arXiv subjects

Jingbo Zhou

Publications and source records attributed to Jingbo Zhou.

At least 19 recordsLinked to original sources

arXiv2026

MarkovTS: Pretrained State-Transition Representations for Zero-Shot Time Series Generation

Across heterogeneous real-world domains, time-series generation supports simulation, model development, and data augmentation by generating sequences that preserve target-domain statistics and temporal dependencies when real observations are scarce or costly. However, existing methods predominantly address in-domain generation, limiting their reuse in unseen domains. We study reference-conditioned zero-shot time series generation: target domains are unseen during pretraining, generation uses a single target-domain reference sequence, and no model parameters are updated. MarkovTS characterizes sequence evolution through local morphologies and their ordered transitions at multiple temporal scales. Its pretrained encoder quantizes normalized time-series patches into multiscale morphological states with a state codebook, while a transition codebook encodes contextual transitions between adjacent intervals. These transferable state-transition representations condition a pretrained flow-matching model. At generation, the frozen model combines a reference-derived condition with independent Gaussian noise to produce stochastic samples that retain the reference's temporal organization. Across 12 unseen target datasets, MarkovTS outperforms strong baselines in most distributional comparisons and generates diverse, reference-consistent sequences. As downstream augmentation, its samples yield overall gains across forecasting, classification, and anomaly detection benchmarks and diverse model families. Our code is available at https://github.com/blisky-li/MarkovTS.

cs.LG↗

arXiv2026

SCARL: Sequence Confidence-Aligned Reinforcement Learning

Reinforcement learning with verifiable rewards (RLVR) improves language-model reasoning by scoring sampled responses with a rule-based verifier and reinforcing those that pass. Where a classifier's training couples predicted probability to labels, nothing ties an RLVR policy's confidence in a response to its reward: aligned training would drive responses with the same advantage toward equal confidence, yet the advantage is blind to confidence. Under this sequence-confidence misalignment, a success the policy barely found earns the same update as one it produces with near certainty, and a confident error is corrected no harder than an exploratory one. We propose SCARL (Sequence Confidence-Aligned Reinforcement Learning), which reshapes, but never re-signs, each advantage with the alignment gap between the response's group-relative confidence and the outcome its advantage certifies, normalized into shares of each class's advantage budget. Misaligned samples absorb the force, responses with the same advantage are driven toward equal confidence, and repairing the misalignment doubles as a remedy for the entropy collapse that erodes exploration. SCARL provably reduces to its base estimator when a class's confidences agree, adds no extra passes and one hyperparameter. On Qwen3-4B-Base it lifts average Pass@32 by 2.4 points over DAPO and is best among nine compute-matched methods on both coverage and per-draw accuracy; applied unchanged across four estimators and four backbones, it improves 14 of 16 settings while preserving policy entropy and widening the confidence-correctness separation. Our code is available at https://github.com/kezhh163/scarl.

cs.LG↗

arXiv2026

FactorEngram: Factorized N-gram Memory with Basis-Level Gating for Language Models

Lookup-based memory has been a promising way to scale the parameters of large language models (LLMs). It retrieves learned representations of local token patterns, such as n-grams, instead of reconstructing them through successive layers of computation. However, existing designs such as Engram treat each retrieved embedding as a monolithic unit. Each embedding is stored in its own hashed slot and modulated by a single scalar gate. As a result, polysemous patterns cannot selectively read out the components of their memory that are relevant to the context. Moreover, parameters are shared only through hash collisions, which are largely unrelated to semantics. We propose FactorEngram, a factorized n-gram memory with basis-level contextual gating. FactorEngram retrieves sparsity-regularized coefficients over a dictionary of basis vectors shared across patterns, so related patterns can reuse common components. The same dictionary is also used for gating. The backbone hidden state is scored against each basis vector to gate the corresponding coefficient before reconstruction, which lets the context modulate each memory component individually. FactorEngram also covers both individual tokens and multi-token n-grams, and we systematically study where the memory branch should be inserted. On 340M- and 1B-parameter Transformer backbones, FactorEngram improves language modeling and downstream task performance. Ablation studies confirm the contribution of each component and identify insertion before the attention sublayer in the middle layers as an effective configuration.

cs.CL↗

arXiv2026

Bison: Cross-Dataset Learning for Unseen-Compound Perturbation Prediction

Predicting transcriptional responses to unseen compounds is limited by fragmented chemical coverage and heterogeneous experimental platforms and gene panels. To assess molecular generalization across these settings, we build on Chem-PerturBridge to benchmark eight datasets with 16,771 compounds, withholding test compounds from every training dataset. This comparison reveals that high overall response agreement can coexist with weak prediction of drug-specific differences, despite reproducible signals across repeated measurements. To exploit complementary chemical supervision while targeting these differences, we introduce Bison: a shared gene representation connects native panels, while two discrete diffusion models compose context-dependent responses with molecular deviations learned through matched drug-contrast supervision. A single Bison model jointly trained across all eight datasets achieves the highest mean overall-response and drug-contrast Pearson correlations on the full benchmark in comparison with 11 methods trained independently per dataset. Compared with dataset-specific training of the same architecture, joint training increases mean drug-contrast correlation by 27.4\%, with gains across all eight datasets and improvements in overall response prediction. These results demonstrate how matched drug contrasts turn complementary screens into shared molecular supervision for unseen-drug response prediction while preserving native gene measurements.

cs.LG↗

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

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

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

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

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

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

HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference

In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding biological processes. Key to this is the robust modeling of hierarchical structures that govern cellular development. Traditional methods face limitations in computational cost, performance, and stability. VAE-based approaches have made strides but still require branch-specific network modules, limiting their scalability and stability, while often suffering from posterior collapse. To overcome these challenges, we introduce HDTree, a generative modeling framework designed for robust lineage inference. HDTree captures tree relationships within a hierarchical latent space using a unified hierarchical codebook and employs a quantized diffusion process to model continuous cell state transitions. By aligning the generative process with the Waddington landscape, this method not only improves stability and scalability but also enhances the biological plausibility of inferred lineages. HDTree's effectiveness is demonstrated through comparisons on both general-purpose and single-cell datasets, where it outperforms existing methods in lineage inference accuracy, reconstruction quality, and hierarchical consistency. These contributions enable accurate and efficient modeling of cellular differentiation paths, offering reliable insights for biological discovery.\footnote{Code is available at https://github.com/zangzelin/code\_HDTree\_icml.

cs.LG↗

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

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

Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired, creating a critical yet unresolved problem in single-cell perturbation modeling. Moreover, the high dimensionality and sparsity of single-cell expression make direct modeling prone to focusing on zeros and neglecting meaningful patterns. To address these problems, we propose a new paradigm for single-cell perturbation modeling. Specifically, we leverage dual diffusion models to learn the control and perturbed distributions separately, and implicitly align them through a shared Gaussian latent space, without requiring explicit cell pairing. Furthermore, we introduce a sparsity masking strategy in which the mask model learns to predict zero-expressed genes, allowing the diffusion model to focus on capturing meaningful patterns among expressed genes and thereby preserving diversity in high-dimensional sparse data. We introduce \textbf{Doloris}, a generative framework that defines a new paradigm for modeling unpaired, high-dimensional, and sparse single-cell perturbation data. It leverages dual conditional diffusion models for separate learning of control and perturbed distributions, complemented by a sparsity masking strategy to enhance prediction of zero-valued genes. The results on publicly available datasets show that our model effectively captures the diversity of single-cell perturbations and achieves state-of-the-art performance. To facilitate reproducibility, we include the code in the supplementary materials.

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↗