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Jingbo Zhou

Publications and source records attributed to Jingbo Zhou.

At least 19 recordsLinked to original sources
arXiv2026

OmegaUse-SOP: SOP Engineering for Professional Computer Use from Human Demonstrations

Large language models (LLMs) are increasingly evolving from conversational assistants into agents capable of operating external digital environments. Graphical user interface (GUI) agents play an important role in this transition, as many real-world workflows remain accessible only through user-facing software interfaces. However, despite recent progress on general computer-use benchmarks, domain-specific professional standard operating procedures (SOPs) remain challenging for GUI agents because they often involve implicit domain knowledge, software-specific conventions, and task-level verification requirements. We introduce OmegaUse-SOP, a human-in-the-loop SOP Engineering system for transforming human demonstrations of professional computer use into reusable SOP skills for GUI agents. Analogous to prompt engineering, SOP Engineering iteratively refines demonstrations, execution rules, and domain knowledge to convert professional SOPs into reusable GUI-agent skills. OmegaUse-SOP consists of four modules: Observe, Reason, Configure, and Execute. Together, these modules record expert operations as multimodal GUI traces, abstract low-level events into semantic step-level instructions, incorporate domain rules and task-specific parameters, and execute the resulting skills in live GUI environments through step-wise grounding, action generation, and verification. To demonstrate its effectiveness, we collaborate with a power-sector client and test OmegaUse-SOP on photovoltaic simulation workflows in PVsyst 7.2. The results suggest that OmegaUse-SOP can improve GUI-agent reliability on professional SOP tasks, highlighting a practical path toward deploying GUI agents in domain-specific professional software environments.

cs.HC↗
arXiv2026

Beyond Success and Failure: Length-Aware Contrastive Learning for GUI Agents

Graphical User Interface (GUI) agents powered by Multimodal Large Language Models (MLLMs) have shown strong potential for automating tasks across diverse digital environments, where reinforcement learning (RL) has become a dominant training paradigm. However, widely used methods such as Group Relative Policy Optimization (GRPO) suffer from reward-gradient misalignment, leading to inefficient and unstable optimization. Recent work addresses this issue by reformulating RL with verifiable rewards (RLVR) as contrastive or classification-based objectives, which improve stability by eliminating problematic gradient behaviors. Despite this progress, existing contrastive RLVR methods rely primarily on outcome-level supervision and fail to capture fine-grained differences in trajectory quality within the same outcome category. In this paper, we propose Length-Aware Contrastive Learning for GUI Agents (LACL-GUI), a contrastive RLVR framework that incorporates trajectory-level quality signals into policy optimization. LACL-GUI introduces structured preferences within both successful and failed trajectories, encouraging concise successful executions and differentiating failure quality based on divergence from successful trajectories, while preserving optimization stability. Experiments on GUI agent benchmarks show that LACL-GUI provides more effective learning signals and consistently improves agent performance over prior methods, highlighting the value of trajectory-level supervision in contrastive RLVR.

cs.AI↗
arXiv2026

Temporal Bridges for Spatial Resolution: Enhancing Climate Data Super-Resolution with Bidirectional Alignment

High-resolution climate data is crucial for meteorological predictions and for informing decision support across diverse domains. However, the acquisition of such high-resolution climate information is often prohibitively costly, necessitating the development of data-driven meteorological prediction models. These models aim to generate fine-grained climate data from low-resolution inputs, a process termed climate data super-resolution (SR). Nevertheless, recent advancements in deep learning for climate data SR have primarily focused on leveraging single-frame spatial information, largely neglecting the temporal correlations between different time frames that could enhance SR outcomes. Furthermore, climate data are inherently stochastic and noisy, rendering widely used temporal alignment methods, such as optical flow models, ineffective in this context. Consequently, the development of a framework tailored for climate data SR that effectively captures implicit temporal correlations remains an unresolved challenge. To this end, we propose a novel Temporal-Enhanced framework with bidirectional temporal alignment. In essence, our framework establishes a temporal bridge to enhance spatial resolution in climate data SR through bidirectional alignment, leading to improved SR performance. Within this framework, Paired Latent Mapping achieves spatial alignment and noise reduction by unifying latent spaces. Then a Bidirectional Temporal Alignment captures temporal correlations by training forward and backward networks on consecutive latent frames. Temporal Enhanced Super-resolution then optimizes the entire framework for climate data SR. Experiments on large-scale real-world datasets demonstrated the superior performance of our framework.

cs.AI↗
arXiv2026

TS-RAG: Retrieval Augmented Generation for Time Series Forecasting

While deep learning models, particularly transformer-based architectures, have shown impressive performance in time series forecasting, the application of retrieval-augmented generation (RAG) in this domain remains limited. Since RAG has proven effective in enhancing the capabilities of large language models by incorporating relevant external information, retrieving similar time series sequences as references might also improve accuracy in time series forecasting tasks. However, most time series models are constrained by limited training data, smaller parameter scales, and a lack of the extensive generative capabilities found in large language models. Simply concatenating reference sequences into the prompt, as done in language models, may not yield the expected results. To address these challenges, we propose a novel approach, TS-RAG, which leverages RAG to enhance forecasting performance. The framework introduces specially designed reference tokens to effectively fuse information from the input sequence with that from retrieved similar sequences, enabling a more robust capture of complex temporal dynamics. Experimental results demonstrate that TS-RAG achieves consistent state-of-the-art performance across several real-world forecasting benchmarks.

cs.AI↗
arXiv2026

OmegaUse-OfficeVal: Benchmarking LLM Agents on Long-Horizon Office-Suite Tasks with Economic Grounding

Large language model (LLM) agents are increasingly expected to assist users in completing tasks. However, existing benchmarks provide limited support for evaluating whether agents can carry out office-suite workflows at a reasonable cost. We introduce OmegaUse-OfficeVal, a benchmark for evaluating LLM agents on long-horizon office-suite tasks with task-level economic grounding. The benchmark comprises 100 tasks derived from office-suite requests proposed by practitioners and adapted through a privacy-preserving process. On average, these tasks require 2.32 hours of human labor to complete. An important feature of the benchmark is that each task is paired with two economic signals: human labor time and task price proxy. These signals enable direct comparisons between human costs and LLM inference costs, as well as value-weighted evaluation. To support stable evaluation, we develop code-based verifiers from fine-grained rubrics. We evaluate several frontier LLMs together with a human baseline. Although all evaluated LLMs are substantially cheaper and faster than human workers, they have not yet approached human-level deliverable quality. The code and dataset are fully open-sourced, and more information is available on our project website: https://omegause-officeval.github.io.

cs.AI↗
arXiv2026

Clarify-Then-Search: A Clarification Benchmark for Deep Search with End-to-End Nugget Restoration

Deep search is brittle on underspecified user queries: missing constraints such as time, location, scope, or definitions can lead to retrieval drift and incomplete answers. We introduce Clarify-Then-Search, a benchmark for evaluating whether LLM-generated clarification questions improve downstream deep-search utility. Built on real-world query data from the Baidu search engine, the benchmark contains 518 curated instances, each with an intent query and a corresponding underspecified query. For each intent query, we run WebDancer once to archive evidence and construct a static golden reference as weighted, evidence-grounded nuggets with traceable source identifiers. At evaluation time, a Clarifier asks k in {1, 2, 3} questions; a closed-book User Answerer replies only with information explicitly stated in the intent query, otherwise returning unknown; and a closed-book Rewriter produces a rewritten query using only the underspecified query and the elicited question-answer pairs. WebDancer then executes on the rewritten query, and we score end-to-end utility using restore_score_100, a weighted nugget-recall score with partial credit against the static gold. Across all evaluated models, clarification improves over the no-interaction baseline at k=1, and larger budgets generally yield further gains. GPT-5.2 achieves the highest mean score at k=1, while ERNIE-4.5-Turbo-128K becomes the overall top-performing model at k=3. Diagnostics reveal a consistent failure mode: many systems over-ask region-only questions that are often unanswerable from the intent and thus elicit unknown. Clarify-Then-Search enables leakage-resistant and reproducible evaluation of clarify-then-search pipelines, with fine-grained analyses of question utility, answerability, and budget effects in deep search.

cs.IR↗
arXiv2026

MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry

De novo peptide sequencing from tandem mass spectrometry is pivotal in proteomics, enabling identification of novel peptides without reference databases. While recent Transformer-based encoder-decoder models have achieved remarkable performance, we uncover a critical pathology in their inference dynamics. Through comprehensive feature scaling experiments, we demonstrate that existing auto-regressive peptide decoders tend to over-rely on generated-sequence priors while progressively under-utilizing fine-grained physical evidence from the input mass spectrum. This phenomenon leads to suboptimal results, where generated peptide sequences are biologically plausible yet not faithful to the input spectrum. To rectify this, we propose MemNovo, a training-free and plug-and-play mechanism that re-balances peptide and spectral contributions at inference time. MemNovo alleviates the information bottleneck by establishing a persistent spectral memory bank and injecting retrieved features directly into the final decoding stage via an ultra-conservative residual connection. Theoretical analysis confirms that this mechanism restores the mutual information between the decoder state and the raw spectrum. Extensive experiments on the Nine Species benchmark with two representative baselines, Casanovo and InstaNovo, demonstrate that MemNovo consistently improves both amino acid precision and peptide precision, achieving up to 39.1% relative improvement in peptide precision for Casanovo and up to 3.9% for InstaNovo, with negligible computational overhead.

cs.LG↗
arXiv2026

scTranslation: A Comprehensive Benchmark for Single-Cell Multi-Omics Modality Translation

Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality translation have emerged in recent years. Despite the development of translation models, there is still a lack of systematic benchmark evaluation in terms of datasets, evaluation metrics, and influencing factors. To address this, we present scTranslation, a comprehensive benchmark for single-cell multi-omics modality translation tasks. It includes diverse translation datasets, integrates state-of-the-art models, and provides a comprehensive evaluation metrics. In addition, we assess model performance under different scenarios, such as feature selection, feature quality, and few-shot settings. These factors significantly affect model performance but have rarely been systematically studied before. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research. The code is anonymously released at https://github.com/Bunnybeibei/scTranslation.

cs.AI↗
arXiv2026

DuIVRS-2: An LLM-based Interactive Voice Response System for Large-scale POI Attribute Acquisition

Accurate Point of Interest (POI) attribute acquisition is essential for location-based services, yet traditional modular Interactive Voice Response (IVR) systems suffer from error accumulation and high maintenance overhead. We present DuIVRS-2, a large language model (LLM)-based end-to-end framework designed for large-scale POI attribute acquisition at Baidu Maps. To address the long-tail distribution of real-world interactions, our methodology first employs a finite state machine (FSM)-guided data augmentation strategy to synthesize a balanced and diverse training dataset. We then streamline dialogue management via a selective generation scheme combined with a Chain-of-Thought (CoT) mechanism, which ensures output stability and effectively eliminates hallucinations in industrial settings. To facilitate continuous policy refinement with minimal manual effort, we design a cooperative iterative learning framework that leverages a dual-evaluator voting system. Deployed in production for two months, DuIVRS-2 processed 0.4 million calls daily and achieved a 83.9\% Task Success Rate (TSR), outperforming its predecessor by 4 percentage points while maintaining a low reaction time of 130ms. This work provides a production-proven reference for developing robust, cost-effective LLM agents for large-scale industrial dialogue applications.

cs.AI↗
arXiv2026

scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest heterogeneously across genes, most existing methods process the transcriptome uniformly, frequently resulting in over-correction and loss of subtle biological signals. To address this, we present scHelix, a dataset-adaptive framework that fundamentally changes how features are processed by explicitly partitioning genes into domain-invariant Anchors and domain-sensitive Variants at the input level. scHelix utilizes a dual-stream sparse diffusion encoder equipped with stop-gradient graph caching to efficiently learn multi-scale structural representations. The core of our approach is a novel asymmetric Align-Refine-Fuse protocol: the unstable Variant stream is first aligned to the robust topology of the Anchor stream, followed by a conservative refinement phase where the Anchor stream absorbs denoised details via bounded residual gating. This divide-and-conquer architecture prevents shortcut learning and ensures robust batch removal without compromising the integrity of biological clusters. Extensive benchmarking demonstrates that scHelix outperforms state-of-the-art methods.

cs.LG↗
arXiv2026

LoReC: Rethinking Large Language Models for Graph Data Analysis

The advent of Large Language Models (LLMs) has fundamentally reshaped the way we interact with graphs, giving rise to a new paradigm called GraphLLM. As revealed in recent studies, graph learning can benefit from LLMs. However, we observe limited benefits when we directly utilize LLMs to make predictions for graph-related tasks within GraphLLM paradigm, which even yields suboptimal results compared to conventional GNN-based approaches. Through in-depth analysis, we find this failure can be attributed to LLMs' limited capability for processing graph data and their tendency to overlook graph information. To address this issue, we propose LoReC (Look, Remember, and Contrast), a novel plug-and-play method for GraphLLM paradigm, which enhances LLM's understanding of graph data through three stages: (1) Look: redistributing attention to graph; (2) Remember: re-injecting graph information into the Feed-Forward Network (FFN); (3) Contrast: rectifying the vanilla logits produced in the decoding process. Extensive experiments demonstrate that LoReC brings notable improvements over current GraphLLM methods and outperforms GNN-based approaches across diverse datasets. The implementation is available at https://github.com/Git-King-Zhan/LoReC.

cs.LG↗
arXiv2026

MAT-Cell: A Multi-Agent Tree-Structured Reasoning Framework for Batch-Level Single-Cell Annotation

Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas. GPTCelltype-style one-shot prompting allows large language models (LLMs) to produce plausible labels from generic expression signals, while reference-based annotators can force unfamiliar states into the nearest known category. We propose MAT-Cell, a prompt-driven framework for batch-level single-cell annotation that separates evidence grounding from label decision. MAT-Cell first uses Reverse Verification Query (RVQ) to combine tissue context, observed differentially expressed genes, and LLM-elicited biological priors into structured candidate-specific premises. Verifier agents then convert these premises into explicit premise-to-claim reasoning trees, and bounded multi-round debate compares,challenges, and revises the resulting claims before consensus or final adjudication.The returned Syllogistic Derivation Tree (SDT) provides an auditable debate trace rather than a formal proof of the annotation. In open-candidate benchmarks across five datasets, a locally deployed Qwen3-30B model with MAT-Cell achieves 75.5% average accuracy, compared with 64.2% for the strongest evaluated CoT baseline and 51.9% for the strongest evaluated scPilot variant. In oracle-candidate bench-marks across three species,MAT-Cell remains competitive across backbones, and local inference substantially reduces monetary cost for batch annotation. Code is available at: https://anonymous.4open.science/r/MATCell-4067

q-bio.QM↗
arXiv2026

VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose \textbf{VecFormer} (the \textbf{Vec}tor Quantized Graph Trans\textbf{former}), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic \texttt{Graph Codes}. In the second stage, attention mechanisms are performed at the \texttt{Graph Token} level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

cs.LG↗
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

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

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↗
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↗