Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage, while recent cross-modal representation learning frameworks often encounter modality misalignment, resulting in suboptimal retrieval accuracy and generalization. To address these limitations, we propose GLMR, a Generative Language Model-based Retrieval framework that mitigates the cross-modal misalignment through a two-stage process. In the pre-retrieval stage, a contrastive learning-based model identifies top candidate molecules as contextual priors for the input mass spectrum. In the generative retrieval stage, these candidate molecules are integrated with the input mass spectrum to guide a generative model in producing refined molecular structures, which are then used to re-rank the candidates based on molecular similarity. Experiments on both MassSpecGym and the proposed MassRET-20k dataset demonstrate that GLMR significantly outperforms existing methods, achieving over 40% improvement in top-1 accuracy and exhibiting strong generalizability.

Yuhang Zhang, Keyan Ding, Peilin Chen, Han Liu, Can Lin, Ruixi Chen, Shiqi Wang, Qi Song. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Kehua Feng, Keyan Ding, Tan Hongzhi, Kede Ma, Zhihua Wang, Shuangquan Guo, Cheng Yuzhou, Ge Sun, Guozhou Zheng, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Yuhao Wang, Keyan Ding, Kehua Feng, Zeyuan Wang, Ming Qin, Xiaotong Li, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Retrieval-augmented generation (RAG) systems often struggle with narrative-rich documents and event-centric reasoning, particularly when synthesizing information across multiple sources. We present EventRAG, a novel framework that enhances text generation through structured event representations. We first construct an Event Knowledge Graph by extracting events and merging semantically equivalent nodes across documents, while expanding under-connected relationships. We then employ an iterative retrieval and inference strategy that explicitly captures temporal dependencies and logical relationships across events. Experiments on UltraDomain and MultiHopRAG benchmarks show EventRAG’s superiority over baseline RAG systems, with substantial gains in generation effectiveness, logical consistency, and multi-hop reasoning accuracy. Our work advances RAG systems by integrating structured event semantics with iterative inference, particularly benefiting scenarios requiring temporal and logical reasoning across documents.

Xiang Zhuang, Bin Wu, Jiyu Cui, Kehua Feng, Xiaotong Li, Huabin Xing, Keyan Ding, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Evaluating the response quality of large language models (LLMs) for open-ended questions poses a significant challenge, especially given the subjectivity and multi-dimensionality of "quality" in natural language generation. Existing LLM evaluators often neglect that different scenarios require distinct evaluation criteria. In this work, we propose **SaMer**, a scenario-aware multi-dimensional evaluator designed to provide both overall and fine-grained assessments of LLM-generated responses. Unlike fixed-dimension evaluation approaches, SaMer adapts to different scenarios by automatically identifying and prioritizing relevant evaluation dimensions tailored to the given query. To achieve this, we construct a large-scale fine-grained preference dataset spanning multiple real-world scenarios, each with distinct evaluation dimensions. We then leverage a text embedding model combined with three specialized heads to predict the appropriate evaluation dimensions and corresponding scores, as well as the respective weights that contribute to the overall score. The resulting model offers fine-grained and interpretable evaluations and shows robust adaptability across diverse scenarios. Extensive experiments on eight single rating and pairwise comparison datasets demonstrate that SaMer outperforms existing baselines in a variety of evaluation tasks, showcasing its robustness, versatility, and generalizability.

Parameter-efficient fine-tuning (PEFT) methods, such as LoRA, have enabled the efficient adaptation of large language models (LLMs) by updating only a small subset of parameters. However, their robustness under out-of-distribution (OOD) conditions remains insufficiently studied. In this paper, we identify the limitations of conventional LoRA in handling distributional shifts and propose $\textbf{HiMoLE}$($\textbf{Hi}$erarchical $\textbf{M}$ixture of $\textbf{L}$oRA $\textbf{E}$xperts), a new framework designed to improve OOD generalization. HiMoLE integrates hierarchical expert modules and hierarchical routing strategies into the LoRA architecture and introduces a two-phase training procedure enhanced by a diversity-driven loss. This design mitigates negative transfer and promotes effective knowledge adaptation across diverse data distributions. We evaluate HiMoLE on three representative tasks in natural language processing. Experimental results evidence that HiMoLE consistently outperforms existing LoRA-based approaches, significantly reducing performance degradation on OOD data while improving in-distribution performance. Our work bridges the gap between parameter efficiency and distributional robustness, advancing the practical deployment of LLMs in real-world applications.

Protein solubility is a critical determinant of biologic candidates' developability, stability, and therapeutic efficacy. However, accurate solubility prediction remains a central challenge in computational protein engineering due to the inherent complexity within protein sequences. In this work, we propose a multimodal prompt learning framework, called MPSol, for protein solubility prediction that integrates complementary representations derived from primary sequences, structural proxies, and textual descriptions generated by large language models (LLMs). MPSol is built upon a unified multimodal backbone with a dedicated cross-modal fusion module that captures fine-grained interactions across modalities. In addition, we design label-aware prompts that encode solubility-specific semantic cues associated with each class. These prompts provide semantic supervision, guiding the alignment of fused protein representations to promote semantic consistency. Extensive experiments demonstrate that MPSol achieves state-of-the-art performance, reaching an accuracy of 0.815, AUC of 0.867 and MCC of 0.642 on the standard PDBSol test set, and generalizes well to the external out-of-distribution test dataset with an accuracy of 0.632, AUC of 0.653 and MCC of 0.332. These results underscore the potential of prompt-driven multimodal learning for interpretable and effective protein property prediction.

Zeyuan Wang, Qiang Zhang, Keyan Ding, Ming Qin, Xiang Zhuang, Xiaotong Li, Huajun Chen. Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2024.

Directed evolution, a cornerstone of protein optimization, is to harness natural mutational processes to enhance protein functionality. Existing Machine Learning-assisted Directed Evolution (MLDE) methodologies typically rely on data-driven strategies and often overlook the profound domain knowledge in biochemical fields. In this paper, we introduce a novel Knowledge-aware Reinforced Language Model (KnowRLM) for MLDE. An Amino Acid Knowledge Graph (AAKG) is constructed to represent the intricate biochemical relationships among amino acids. We further propose a Protein Language Model (PLM)-based policy network that iteratively samples mutants through preferential random walks on the AAKG using a dynamic sliding window mechanism. The novel mutants are actively sampled to fine-tune a fitness predictor as the reward model, providing feedback to the knowledge-aware policy. Finally, we optimize the whole system in an active learning approach that mimics biological settings in practice.KnowRLM stands out for its ability to utilize contextual amino acid information from knowledge graphs, thus attaining advantages from both statistical patterns of protein sequences and biochemical properties of amino acids.Extensive experiments demonstrate the superior performance of KnowRLM in more efficiently identifying high-fitness mutants compared to existing methods.

Protein optimization is a fundamental biological task aimed at enhancing theperformance of proteins by modifying their sequences. Computational methodsprimarily rely on evolutionary information (EI) encoded by protein languagemodels (PLMs) to predict fitness landscape for optimization. However, thesemethods suffer from a few limitations. (1) Evolutionary processes involve thesimultaneous consideration of multiple functional properties, often overshadowingthe specific property of interest. (2) Measurements of these properties tend to betailored to experimental conditions, leading to reduced generalizability of trainedmodels to novel proteins. To address these limitations, we introduce DenoisingProtein Language Models (DePLM), a novel approach that refines the evolutionaryinformation embodied in PLMs for improved protein optimization. Specifically, weconceptualize EI as comprising both property-relevant and irrelevant information,with the latter acting as “noise” for the optimization task at hand. Our approachinvolves denoising this EI in PLMs through a diffusion process conducted in therank space of property values, thereby enhancing model generalization and ensuringdataset-agnostic learning. Extensive experimental results have demonstrated thatDePLM not only surpasses the state-of-the-art in mutation effect prediction butalso exhibits strong generalization capabilities for novel proteins.

Objective Image Quality Assessment (IQA) aims to design computational models that can automatically predict the perceived quality of images. The state-of-the-art full-reference IQA metric – Deep Image Structure and Texture Similarity (DISTS), neglects the fact that natural images often consist of local structure and texture, and requires supervised training on the annotated dataset. In this article, we introduce multiple adaptive strategies to improve DISTS, resulting in an opinion-unaware IQA metric, named A-DISTS. Specifically, A-DISTS first uses the dispersion index as a statistical feature to adaptively localize structure and texture regions at different scales. Second, it adaptively assigns the spatial weights between local structure and texture similarity measurements according to the estimated structure or texture probability maps. Finally, it calculates the entropy of image representation to adaptively weigh the importance of each feature map. As a result, A-DISTS is adapted to local image content and does not require any training. The experimental results demonstrated that the proposed metric correlates well with human rating in the standard and algorithm-dependent IQA databases, and exhibits competitive performance in the optimization tasks of single image super-resolution, motion deblurring, and multi-distortion removal.

Deep learning-based methods have significantly influenced the blind image quality assessment (BIQA) field, however, these methods often require training using large amounts of human rating data. In contrast, traditional knowledge-based methods are cost-effective for training but face challenges in effectively extracting features aligned with human visual perception. To bridge these gaps, we propose integrating deep features from pre-trained visual models with a statistical analysis model into a Multi-scale Deep Feature Statistics (MDFS) model for achieving opinion-unaware BIQA (OU-BIQA), thereby eliminating the reliance on human rating data and significantly improving training efficiency. Specifically, we extract patch-wise multi-scale features from pre-trained vision models, which are subsequently fitted into a multivariate Gaussian (MVG) model. The final quality score is determined by quantifying the distance between the MVG model derived from the test image and the benchmark MVG model derived from the high-quality image set. A comprehensive series of experiments conducted on various datasets show that our proposed model exhibits superior consistency with human visual perception compared to state-of-the-art BIQA models. Furthermore, it shows improved generalizability across diverse target-specific BIQA tasks. Our code is available at:https://github.com/eezkni/MDFS

Opinion-Unaware Blind Image Quality Assessment (OU-BIQA) models aim to predict image quality without training on reference images and subjective quality scores. Thereinto, image statistical comparison is a classic paradigm, while the performance is limited by the representation ability of visual descriptors. Deep features as visual descriptors have advanced IQA in recent research, but they are discovered to be highly texture-biased and lack shape-bias. On this basis, we find out that image shape and texture cues respond differently toward distortions, and the absence of either one results in an incomplete image representation. Therefore, to formulate a well-rounded statistical description for images, we utilize the shape-biased and texture-biased deep features produced by Deep Neural Networks (DNNs) simultaneously. More specifically, we design a Shape-Texture Adaptive Fusion (STAF) module to merge shape and texture information, based on which we formulate quality-relevant image statistics. The perceptual quality is quantified by the variant Mahalanobis distance between the inner and outer Deep Shape-Texture Statistics (DSTS), wherein the inner and outer statistics respectively describe the quality fingerprints of the distorted image and natural images. The proposed DSTS delicately utilizes shape-texture statistical relations between different data scales in the deep domain and achieves state-of-the-art (SOTA) quality prediction performance on images with artificial and authentic distortions.

Directed evolution is a widely-used strategy of protein engineering to improve protein function via mimicking natural mutation and selection. Machine learning-assisted directed evolution (MLDE) approaches aim to learn a fitness predictor, thereby efficiently searching for optimal mutants within the vast combinatorial mutation space. Since annotating mutants is both costly and labor-intensive, how to efficiently sample and utilize informative protein mutants to train the predictor is a critical problem in MLDE. Previous MLDE works just simply utilized pre-trained protein language models (PPLMs) for sampling without tailoring to the specific target protein of interest, which has not fully exploited the potential of PPLMs. In this work, we propose a novel method, the Actively-Finetuned Protein language model for Directed Evolution(AFP-DE), which leverages PPLMs to actively sample and fine-tune themselves, continuously improving the model’s sampling and overall performance through iterations, to achieve efficient directed protein evolution. Extensive experiments have shown the effectiveness of our method in generating optimal mutants with minimal annotation effort, outperforming previous works even with fewer annotated mutants, making it budget-friendly for biological experiments.

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of subgraphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.

Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for learning molecular representations that exhibit invariance and robustness against distribution shifts. Specifically, we propose a strategy called ``first-encoding-then-separation'' to identify invariant molecule features in the latent space, which deviates from conventional practices. Prior to the separation step, we introduce a residual vector quantization module that mitigates the over-fitting to training data distributions while preserving the expressivity of encoders. Furthermore, we design a task-agnostic self-supervised learning objective to encourage precise invariance identification, which enables our method widely applicable to a variety of tasks, such as regression and multi-label classification. Extensive experiments on 18 real-world molecular datasets demonstrate that our model achieves stronger generalization against state-of-the-art baselines in the presence of various distribution shifts. Our code is available at https://github.com/HICAI-ZJU/iMoLD.

Objective measures of image quality generally operate by comparing pixels of a "degraded" image to those of the original. Relative to human observers, these measures are overly sensitive to resampling of texture regions (e.g., replacing one patch of grass with another). Here, we develop the first full-reference image quality model with explicit tolerance to texture resampling. Using a convolutional neural network, we construct an injective and differentiable function that transforms images to multi-scale overcomplete representations. We demonstrate empirically that the spatial averages of the feature maps in this representation capture texture appearance, in that they provide a set of sufficient statistical constraints to synthesize a wide variety of texture patterns. We then describe an image quality method that combines correlations of these spatial averages ("texture similarity") with correlations of the feature maps ("structure similarity"). The parameters of the proposed measure are jointly optimized to match human ratings of image quality, while minimizing the reported distances between subimages cropped from the same texture images. Experiments show that the optimized method explains human perceptual scores, both on conventional image quality databases, as well as on texture databases. The measure also offers competitive performance on related tasks such as texture classification and retrieval. Finally, we show that our method is relatively insensitive to geometric transformations (e.g., translation and dilation), without use of any specialized training or data augmentation. Code is available at https://github.com/dingkeyan93/DISTS.

The latest advances in full-reference image quality assessment (IQA) involve unifying structure and texture similarity based on deep representations. The resulting Deep Image Structure and Texture Similarity (DISTS) metric, however, makes rather global quality measurements, ignoring the fact that natural photographic images are locally structured and textured across space and scale. In this paper, we describe a locally adaptive structure and texture similarity index for full-reference IQA, which we term A-DISTS. Specifically, we rely on a single statistical feature, namely the dispersion index, to localize texture regions at different scales. The estimated probability (of one patch being texture) is in turn used to adaptively pool local structure and texture measurements. The resulting A-DISTS is adapted to local image content, and is free of expensive human perceptual scores for supervised training. We demonstrate the advantages of A-DISTS in terms of correlation with human data on ten IQA databases and optimization of single image super-resolution methods.

The goal of research in automatic image popularity assessment (IPA) is to develop computational models that can accurately predict the potential of a social image to go viral on the Internet. Here, we aim to single out the contribution of visual content to image popularity, \ie, intrinsic image popularity. Specifically, we first describe a probabilistic method to generate massive popularity-discriminable image pairs, based on which the first large-scale image database for intrinsic IPA (I$^2$PA) is established. We then develop computational models for I$^2$PA based on deep neural networks, optimizing for ranking consistency with millions of popularity-discriminable image pairs. Experiments on Instagram and other social platforms demonstrate that the optimized model performs favorably against existing methods, exhibits reasonable generalizability on different databases, and even surpasses human-level performance on Instagram. In addition, we conduct a psychophysical experiment to analyze various aspects of human behavior in I$^2$PA.

Social media popularity prediction (SMPD) aims to predict the popularity of the post shared on online social media platforms. This task is crucial for content providers and consumers in a wide range of real-world applications, including multimedia advertising, recommendation system and trend analysis. In this paper, we propose to fuse features from multiple sources by deep neural networks (DNNs) for popularity prediction. Specifically, high-level image and text features are extracted by the advanced pretrained DNN, and numerical features are captured from the metadata of the posts. All of the features are concatenated and fed into a regressor with multiple dense layers. Experiments have demonstrated the effectiveness of the proposed model on the ACM Multimedia Challenge SMPD2019 dataset. We also verify the importance of each feature via univariate test and ablation study, and provide the insights of feature combination for social media popularity prediction.