance with GPT-4, while only using 2,000 training samples.

cs.CL↗

arXiv2024

Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptive Residual Module

Graph Neural Networks (GNNs), a type of neural network that can learn from graph-structured data through neighborhood information aggregation, have shown superior performance in various downstream tasks. However, as the number of layers increases, node representations become indistinguishable, which is known as over-smoothing. To address this issue, many residual methods have emerged. In this paper, we focus on the over-smoothing issue and related residual methods. Firstly, we revisit over-smoothing from the perspective of overlapping neighborhood subgraphs, and based on this, we explain how residual methods can alleviate over-smoothing by integrating multiple orders neighborhood subgraphs to avoid the indistinguishability of the single high-order neighborhood subgraphs. Additionally, we reveal the drawbacks of previous residual methods, such as the lack of node adaptability and severe loss of high-order neighborhood subgraph information, and propose a \textbf{Posterior-Sampling-based, Node-Adaptive Residual module (PSNR)}. We theoretically demonstrate that PSNR can alleviate the drawbacks of previous residual methods. Furthermore, extensive experiments verify the superiority of the PSNR module in fully observed node classification and missing feature scenarios. Our code is available at https://github.com/jingbo02/PSNR-GNN.

cs.LG↗