arXiv subjects

Jun Xia

Publications and source records attributed to Jun Xia.

At least 19 recordsLinked to original sources

arXiv2026

MM-Spectrum: Multimodal Multi-spectral Molecular Structural Elucidation with a Stable MoE Framework

Inferring molecular structures from multimodal spectroscopic measurements requires integrating complementary yet highly heterogeneous signals. However, the common paradigm of directly concatenating multispectral sequences can exhibit anomalous performance degradation, primarily due to pronounced heterogeneity and the resulting multimodal imbalance across modalities. As a remedy, we propose MM-Spectrum, a sparse Mixture-of-Experts framework tailored for multimodal multispectral spectra-to-structure elucidation. To better match the information characteristics under multispectral imbalance, MM-Spectrum introduces an explicit modality-aware routing mechanism that exposes spectral identity to the router in addition to token content representations. Moreover, it incorporates shared and interaction experts, together with heterogeneous expert capacities, to extract multispectral modality-unique and cross-modal synergistic information while suppressing noise-induced interference. Across full-modality, bimodal, and missing-modality settings on molecular structural elucidation, MM-Spectrum achieves consistent and substantial improvements, supported by ablation studies and interpretability analyses.

cs.LG↗

arXiv2026

Unlocking Multimodal Protein Language Models at Inference Time

Multimodal protein language models (pLMs) learn joint protein sequence-structure distributions, and their generation performance should also depend critically on inference-time sampling strategies. Yet prior work has focused more on model training than on how inference-time strategies behave. In this paper, we establish a three-stage investigation framework to empirically study the inference design space of multimodal pLMs across three representative pLMs and four fundamental tasks. We evaluate vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search on multimodal pLMs, corresponding to controls over sampling distributions, per-step logits, and parallel trajectories. Throughout the complementary advancements centered on exploration-exploitation trade-off, we (1) reveal the suboptimality of default inference protocols and identify task-oriented sampling preferences; (2) observe substantial quantitative gains across tasks, consistently boosting the upper bound performance of multimodal pLMs without updating model parameters; (3) derive conclusions about base models that differ from prior consensus.

cs.CE↗

arXiv2026

Towards Reasonable Molecular Structure Elucidation from Infrared Spectroscopy with Chemical Feedback

Infrared (IR) spectra provide characteristic signals of molecular structure, which are often interpreted by experts via functional-group identification or library matching, making the process time-consuming and ambiguous. Recent machine learning methods have made progress in molecular structure elucidation using molecular formulas and IR spectra. However, these models often infer unreasonable candidate molecular structures, including top-ranked predictions. More specifically, the molecular formula implied by a candidate structure often fails to match the input molecular formula, and the candidate's theoretical IR spectrum is often inconsistent with the observed IR spectrum. To address these issues, we propose Formula- and IR-Matched Preference Optimization (FIRMPO), a general and plug-and-play chemical feedback-driven preference optimization framework for molecular structure elucidation. FIRMPO incorporates chemical feedback as preference signals based on exact molecular formula matching and IR spectral consistency to guide reasonable structure predictions. Unlike generic preference optimization methods, FIRMPO is tailored to molecular structure elucidation while remaining model-agnostic, enabling it to be readily integrated with different structure prediction models in this class. This encourages models to prioritize structures that satisfy the chemical feedback, leading to a substantial improvement in the accuracy of top-ranked predictions. Extensive experiments on three widely used IR datasets show that FIRMPO significantly improves molecular structure elucidation accuracy over existing baselines.

cs.LG↗

arXiv2026

FinFraudBench: A Heterogeneous Graph Benchmark for Financial Fraud Detection

The increasing complexity of digital financial systems has reshaped financial fraud detection from isolated transaction classification into relational risk reasoning over interconnected financial entities. This shift has motivated graph-based fraud detection, where models identify fraudulent nodes by exploiting dependencies among customers, cards, merchants, categories, and locations. However, despite rapid progress in graph-based methods, existing public benchmarks remain misaligned with real-world financial systems in two important aspects. First, they often simplify financial ecosystems into homogeneous or single-node-type multi-relational graphs, failing to preserve the multi-entity and multi-relational nature of financial data. Second, they rarely provide large-scale heterogeneous financial graph datasets with realistic operating conditions such as extreme class imbalance and limited label availability, making it difficult to assess the practical effectiveness of current methods. To address these gaps, we present FinFraudBench, a heterogeneous graph benchmark for financial fraud detection. FinFraudBench contains two heterogeneous graph datasets (CreditCard-Fraud and BankTrans-Fraud) with up to 8.99M nodes and 89.23M directed typed edges. Each dataset preserves six financial entity types, fourteen directed edge types, and natural fraud rates that mirror deployment constraints. With these datasets, we establish a standardized evaluation protocol covering both ranking and imbalance-sensitive classification metrics, and evaluate representative baselines. Extensive experiments yield empirical insights into current methods' limitations and suggest promising avenues for future research. FinFraudBench is available at https://anonymous.4open.science/r/FinFraudBench-B002.

cs.LG↗

arXiv2026

Simulation-to-real transfer learning for infrared spectroscopic chemical sensing and analysis from molecules to complex samples

Infrared (IR) spectroscopy is widely used for chemical sensing, but extracting reliable chemical information from spectra remains challenging. Conventional interpretation is labor-intensive, relies on prior knowledge and reference spectra, and is difficult to scale, whereas most machine-learning methods are tailored to individual tasks or datasets, require large labeled training sets, and transfer poorly across analytical objectives and experimental datasets. Here we introduce UltraIR, a foundation model for IR spectroscopy with more than 100 million parameters that enables simulation-to-real transfer learning for chemical sensing and analysis from molecules to complex samples. UltraIR is pretrained on approximately 60 million simulated IR spectra using spectral reconstruction, molecular fingerprint similarity alignment, and functional-group prediction, then adapted to downstream objectives with task-specific labels or targets. Across functional-group prediction, molecular structure elucidation, physicochemical property prediction, mixture-component identification and quantification, bacterial classification, medicinal-herb geographic origin traceability and constituent quantification, microplastics classification, and soil property prediction, UltraIR outperforms conventional machine-learning and task-specific deep-learning baselines. It performs strongly with limited labeled experimental spectra and in zero-shot inference for the same analytical task across Fourier-transform infrared spectrometers and laboratories, providing a route to adaptable, data-efficient chemical sensing from complex real-world samples.

cs.LG↗

arXiv2026

SpecCal: Ambiguity-Aware Candidate Calibration for Infrared Spectrum-Based Molecular Structure Reconstruction

Inferring molecular structures from infrared (IR) spectra is a fundamental yet challenging problem. A key difficulty is that an IR spectrum provides limited structural information: different molecules may share similar functional groups and local vibrational patterns, leading to highly similar spectral responses. Thus, even when an observed spectrum has a unique underlying structure, reconstructing it from the spectrum remains ambiguous. Existing IR-to-molecule models usually generate a ranked set of candidate molecules, but this set is largely determined by the model's learned generation preference and may not fully capture the structures that best satisfy the observed spectral constraints. To address this limitation, we propose SpecCal, a training-free candidate calibration framework for IR-to-molecule prediction. SpecCal operates on the candidate outputs of existing base models and improves the prediction set by re-ranking current candidates while introducing additional structurally plausible alternatives guided by spectral consistency. The framework is plug-and-play and model-agnostic, requiring no parameter updates for integration with diverse base models. Experiments on multiple benchmarks show that SpecCal consistently improves top-k reconstruction at both SMILES and scaffold levels across different base models. Further analyses demonstrate that calibrating candidate sets under spectral ambiguity provides a practical way to improve molecular reconstruction from IR spectra. The code is available at: https://anonymous.4open.science/r/SpecCal-B18A.

cs.AI↗

arXiv2026

Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

Nuclear Magnetic Resonance (NMR) spectroscopy is the gold standard for molecular structure elucidation, yet interpreting complex spectra for unknown molecules remains a bottleneck reliant on human expertise. While artificial intelligence has advanced this field, current methods face a critical trade-off: database retrieval cannot identify novel scaffolds, while de novo molecular structure elucidation models operate as black boxes, lacking the atom-level interpretability required for rigorous scientific validation. Here, we present NMRAgent, an evidential reasoning agent powered by large language models (LLMs) that bridges this gap by integrating specialized spectral analysis tools with chemical knowledge graphs. Unlike previous approaches, NMRAgent mimics the deductive reasoning of human experts: it takes experimental NMR spectra and molecular formula as input, plans the elucidation process, proposes candidate structures, verifies peak-atom consistency, and refines misaligned substructure through formula-aware fragment optimization. Enabled by its evidential reasoning, NMRAgent outperforms state-of-the-art methods, improving top-1 accuracy by 46.5% and Tanimoto similarity by 0.502 on a scaffold-split benchmark with novel scaffolds in the test set. Besides, we demonstrate the agent's practical utility by elucidating the structures of two previously unknown natural products isolated from Hydrangea davidii and Vitex trifolia, and by correcting structural misassignments in established literature. By combining high-accuracy prediction with transparent and evidence-based reasoning, NMRAgent establishes a new paradigm for interpretable AI in analytical chemistry.

cs.LG↗

arXiv2026

HG-Bench: A Benchmark for Multi-Page Handwritten Answer-Region Grounding in Automated Homework Assessment

Automated homework assessment depends not only on recognizing student answers, but also on accurately locating where each answer and each intermediate reasoning step appears in noisy, multi-page handwritten work. This paper addresses the missing evaluation setting of page-aware, two-level answer-region grounding: given a sequence of homework page images, a model must localize complete answer regions and their ordered step-level subregions. We introduce HG-Bench, a benchmark of 500 human-annotated K-12 homework samples curated from a 1,489,278-image source pool, with question-level and step-level boxes linked by a hierarchical containment constraint. HG-Bench is paired with a page-aware evaluation protocol that separately measures complete-answer localization (FA) and step-level decomposition (FSm), revealing whether models truly ground the spatial structure of student reasoning rather than merely parse visible text. Across frontier closed-source APIs and competitive open-weight VLMs, no zero-shot system exceeds 55.22% on FA or 48.22% on FSm, while a GLM-4.6V 9B reference model fine-tuned on ~10k in-domain examples reaches 74.97/72.26. These results identify step-level handwritten grounding as a concrete capability gap and provide a reproducible benchmark, evaluation protocol, and trained reference point for future work on automated homework assessment.

cs.CV↗

arXiv2026

Attention-Spectrum Regularization for Replay-Free Continual Multimodal LLMs

Multimodal large language models (MLLMs) are increasingly required to adapt to non-stationary streams of visual domains, question types, and user instructions, yet continual fine-tuning often causes severe forgetting of previously acquired multimodal skills. Existing continual vision-language methods mainly preserve outputs, replay data or pseudo-data, regularize embedding geometry, or allocate task-specific parameters, but they provide limited control over how internal cross-modal attention patterns supporting old skills drift during adaptation. We propose Attention-Spectrum Regularization (ASR), a replay-free continual learning framework that preserves skill-conditioned structures of cross-modal attention. ASR treats cross-attention maps as two-dimensional signals, summarizes their scale and directional properties into compact spectral statistics, and stores only skill-wise prototype distributions instead of replaying past image-question pairs, generated pseudo-examples, or old-stage teacher snapshots. In later stages, a phase-invariant spectral regularizer constrains harmful drift of these prototypes while allowing instance-level attention to adapt to new tasks. We provide theoretical analysis showing that skill-conditioned spectral drift controls forgetting under a spectral sufficiency assumption, and that Fourier power spectra are stable to spatial translations and bounded perturbations. Experiments on continual VQA and multimodal instruction-tuning benchmarks, including VQA v2, VQACL, CLT-VQA, CoIN, and UCIT, show that ASR consistently improves final performance and reduces forgetting over strong replay-, regularization-, and adapter-based baselines. Preserving skill-level attention structure is an effective and lightweight mechanism for continual MLLMs. Code is available at https://github.com/Creative-zcx/attention-spectrum-replay

cs.CV↗

arXiv2026

A large-scale foundation model enables simulation-to-real adaptation for nuclear magnetic resonance-based molecular structure analysis

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for molecular structure analysis, and spectral artificial intelligence offers great potential for its rapid and automated interpretation. However, the scarcity of experimental NMR datasets has constrained deep learning in this domain to narrow, task-specific applications that lack broad generalization. Here, we introduce UltraNMR, a large-scale foundation model for NMR that leverages the intrinsic properties of NMR spectra to learn generalizable spectral representations. We collected 158 million paired simulated $^{1}$H and $^{13}$C NMR spectra to train UltraNMR, employing multiple domain-specific pre-training objectives. UltraNMR captures both intra-spectral and inter-spectral dependencies, enabling seamless simulation-to-real adaptation. We demonstrate that adapting UltraNMR to a range of molecular structure analysis tasks on experimental NMR spectra consistently yields state-of-the-art performance and clearly outperforms UltraNMR variants trained directly on downstream data without simulation pre-training. We also construct a large-scale NMR spectral vector library by encoding simulated NMR spectra using UltraNMR, covering 94 million unique molecules and enabling effective structure-aware retrieval. In real-world applications, UltraNMR facilitates the structural elucidation of two previously unknown natural products from Chinese herbal medicines recorded in the Chinese Pharmacopoeia. These results suggest that large-scale simulation pre-training can effectively bridge the simulation-to-real gap, enabling robust and generalizable molecular structure analysis of real-world NMR spectra.

physics.chem-ph↗

arXiv2026

FastMix: Fast Data Mixture Optimization via Gradient Descent

While large and diverse datasets have driven recent advances in large models, identifying the optimal data mixture for pre-training and post-training remains a significant open problem. We address this challenge with FASTMIX, a novel framework that automates data mixture discovery while training only a single proxy model. Instead of relying on predefined heuristics or resource-intensive simulations, FASTMIX jointly optimizes mixture coefficients and model parameters, substantially improving efficiency and scalability over prior approaches. At the core of FASTMIX is a reformulation of mixture selection as a bilevel optimization problem. Under this reformulation, we show that optimizing mixture ratios is mathematically equivalent to assigning per-source loss weights under uniform source sampling. This embeds the mixture coefficients directly into the differentiable iterative optimization objective, enabling efficient, gradient-based optimization of both mixture and model. To solve the optimization problem, FASTMIX implements an approximate iterative optimization procedure, alternating between (i) updating model parameters on data sampled according to current mixture ratios (inner loop) and (ii) updating mixture ratios based on validation feedback (outer loop). Across pre- and post-training, FASTMIX outperforms baselines while drastically reducing search cost. Code (https://github.com/hrtan/fastmix)

cs.LG↗

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

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

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

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

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↗