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Jun Xia

Publications and source records attributed to Jun Xia.

At least 37 records · Page 2Linked to original sources
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

ERNIE-Image Technical Report

We introduce ERNIE-Image, an open-source text-to-image generation model built upon an 8B single-stream DiT architecture. ERNIE-Image aims to bridge the gap between current open-source models and leading closed-source systems through more effective mining of large-scale pre-training data and improved supervision quality throughout training. During pre-training, we adopt a bottom-up data construction pipeline that combines fine-grained image categorization, rich caption annotation, aesthetic assessment, and hierarchical sampling. This strategy reduces data noise while preserving long-tail concepts and detailed real-world knowledge, providing a stronger foundation for complex generation tasks. In the post-training stage, we use a top-down data construction pipeline for high-demand scenarios, diversify prompt annotations to better match real user inputs, and apply a stabilized DPO strategy to align the model with human aesthetic preferences. We further train ERNIE-Image-Turbo for efficient 8-NFE generation and propose MT-DMD to mitigate capability drift during distillation. To make the model easier to use in practical scenarios, we equip it with a lightweight Prompt Enhancer that expands concise user intents into structured visual descriptions. In addition, we develop ERNIE-Image-Aes, an industrial-grade aesthetic model, together with ERNIE-Image-Aes-1K, a human-annotated benchmark for realistic aesthetic evaluation. Extensive qualitative and quantitative experiments show that ERNIE-Image achieves leading performance among open-source models and approaches top-tier commercial models in instruction following, text rendering, and aesthetic quality. We release the trained models and aesthetic resources to facilitate further academic research and technical progress in the AIGC community.

cs.CV↗
arXiv2026

PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Tandem mass spectrometry provides a high-throughput framework for identifying and quantifying proteins in complex biological samples. In computational proteomics, predicting peptide MS/MS spectra is a critical task, enabling downstream applications such as large-scale peptide identification and quantification. While deep learning architectures have substantially improved prediction accuracy, three evaluation challenges obscure the true progress of the field. First, inconsistent data preprocessing and incompatible model output spaces hinder fair model comparison. Second, flawed data splitting strategies can permit hidden sequence leakage and inflate reported performance. Third, existing evaluations typically lack comprehensive cross-species benchmarking and systematic assessment of model robustness to influential experimental conditions. To address these challenges, we propose PepSpecBench, a unified benchmark for peptide MS/MS spectrum prediction. PepSpecBench standardizes data preprocessing across complementary public datasets, enforces a strict backbone-disjoint splitting strategy to eliminate sequence leakage, and evaluates diverse architectures within a shared fragment-ion representation space. It further introduces a comprehensive multi-species evaluation suite and physically grounded metadata perturbation probes to assess model robustness and instrument awareness. We uncover previously unrecognized performance discrepancies and robustness limitations across six representative models, providing actionable insights for future model design, evaluation and practical deployment.

cs.LG↗
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↗
arXiv2026

DuoTeach: Dual Role Self-Teaching for Coarse-to-Fine Decision Coordination in Vision--Language Models

Coarse-to-fine path decision-making requires predicting a valid taxonomy path in which earlier decisions constrain later ones. However, existing benchmarks score each level independently, obscuring cross-level validity and consistency. To better align evaluation with this setting, we introduce a Joint Path Decision (JPD) protocol that requires predicting the full path in one call, together with Depth-Weighted Prefix Accuracy (DWPA), a metric family that measures path reliability with tunable emphasis on deeper levels. Under JPD, strong vision-language models (VLMs) frequently produce invalid parent-child pairs and brittle full-path predictions, suggesting that their failures stem not only from incomplete taxonomic knowledge but also from unstable cross-level decision coordination. To address this problem, we propose DuoTeach, a dual-role self-teaching distillation framework that requires no ground-truth labels and reuses the same pretrained VLM in two roles. Its Decision-Conditioned Rollout (DCR) generates more coherent teacher traces by conditioning each level on prior decisions, and distills this coordinated behavior into the student without additional test-time rollouts. Across multiple taxonomy-structured benchmarks and VLM base models, DuoTeach improves in-domain DWPA (alpha = 0.95) by up to 30.24 points and boosts zero-shot performance on unseen taxonomies from 17.17% to 43.66%. Further analyses attribute these gains to improved within-call multi-level decision coordination.

cs.MM↗
arXiv2026

Refold: Refining Protein Inverse Folding with Efficient Structural Matching and Fusion

Protein inverse folding aims to design an amino acid sequence that will fold into a given backbone structure, serving as a central task in protein design. Two main paradigms have been widely explored. Template-based methods exploit database-derived structural priors and can achieve high local precision when close structural neighbors are available, but their dependence on database coverage and match quality often degrades performance on out-of-distribution (OOD) targets. Deep learning approaches, in contrast, learn general structure-to-sequence regularities and usually generalize better to new backbones. However, they struggle to capture fine-grained local structure, which can cause uncertain residue predictions and missed local motifs in ambiguous regions. We introduce Refold, a novel framework that synergistically integrates the strengths of database-derived structural priors and deep learning prediction to enhance inverse folding. Refold obtains structural priors from matched neighbors and fuses them with model predictions to refine residue probabilities. In practice, low-quality neighbors can introduce noise, potentially degrading model performance. We address this issue with a Dynamic Utility Gate that controls prior injection and falls back to the base prediction when the priors are untrustworthy. Comprehensive evaluations on standard benchmarks demonstrate that Refold achieves state-of-the-art native sequence recovery of 0.63 on both CATH 4.2 and CATH 4.3. Also, analysis indicates that Refold delivers larger gains on high-uncertainty regions, reflecting the complementarity between structural priors and deep learning predictions.

cs.LG↗
arXiv2026

SGI: Structured 2D Gaussians for Efficient and Compact Large Image Representation

2D Gaussian Splatting has emerged as a novel image representation technique that can support efficient rendering on low-end devices. However, scaling to high-resolution images requires optimizing and storing millions of unstructured Gaussian primitives independently, leading to slow convergence and redundant parameters. To address this, we propose Structured Gaussian Image (SGI), a compact and efficient framework for representing high-resolution images. SGI decomposes a complex image into multi-scale local spaces defined by a set of seeds. Each seed corresponds to a spatially coherent region and, together with lightweight multi-layer perceptrons (MLPs), generates structured implicit 2D neural Gaussians. This seed-based formulation imposes structural regularity on otherwise unstructured Gaussian primitives, which facilitates entropy-based compression at the seed level to reduce the total storage. However, optimizing seed parameters directly on high-resolution images is a challenging and non-trivial task. Therefore, we designed a multi-scale fitting strategy that refines the seed representation in a coarse-to-fine manner, substantially accelerating convergence. Quantitative and qualitative evaluations demonstrate that SGI achieves up to 7.5x compression over prior non-quantized 2D Gaussian methods and 1.6x over quantized ones, while also delivering 1.6x and 6.5x faster optimization, respectively, without degrading, and often improving, image fidelity. Code is available at https://github.com/zx-pan/SGI.

cs.CV↗
arXiv2026

SurgFed: Language-guided Multi-Task Federated Learning for Surgical Video Understanding

Surgical scene Multi-Task Federated Learning (MTFL) is essential for robot-assisted minimally invasive surgery (RAS) but remains underexplored in surgical video understanding due to two key challenges: (1) Tissue Diversity: Local models struggle to adapt to site-specific tissue features, limiting their effectiveness in heterogeneous clinical environments and leading to poor local predictions. (2) Task Diversity: Server-side aggregation, relying solely on gradient-based clustering, often produces suboptimal or incorrect parameter updates due to inter-site task heterogeneity, resulting in inaccurate localization. In light of these two issues, we propose SurgFed, a multi-task federated learning framework, enabling federated learning for surgical scene segmentation and depth estimation across diverse surgical types. SurgFed is powered by two appealing designs, i.e., Language-guided Channel Selection (LCS) and Language-guided Hyper Aggregation (LHA), to address the challenge of fully exploration on corss-site and cross-task. Technically, the LCS is first designed a lightweight personalized channel selection network that enhances site-specific adaptation using pre-defined text inputs, which optimally the local model learn the specific embeddings. We further introduce the LHA that employs a layer-wise cross-attention mechanism with pre-defined text inputs to model task interactions across sites and guide a hypernetwork for personalized parameter updates. Extensive empirical evidence shows that SurgFed yields improvements over the state-of-the-art methods in five public datasets across four surgical types. The code is available at https://anonymous.4open.science/r/SurgFed-070E/.

cs.CV↗
arXiv2026

Is Exchangeability better than I.I.D to handle Data Distribution Shifts while Pooling Data for Data-scarce Medical image segmentation?

Data scarcity is a major challenge in medical imaging, particularly for deep learning models. While data pooling (combining datasets from multiple sources) and data addition (adding more data from a new dataset) have been shown to enhance model performance, they are not without complications. Specifically, increasing the size of the training dataset through pooling or addition can induce distributional shifts, negatively affecting downstream model performance, a phenomenon known as the "Data Addition Dilemma". While the traditional i.i.d. assumption may not hold in multi-source contexts, assuming exchangeability across datasets provides a more practical framework for data pooling. In this work, we investigate medical image segmentation under these conditions, drawing insights from causal frameworks to propose a method for controlling foreground-background feature discrepancies across all layers of deep networks. This approach improves feature representations, which are crucial in data-addition scenarios. Our method achieves state-of-the-art segmentation performance on histopathology and ultrasound images across five datasets, including a novel ultrasound dataset that we have curated and contributed. Qualitative results demonstrate more refined and accurate segmentation maps compared to prominent baselines across three model architectures.

cs.CV↗
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

NMRGym: A Comprehensive Benchmark for Nuclear Magnetic Resonance Based Molecular Structure Elucidation

Nuclear Magnetic Resonance (NMR) spectroscopy is the cornerstone of small-molecule structure elucidation. While deep learning has demonstrated significant potential in automating structure elucidation and spectral simulation, current progress is severely impeded by the reliance on synthetic datasets, which introduces significant domain shifts when applied to real-world experimental spectra. Furthermore, the lack of standardized evaluation protocols and rigorous data splitting strategies frequently leads to unfair comparisons and data leakage. To address these challenges, we introduce \textbf{NMRGym}, the largest and most comprehensive standardized dataset and benchmark derived from high-quality experimental NMR data to date. Comprising \textbf{269,999} unique molecules paired with high-fidelity $^1$H and $^{13}$C spectra, NMRGym bridges the critical gap between synthetic approximations and real-world diversity. We implement a strict quality control pipeline and unify data formats to ensure fair comparison. To strictly prevent data leakage, we enforce a scaffold-based split. Additionally, we provide fine-grained peak-atom level annotations to support future usage. Leveraging this resource, we establish a comprehensive evaluation suite covering diverse downstream tasks, including structure elucidation, functional group prediction from NMR, toxicity prediction from NMR, and spectral simulation, benchmarking representative state-of-the-art methodologies. Finally, we release an open-source leadboard with an automated leaderboard to foster community collaboration and standardize future research. The dataset, benchmark and leaderboard are publicly available at \textcolor{blue}{https://AIMS-Lab-HKUSTGZ.github.io/NMRGym/}.

cs.CE↗
arXiv2026

Patient-Conditioned Adaptive Offsets for Reliable Diagnosis across Subgroups

AI models for medical diagnosis often exhibit uneven performance across patient populations due to heterogeneity in disease prevalence, imaging appearance, and clinical risk profiles. Existing algorithmic fairness approaches typically seek to reduce such disparities by suppressing sensitive attributes. However, in medical settings these attributes often carry essential diagnostic information, and removing them can degrade accuracy and reliability, particularly in high-stakes applications. In contrast, clinical decision making explicitly incorporates patient context when interpreting diagnostic evidence, suggesting a different design direction for subgroup-aware models. In this paper, we introduce HyperAdapt, a patient-conditioned adaptation framework that improves subgroup reliability while maintaining a shared diagnostic model. Clinically relevant attributes such as age and sex are encoded into a compact embedding and used to condition a hypernetwork-style module, which generates small residual modulation parameters for selected layers of a shared backbone. This design preserves the general medical knowledge learned by the backbone while enabling targeted adjustments that reflect patient-specific variability. To ensure efficiency and robustness, adaptations are constrained through low-rank and bottlenecked parameterizations, limiting both model complexity and computational overhead. Experiments across multiple public medical imaging benchmarks demonstrate that the proposed approach consistently improves subgroup-level performance without sacrificing overall accuracy. On the PAD-UFES-20 dataset, our method outperforms the strongest competing baseline by 4.1% in recall and 4.4% in F1 score, with larger gains observed for underrepresented patient populations.

cs.CV↗
arXiv2026

MiMo-V2-Flash Technical Report

We present MiMo-V2-Flash, a Mixture-of-Experts (MoE) model with 309B total parameters and 15B active parameters, designed for fast, strong reasoning and agentic capabilities. MiMo-V2-Flash adopts a hybrid attention architecture that interleaves Sliding Window Attention (SWA) with global attention, with a 128-token sliding window under a 5:1 hybrid ratio. The model is pre-trained on 27 trillion tokens with Multi-Token Prediction (MTP), employing a native 32k context length and subsequently extended to 256k. To efficiently scale post-training compute, MiMo-V2-Flash introduces a novel Multi-Teacher On-Policy Distillation (MOPD) paradigm. In this framework, domain-specialized teachers (e.g., trained via large-scale reinforcement learning) provide dense and token-level reward, enabling the student model to perfectly master teacher expertise. MiMo-V2-Flash rivals top-tier open-weight models such as DeepSeek-V3.2 and Kimi-K2, despite using only 1/2 and 1/3 of their total parameters, respectively. During inference, by repurposing MTP as a draft model for speculative decoding, MiMo-V2-Flash achieves up to 3.6 acceptance length and 2.6x decoding speedup with three MTP layers. We open-source both the model weights and the three-layer MTP weights to foster open research and community collaboration.

cs.CL↗
arXiv2025

Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges

Predicting single-cell perturbation outcomes directly advances gene function analysis and facilitates drug candidate selection, making it a key driver of both basic and translational biomedical research. However, a major bottleneck in this task is the unpaired nature of single-cell data, as the same cell cannot be observed both before and after perturbation due to the destructive nature of sequencing. Although some neural generative transport models attempt to tackle unpaired single-cell perturbation data, they either lack explicit conditioning or depend on prior spaces for indirect distribution alignment, limiting precise perturbation modeling. In this work, we approximate Schrödinger Bridge (SB), which defines stochastic dynamic mappings recovering the entropy-regularized optimal transport (OT), to directly align the distributions of control and perturbed single-cell populations across different perturbation conditions. Unlike prior SB approximations that rely on bidirectional modeling to infer optimal source-target sample coupling, we leverage Minibatch-OT based pairing to avoid such bidirectional inference and the associated ill-posedness of defining the reverse process. This pairing directly guides bridge learning, yielding a scalable approximation to the SB. We approximate two SB models, one modeling discrete gene activation states and the other continuous expression distributions. Joint training enables accurate perturbation modeling and captures single-cell heterogeneity. Experiments on public genetic and drug perturbation datasets show that our model effectively captures heterogeneous single-cell responses and achieves state-of-the-art performance.

cs.LG↗
arXiv2025

GuardReasoner: Towards Reasoning-based LLM Safeguards

As LLMs increasingly impact safety-critical applications, ensuring their safety using guardrails remains a key challenge. This paper proposes GuardReasoner, a new safeguard for LLMs, by guiding the guard model to learn to reason. Concretely, we first create the GuardReasonerTrain dataset, which consists of 127K samples with 460K detailed reasoning steps. Then, we introduce reasoning SFT to unlock the reasoning capability of guard models. In addition, we present hard sample DPO to further strengthen their reasoning ability. In this manner, GuardReasoner achieves better performance, explainability, and generalizability. Extensive experiments and analyses on 13 benchmarks of 3 guardrail tasks demonstrate its superiority. Remarkably, GuardReasoner 8B surpasses GPT-4o+CoT by 5.74% and LLaMA Guard 3 8B by 20.84% F1 score on average. We release the training data, code, and models with different scales (1B, 3B, 8B) of GuardReasoner : https://github.com/yueliu1999/GuardReasoner/.

cs.CR↗
arXiv2025

Rethinking Medical Anomaly Detection in Brain MRI: An Image Quality Assessment Perspective

Reconstruction-based methods, particularly those leveraging autoencoders, have been widely adopted for anomaly detection task in brain MRI. Unlike most existing works try to improve the task accuracy through architectural or algorithmic innovations, we tackle this task from image quality assessment (IQA) perspective, an under-explored direction in the field. Due to the limitations of conventional metrics such as l1 in capturing the nuanced differences in reconstructed images for medical anomaly detection, we propose fusion quality, a novel metric that wisely integrates the structure-level sensitivity of Structural Similarity Index Measure (SSIM) with the pixel-level precision of l1. The metric offers a more comprehensive assessment of reconstruction quality, considering intensity (subtractive property of l1 and divisive property of SSIM), contrast, and structural similarity. Furthermore, the proposed metric makes subtle regional variations more impactful in the final assessment. Thus, considering the inherent divisive properties of SSIM, we design an average intensity ratio (AIR)-based data transformation that amplifies the divisive discrepancies between normal and abnormal regions, thereby enhancing anomaly detection. By fusing the aforementioned two components, we devise the IQA approach. Experimental results on two distinct brain MRI datasets show that our IQA approach significantly enhances medical anomaly detection performance when integrated with state-of-the-art baselines.

eess.IV↗