Ling Luo

Ling Luo, Chih-Hsuan Wei, Po-Ting Lai et al.

The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or identifier by a text-mining algorithm. Existing methods typically rely on heuristic rules based on gene and species co-occurrence in the article, but their accuracy is suboptimal. We therefore developed a high-performance method, using a novel deep learning-based framework, to classify whether there is a relation between a gene and a species. Instead of the traditional binary classification framework in which all possible pairs of genes and species in the same article are evaluated, we treat the problem as a sequence-labeling task such that only a fraction of the pairs needs to be considered. Our benchmarking results show that our approach obtains significantly higher performance compared to that of the rule-based baseline method for the species assignment task (from 65.8% to 81.3% in accuracy). The source code and data for species assignment are freely available at https://github.com/ncbi/SpeciesAssignment.

Po-Ting Lai, Chih-Hsuan Wei, Ling Luo et al.

Biomedical relation extraction (RE) is the task of automatically identifying and characterizing relations between biomedical concepts from free text. RE is a central task in biomedical natural language processing (NLP) research and plays a critical role in many downstream applications, such as literature-based discovery and knowledge graph construction. State-of-the-art methods were used primarily to train machine learning models on individual RE datasets, such as protein-protein interaction and chemical-induced disease relation. Manual dataset annotation, however, is highly expensive and time-consuming, as it requires domain knowledge. Existing RE datasets are usually domain-specific or small, which limits the development of generalized and high-performing RE models. In this work, we present a novel framework for systematically addressing the data heterogeneity of individual datasets and combining them into a large dataset. Based on the framework and dataset, we report on BioREx, a data-centric approach for extracting relations. Our evaluation shows that BioREx achieves significantly higher performance than the benchmark system trained on the individual dataset, setting a new SOTA from 74.4% to 79.6% in F-1 measure on the recently released BioRED corpus. We further demonstrate that the combined dataset can improve performance for five different RE tasks. In addition, we show that on average BioREx compares favorably to current best-performing methods such as transfer learning and multi-task learning. Finally, we demonstrate BioREx's robustness and generalizability in two independent RE tasks not previously seen in training data: drug-drug N-ary combination and document-level gene-disease RE. The integrated dataset and optimized method have been packaged as a stand-alone tool available at https://github.com/ncbi/BioREx.

Ling Luo, Pinaki Nath Chowdhury, Tao Xiang et al.

3D shape modeling is labor-intensive, time-consuming, and requires years of expertise. To facilitate 3D shape modeling, we propose a 3D shape generation network that takes a 3D VR sketch as a condition. We assume that sketches are created by novices without art training and aim to reconstruct geometrically realistic 3D shapes of a given category. To handle potential sketch ambiguity, our method creates multiple 3D shapes that align with the original sketch's structure. We carefully design our method, training the model step-by-step and leveraging multi-modal 3D shape representation to support training with limited training data. To guarantee the realism of generated 3D shapes we leverage the normalizing flow that models the distribution of the latent space of 3D shapes. To encourage the fidelity of the generated 3D shapes to an input sketch, we propose a dedicated loss that we deploy at different stages of the training process. The code is available at https://github.com/Rowl1ng/3Dsketch2shape.

Ling Luo, Yulia Gryaditskaya, Tao Xiang et al.

We study the practical task of fine-grained 3D-VR-sketch-based 3D shape retrieval. This task is of particular interest as 2D sketches were shown to be effective queries for 2D images. However, due to the domain gap, it remains hard to achieve strong performance in 3D shape retrieval from 2D sketches. Recent work demonstrated the advantage of 3D VR sketching on this task. In our work, we focus on the challenge caused by inherent inaccuracies in 3D VR sketches. We observe that retrieval results obtained with a triplet loss with a fixed margin value, commonly used for retrieval tasks, contain many irrelevant shapes and often just one or few with a similar structure to the query. To mitigate this problem, we for the first time draw a connection between adaptive margin values and shape similarities. In particular, we propose to use a triplet loss with an adaptive margin value driven by a "fitting gap", which is the similarity of two shapes under structure-preserving deformations. We also conduct a user study which confirms that this fitting gap is indeed a suitable criterion to evaluate the structural similarity of shapes. Furthermore, we introduce a dataset of 202 VR sketches for 202 3D shapes drawn from memory rather than from observation. The code and data are available at https://github.com/Rowl1ng/Structure-Aware-VR-Sketch-Shape-Retrieval.

Ling Luo, Po-Ting Lai, Chih-Hsuan Wei et al.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

Ling Luo, Chih-Hsuan Wei, Po-Ting Lai et al.

Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction and question answering. Manually labeling training data for the BioNER task is costly, however, due to the significant domain expertise required for accurate annotation. The resulting data scarcity causes current BioNER approaches to be prone to overfitting, to suffer from limited generalizability, and to address a single entity type at a time (e.g., gene or disease). We therefore propose a novel all-in-one (AIO) scheme that uses external data from existing annotated resources to enhance the accuracy and stability of BioNER models. We further present AIONER, a general-purpose BioNER tool based on cutting-edge deep learning and our AIO schema. We evaluate AIONER on 14 BioNER benchmark tasks and show that AIONER is effective, robust, and compares favorably to other state-of-the-art approaches such as multi-task learning. We further demonstrate the practical utility of AIONER in three independent tasks to recognize entity types not previously seen in training data, as well as the advantages of AIONER over existing methods for processing biomedical text at a large scale (e.g., the entire PubMed data).

Ling Luo, Yulia Gryaditskaya, Yongxin Yang et al.

Growing free online 3D shapes collections dictated research on 3D retrieval. Active debate has however been had on (i) what the best input modality is to trigger retrieval, and (ii) the ultimate usage scenario for such retrieval. In this paper, we offer a different perspective towards answering these questions -- we study the use of 3D sketches as an input modality and advocate a VR-scenario where retrieval is conducted. Thus, the ultimate vision is that users can freely retrieve a 3D model by air-doodling in a VR environment. As a first stab at this new 3D VR-sketch to 3D shape retrieval problem, we make four contributions. First, we code a VR utility to collect 3D VR-sketches and conduct retrieval. Second, we collect the first set of $167$ 3D VR-sketches on two shape categories from ModelNet. Third, we propose a novel approach to generate a synthetic dataset of human-like 3D sketches of different abstract levels to train deep networks. At last, we compare the common multi-view and volumetric approaches: We show that, in contrast to 3D shape to 3D shape retrieval, volumetric point-based approaches exhibit superior performance on 3D sketch to 3D shape retrieval due to the sparse and abstract nature of 3D VR-sketches. We believe these contributions will collectively serve as enablers for future attempts at this problem. The VR interface, code and datasets are available at https://tinyurl.com/3DSketch3DV.

Ling Luo, Yulia Gryaditskaya, Yongxin Yang et al.

We present the first fine-grained dataset of 1,497 3D VR sketch and 3D shape pairs of a chair category with large shapes diversity. Our dataset supports the recent trend in the sketch community on fine-grained data analysis, and extends it to an actively developing 3D domain. We argue for the most convenient sketching scenario where the sketch consists of sparse lines and does not require any sketching skills, prior training or time-consuming accurate drawing. We then, for the first time, study the scenario of fine-grained 3D VR sketch to 3D shape retrieval, as a novel VR sketching application and a proving ground to drive out generic insights to inform future research. By experimenting with carefully selected combinations of design factors on this new problem, we draw important conclusions to help follow-on work. We hope our dataset will enable other novel applications, especially those that require a fine-grained angle such as fine-grained 3D shape reconstruction. The dataset is available at tinyurl.com/VRSketch3DV21.

Ling Luo, Jinzhong Ning, Yingwen Zhao et al.

Objective: Most existing fine-tuned biomedical large language models (LLMs) focus on enhancing performance in monolingual biomedical question answering and conversation tasks. To investigate the effectiveness of the fine-tuned LLMs on diverse biomedical NLP tasks in different languages, We present Taiyi, a bilingual fine-tuned LLM for diverse biomedical tasks. Materials and Methods: We first curated a comprehensive collection of 140 existing biomedical text mining datasets (102 English and 38 Chinese datasets) across over 10 task types. Subsequently, a two-stage strategy is proposed for supervised fine-tuning to optimize the model performance across varied tasks. Results: Experimental results on 13 test sets covering named entity recognition, relation extraction, text classification, question answering tasks demonstrate that Taiyi achieves superior performance compared to general LLMs. The case study involving additional biomedical NLP tasks further shows Taiyi's considerable potential for bilingual biomedical multi-tasking. Conclusion: Leveraging rich high-quality biomedical corpora and developing effective fine-tuning strategies can significantly improve the performance of LLMs within the biomedical domain. Taiyi shows the bilingual multi-tasking capability through supervised fine-tuning. However, those tasks such as information extraction that are not generation tasks in nature remain challenging for LLM-based generative approaches, and they still underperform the conventional discriminative approaches of smaller language models.

Feiyang Pan, Tongzhe Zhang, Ling Luo et al.

Optimal execution is a sequential decision-making problem for cost-saving in algorithmic trading. Studies have found that reinforcement learning (RL) can help decide the order-splitting sizes. However, a problem remains unsolved: how to place limit orders at appropriate limit prices? The key challenge lies in the "continuous-discrete duality" of the action space. On the one hand, the continuous action space using percentage changes in prices is preferred for generalization. On the other hand, the trader eventually needs to choose limit prices discretely due to the existence of the tick size, which requires specialization for every single stock with different characteristics (e.g., the liquidity and the price range). So we need continuous control for generalization and discrete control for specialization. To this end, we propose a hybrid RL method to combine the advantages of both of them. We first use a continuous control agent to scope an action subset, then deploy a fine-grained agent to choose a specific limit price. Extensive experiments show that our method has higher sample efficiency and better training stability than existing RL algorithms and significantly outperforms previous learning-based methods for order execution.

Xuan-May Le, Ling Luo, Uwe Aickelin et al.

Multivariate time series classification (MTSC) has attracted significant research attention due to its diverse real-world applications. Recently, exploiting transformers for MTSC has achieved state-of-the-art performance. However, existing methods focus on generic features, providing a comprehensive understanding of data, but they ignore class-specific features crucial for learning the representative characteristics of each class. This leads to poor performance in the case of imbalanced datasets or datasets with similar overall patterns but differing in minor class-specific details. In this paper, we propose a novel Shapelet Transformer (ShapeFormer), which comprises class-specific and generic transformer modules to capture both of these features. In the class-specific module, we introduce the discovery method to extract the discriminative subsequences of each class (i.e. shapelets) from the training set. We then propose a Shapelet Filter to learn the difference features between these shapelets and the input time series. We found that the difference feature for each shapelet contains important class-specific features, as it shows a significant distinction between its class and others. In the generic module, convolution filters are used to extract generic features that contain information to distinguish among all classes. For each module, we employ the transformer encoder to capture the correlation between their features. As a result, the combination of two transformer modules allows our model to exploit the power of both types of features, thereby enhancing the classification performance. Our experiments on 30 UEA MTSC datasets demonstrate that ShapeFormer has achieved the highest accuracy ranking compared to state-of-the-art methods. The code is available at https://github.com/xuanmay2701/shapeformer.

Juntao Li, Haobin Yuan, Ling Luo et al.

Discharge medication recommendation plays a critical role in ensuring treatment continuity, preventing readmission, and improving long-term management for patients with chronic metabolic diseases. This paper present an overview of the CHIP 2025 Shared Task 2 competition, which aimed to develop state-of-the-art approaches for automatically recommending appro-priate discharge medications using real-world Chinese EHR data. For this task, we constructed CDrugRed, a high-quality dataset consisting of 5,894 de-identified hospitalization records from 3,190 patients in China. This task is challenging due to multi-label nature of medication recommendation, het-erogeneous clinical text, and patient-specific variability in treatment plans. A total of 526 teams registered, with 167 and 95 teams submitting valid results to the Phase A and Phase B leaderboards, respectively. The top-performing team achieved the highest overall performance on the final test set, with a Jaccard score of 0.5102, F1 score of 0.6267, demonstrating the potential of advanced large language model (LLM)-based ensemble systems. These re-sults highlight both the promise and remaining challenges of applying LLMs to medication recommendation in Chinese EHRs. The post-evaluation phase remains open at https://tianchi.aliyun.com/competition/entrance/532411/.

Juntao Li, Haobin Yuan, Ling Luo et al.

Intelligent drug recommendation based on Electronic Health Records (EHRs) is critical for improving for improving the quality and efficiency of clinical decision-making. By leveraging large-scale patient data, drug recommendation systems can assist physicians in selecting the most appropriate medications according to a patient's medical history, diagnoses, laboratory results, and comorbidities. However, the advancement of such systems is significantly hampered by the scarcity of publicly available, real-world EHR datasets, particularly in languages other than English. In this work, we present CDrugRed, a first publicly available Chinese drug recommendation dataset focused on discharge medications for metabolic diseases. The dataset includes 5,894 de-identified records from 3,190 patients, containing comprehensive information such as patient demographics, medical history, clinical course, and discharge diagnoses. We assess the utility of CDrugRed by benchmarking several state-of-the-art large language models (LLMs) on the discharge medication recommendation task. Experimental results show that while supervised fine-tuning improves model performance, there remains substantial room for improvement, with the best model achieving the F1 score of 0.5648 and Jaccard score of 0.4477. This result highlights the complexity of the clinical drug recommendation task and establishes CDrugRed as a challenging and valuable resource for developing more robust and accurate drug recommendation systems. The dataset is publicly available to the research community under the data usage agreements at https://github.com/DUTIR-BioNLP/CDrugRed.

Zhijun Wang, Ling Luo, Dinghao Pan et al.

Automated Drug Combination Extraction (DCE) from large-scale biomedical literature is crucial for advancing precision medicine and pharmacological research. However, existing relation extraction methods primarily focus on binary interactions and struggle to model variable-length n-ary drug combinations, where complex compatibility logic and distributed evidence need to be considered. To address these limitations, we propose RexDrug, an end-to-end reasoning-enhanced relation extraction framework for n-ary drug combination extraction based on large language models. RexDrug adopts a two-stage training strategy. First, a multi-agent collaborative mechanism is utilized to automatically generate high-quality expert-like reasoning traces for supervised fine-tuning. Second, reinforcement learning with a multi-dimensional reward function specifically tailored for DCE is applied to further refine reasoning quality and extraction accuracy. Extensive experiments on the DrugComb dataset show that RexDrug consistently outperforms state-of-the-art baselines for n-ary extraction. Additional evaluation on the DDI13 corpus confirms its generalizability to binary drugdrug interaction tasks. Human expert assessment and automatic reasoning metrics further indicates that RexDrug produces coherent medical reasoning while accurately identifying complex therapeutic regimens. These results establish RexDrug as a scalable and reliable solution for complex biomedical relation extraction from unstructured text. The source code and data are available at https://github.com/DUTIR-BioNLP/RexDrug

Tengxiao Lv, Ling Luo, Juntao Li et al.

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual generalization. In this paper, we propose a unified Biomedical Named Entity Recognition (BioNER) framework based on Large Language Models (LLMs). We first reformulate BioNER as a text generation task and design a symbolic tagging strategy to jointly handle both flat and nested entities with explicit boundary annotation. To enhance multilingual and multi-task generalization, we perform bilingual joint fine-tuning across multiple Chinese and English datasets. Additionally, we introduce a contrastive learning-based entity selector that filters incorrect or spurious predictions by leveraging boundary-sensitive positive and negative samples. Experimental results on four benchmark datasets and two unseen corpora show that our method achieves state-of-the-art performance and robust zero-shot generalization across languages. The source codes are freely available at https://github.com/dreamer-tx/LLMNER.

Chao Liu, Ling Luo, Tengxiao Lv et al.

With the rapid development of online medical platforms, consumer health questions (CHQs) are inefficient in diagnosis due to redundant information and frequent non-professional terms. The medical question summary (MQS) task aims to transform CHQs into streamlined doctors' frequently asked questions (FAQs), but existing methods still face challenges such as poor identification of question focus and model hallucination. This paper explores the potential of large language models (LLMs) in the MQS task and finds that direct fine-tuning is prone to focus identification bias and generates unfaithful content. To this end, we propose an optimization framework based on core focus guidance. First, a prompt template is designed to drive the LLMs to extract the core focus from the CHQs that is faithful to the original text. Then, a fine-tuning dataset is constructed in combination with the original CHQ-FAQ pairs to improve the ability to identify the focus of the question. Finally, a multi-dimensional quality evaluation and selection mechanism is proposed to comprehensively improve the quality of the summary from multiple dimensions. We conduct comprehensive experiments on two widely-adopted MQS datasets using three established evaluation metrics. The proposed framework achieves state-of-the-art performance across all measures, demonstrating a significant boost in the model's ability to identify critical focus of questions and a notable mitigation of hallucinations. The source codes are freely available at https://github.com/DUT-LiuChao/FocusMed.

Ling Luo, Dingyu Xue, Xinglong Feng et al.

Modern approaches for semantic segmention usually pay too much attention to the accuracy of the model, and therefore it is strongly recommended to introduce cumbersome backbones, which brings heavy computation burden and memory footprint. To alleviate this problem, we propose an efficient segmentation method based on deep convolutional neural networks (DCNNs) for the task of hair and facial skin segmentation, which achieving remarkable trade-off between speed and performance on three benchmark datasets. As far as we know, the accuracy of skin tones classification is usually unsatisfactory due to the influence of external environmental factors such as illumination and background noise. Therefore, we use the segmentated face to obtain a specific face area, and further exploit the color moment algorithm to extract its color features. Specifically, for a 224 x 224 standard input, using our high-resolution spatial detail information and low-resolution contextual information fusion network (HLNet), we achieve 90.73% Pixel Accuracy on Figaro1k dataset at over 16 FPS in the case of CPU environment. Additional experiments on CamVid dataset further confirm the universality of the proposed model. We further use masked color moment for skin tones grade evaluation and approximate 80% classification accuracy demonstrate the feasibility of the proposed scheme.Code is available at https://github.com/JACKYLUO1991/Face-skin-hair-segmentaiton-and-skin-color-evaluation.

Navid Akhavan Attar, Hesam Asadollahzadeh, Ling Luo et al.

The merit of Conformal Prediction (CP), as a distribution-free framework for uncertainty quantification, depends on generating prediction sets that are efficient, reflected in small average set sizes, while adaptive, meaning they signal uncertainty by varying in size according to input difficulty. A central limitation for deep conformal classifiers is that the nonconformity scores are derived from softmax outputs, which can be unreliable indicators of how certain the model truly is about a given input, sometimes leading to overconfident misclassifications or undue hesitation. In this work, we argue that this unreliability can be inherited by the prediction sets generated by CP, limiting their capacity for adaptiveness. We propose a new approach that leverages information from the pre-softmax logit space, using the Helmholtz Free Energy as a measure of model uncertainty and sample difficulty. By reweighting nonconformity scores with a monotonic transformation of the energy score of each sample, we improve their sensitivity to input difficulty. Our experiments with four state-of-the-art score functions on multiple datasets and deep architectures show that this energy-based enhancement improves the adaptiveness of the prediction sets, leading to a notable increase in both efficiency and adaptiveness compared to baseline nonconformity scores, without introducing any post-hoc complexity.

Yuxiang Lin, Ling Luo, Ying Chen et al.

Spatial transcriptomics (ST) provides high-resolution pathological images and whole-transcriptomic expression profiles at individual spots across whole-slide scales. This setting makes it an ideal data source to develop multimodal foundation models. Although recent studies attempted to fine-tune visual encoders with trainable gene encoders based on spot-level, the absence of a wider slide perspective and spatial intrinsic relationships limits their ability to capture ST-specific insights effectively. Here, we introduce ST-Align, the first foundation model designed for ST that deeply aligns image-gene pairs by incorporating spatial context, effectively bridging pathological imaging with genomic features. We design a novel pretraining framework with a three-target alignment strategy for ST-Align, enabling (1) multi-scale alignment across image-gene pairs, capturing both spot- and niche-level contexts for a comprehensive perspective, and (2) cross-level alignment of multimodal insights, connecting localized cellular characteristics and broader tissue architecture. Additionally, ST-Align employs specialized encoders tailored to distinct ST contexts, followed by an Attention-Based Fusion Network (ABFN) for enhanced multimodal fusion, effectively merging domain-shared knowledge with ST-specific insights from both pathological and genomic data. We pre-trained ST-Align on 1.3 million spot-niche pairs and evaluated its performance through two downstream tasks across six datasets, demonstrating superior zero-shot and few-shot capabilities. ST-Align highlights the potential for reducing the cost of ST and providing valuable insights into the distinction of critical compositions within human tissue.

Ling Luo, Qiangian Bai

Vision-Language Navigation (VLN) is evolving from single-point pathfinding toward the more challenging Multi-Goal VLN. This task requires agents to accurately identify multiple entities while collaboratively reasoning over their spatial-physical constraints and sequential execution order. However, generic Retrieval-Augmented Generation (RAG) paradigms often suffer from spatial hallucinations and planning drift when handling multi-object associations due to the lack of explicit spatial modeling.To address these challenges, we propose RAGNav, a framework that bridges the gap between semantic reasoning and physical structure. The core of RAGNav is a Dual-Basis Memory system, which integrates a low-level topological map for maintaining physical connectivity with a high-level semantic forest for hierarchical environment abstraction. Building on this representation, the framework introduces an anchor-guided conditional retrieval and a topological neighbor score propagation mechanism. This approach facilitates the rapid screening of candidate targets and the elimination of semantic noise, while performing semantic calibration by leveraging the physical associations inherent in the topological neighborhood.This mechanism significantly enhances the capability of inter-target reachability reasoning and the efficiency of sequential planning. Experimental results demonstrate that RAGNav achieves state-of-the-art (SOTA) performance in complex multi-goal navigation tasks.

Ling Luo, Qianqian Bai

Vision-Language Navigation (VLN) aims to empower robots with the ability to perform long-horizon navigation in unfamiliar environments based on complex linguistic instructions. Its success critically hinges on establishing an efficient ``language-understanding -- visual-perception -- embodied-execution'' closed loop. Existing methods often suffer from perceptual distortion and decision drift in complex, long-distance tasks due to the cognitive overload of a single agent. Inspired by distributed cognition theory, this paper proposes MA-CoNav, a Multi-Agent Collaborative Navigation framework. This framework adopts a ``Master-Slave'' hierarchical agent collaboration architecture, decoupling and distributing the perception, planning, execution, and memory functions required for navigation tasks to specialized agents. Specifically, the Master Agent is responsible for global orchestration, while the Subordinate Agent group collaborates through a clear division of labor: an Observation Agent generates environment descriptions, a Planning Agent performs task decomposition and dynamic verification, an Execution Agent handles simultaneous mapping and action, and a Memory Agent manages structured experiences. Furthermore, the framework introduces a ``Local-Global'' dual-stage reflection mechanism to dynamically optimize the entire navigation pipeline. Empirical experiments were conducted using a real-world indoor dataset collected by a Limo Pro robot, with no scene-specific fine-tuning performed on the models throughout the process. The results demonstrate that MA-CoNav comprehensively outperforms existing mainstream VLN methods across multiple metrics.

Chenhao Gu, Ling Luo, Zainab Razia Zaidi et al.

The rise of echo chambers on social media platforms has heightened concerns about polarization and the reinforcement of existing beliefs. Traditional approaches for simulating echo chamber formation have often relied on predefined rules and numerical simulations, which, while insightful, may lack the nuance needed to capture complex, real-world interactions. In this paper, we present a novel framework that leverages large language models (LLMs) as generative agents to simulate echo chamber dynamics within social networks. The novelty of our approach is that it incorporates both opinion updates and network rewiring behaviors driven by LLMs, allowing for a context-aware and semantically rich simulation of social interactions. Additionally, we utilize real-world Twitter (now X) data to benchmark the LLM-based simulation against actual social media behaviors, providing insights into the accuracy and realism of the generated opinion trends. Our results demonstrate the efficacy of LLMs in modeling echo chamber formation, capturing both structural and semantic dimensions of opinion clustering. %This work contributes to a deeper understanding of social influence dynamics and offers a new tool for studying polarization in online communities.

Po-Ting Lai, Elisabeth Coudert, Lucila Aimo et al.

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts in which enzymes and the chemical reactions they catalyze are annotated using identifiers from the UniProt Knowledgebase (UniProtKB) and the ontology of Chemical Entities of Biological Interest (ChEBI). We show that fine-tuning pre-trained language models with EnzChemRED can significantly boost their ability to identify mentions of proteins and chemicals in text (Named Entity Recognition, or NER) and to extract the chemical conversions in which they participate (Relation Extraction, or RE), with average F1 score of 86.30% for NER, 86.66% for RE for chemical conversion pairs, and 83.79% for RE for chemical conversion pairs and linked enzymes. We combine the best performing methods after fine-tuning using EnzChemRED to create an end-to-end pipeline for knowledge extraction from text and apply this to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea. The EnzChemRED corpus is freely available at https://ftp.expasy.org/databases/rhea/nlp/.

Ling Luo, Wenbin Jiang, Xushi Zhang et al.

Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present AFD-Instruction, the first large-scale instruction dataset with functional annotations tailored to antibodies. This dataset encompasses two key components: antibody understanding, which infers functional attributes directly from sequences, and antibody design, which enables de novo sequence generation under functional constraints. These components provide explicit sequence-function alignment and support antibody design guided by natural language instructions. Extensive instruction-tuning experiments on general-purpose LLMs demonstrate that AFD-Instruction consistently improves performance across diverse antibody-related tasks. By linking antibody sequences with textual descriptions of function, AFD-Instruction establishes a new foundation for advancing antibody modeling and accelerating therapeutic discovery.

Xianzhe Meng, Qiangsheng Zeng, Ling Luo et al.

Training stability is typically regarded as a prerequisite for reliable optimization in large language models. In this work, we analyze how stabilizing training dynamics affects the induced generation distribution. We show that under standard maximum likelihood training, stable parameter trajectories lead stationary solutions to approximately minimize the forward KL divergence to the empirical distribution, while implicitly reducing generative entropy. As a consequence, the learned model can concentrate probability mass on a limited subset of empirical modes, exhibiting systematic degeneration despite smooth loss convergence. We empirically validate this effect using a controlled feedback-based training framework that stabilizes internal generation statistics, observing consistent low-entropy outputs and repetitive behavior across architectures and random seeds. It indicates that optimization stability and generative expressivity are not inherently aligned, and that stability alone is an insufficient indicator of generative quality.

Yingpeng Ning, Yuanyuan Sun, Ling Luo et al.

Biomedical question answering (QA) requires accurate interpretation of complex medical knowledge. Large language models (LLMs) have shown promising capabilities in this domain, with retrieval-augmented generation (RAG) systems enhancing performance by incorporating external medical literature. However, RAG-based approaches in biomedical QA suffer from hallucinations due to post-retrieval noise and insufficient verification of retrieved evidence, undermining response reliability. We propose MedTrust-Guided Iterative RAG, a framework designed to enhance factual consistency and mitigate hallucinations in medical QA. Our method introduces three key innovations. First, it enforces citation-aware reasoning by requiring all generated content to be explicitly grounded in retrieved medical documents, with structured Negative Knowledge Assertions used when evidence is insufficient. Second, it employs an iterative retrieval-verification process, where a verification agent assesses evidence adequacy and refines queries through Medical Gap Analysis until reliable information is obtained. Third, it integrates the MedTrust-Align Module (MTAM) that combines verified positive examples with hallucination-aware negative samples, leveraging Direct Preference Optimization to reinforce citation-grounded reasoning while penalizing hallucination-prone response patterns.

Chuang Wang, Haitao Zhou, Ling Luo et al.

3D vector graphics play a crucial role in various applications including 3D shape retrieval, conceptual design, and virtual reality interactions due to their ability to capture essential structural information with minimal representation. While recent approaches have shown promise in generating 3D vector graphics, they often suffer from lengthy processing times and struggle to maintain view consistency. To address these limitations, we propose ViewCraft3D (VC3D), an efficient method that leverages 3D priors to generate 3D vector graphics. Specifically, our approach begins with 3D object analysis, employs a geometric extraction algorithm to fit 3D vector graphics to the underlying structure, and applies view-consistent refinement process to enhance visual quality. Our comprehensive experiments demonstrate that VC3D outperforms previous methods in both qualitative and quantitative evaluations, while significantly reducing computational overhead. The resulting 3D sketches maintain view consistency and effectively capture the essential characteristics of the original objects.

Yuhao Li, Ling Luo, Uwe Aickelin

Medical research, particularly in predicting patient outcomes, heavily relies on medical time series data extracted from Electronic Health Records (EHR), which provide extensive information on patient histories. Despite rigorous examination, labeling errors are inevitable and can significantly impede accurate predictions of patient outcome. To address this challenge, we propose an \textbf{A}ttention-based Learning Framework with Dynamic \textbf{C}alibration and Augmentation for \textbf{T}ime series Noisy \textbf{L}abel \textbf{L}earning (ACTLL). This framework leverages a two-component Beta mixture model to identify the certain and uncertain sets of instances based on the fitness distribution of each class, and it captures global temporal dynamics while dynamically calibrating labels from the uncertain set or augmenting confident instances from the certain set. Experimental results on large-scale EHR datasets eICU and MIMIC-IV-ED, and several benchmark datasets from the UCR and UEA repositories, demonstrate that our model ACTLL has achieved state-of-the-art performance, especially under high noise levels.

Xuan-May Le, Ling Luo, Uwe Aickelin et al.

Patient-ventilator asynchrony (PVA) is a common and critical issue during mechanical ventilation, affecting up to 85% of patients. PVA can result in clinical complications such as discomfort, sleep disruption, and potentially more severe conditions like ventilator-induced lung injury and diaphragm dysfunction. Traditional PVA management, which relies on manual adjustments by healthcare providers, is often inadequate due to delays and errors. While various computational methods, including rule-based, statistical, and deep learning approaches, have been developed to detect PVA events, they face challenges related to dataset imbalances and lack of interpretability. In this work, we propose a shapelet-based approach SHIP for PVA detection, utilizing shapelets - discriminative subsequences in time-series data - to enhance detection accuracy and interpretability. Our method addresses dataset imbalances through shapelet-based data augmentation and constructs a shapelet pool to transform the dataset for more effective classification. The combined shapelet and statistical features are then used in a classifier to identify PVA events. Experimental results on medical datasets show that SHIP significantly improves PVA detection while providing interpretable insights into model decisions.

Dongli Wu, Ling Luo

With the advancement of Internet of Things (IoT) technology, underwater target detection and tracking have become increasingly important for ocean monitoring and resource management. Existing methods often fall short in handling high-noise and low-contrast images in complex underwater environments, lacking precision and robustness. This paper introduces a novel SVGS-DSGAT model that combines GraphSage, SVAM, and DSGAT modules, enhancing feature extraction and target detection capabilities through graph neural networks and attention mechanisms. The model integrates IoT technology to facilitate real-time data collection and processing, optimizing resource allocation and model responsiveness. Experimental results demonstrate that the SVGS-DSGAT model achieves an mAP of 40.8% on the URPC 2020 dataset and 41.5% on the SeaDronesSee dataset, significantly outperforming existing mainstream models. This IoT-enhanced approach not only excels in high-noise and complex backgrounds but also improves the overall efficiency and scalability of the system. This research provides an effective IoT solution for underwater target detection technology, offering significant practical application value and broad development prospects.

Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai et al.

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases, and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

Amila Silva, Ling Luo, Shanika Karunasekera et al.

The emergence of social media as one of the main platforms for people to access news has enabled the wide dissemination of fake news. This has motivated numerous studies on automating fake news detection. Although there have been limited attempts at unsupervised fake news detection, their performance suffers due to not exploiting the knowledge from various modalities related to news records and due to the presence of various latent biases in the existing news datasets. To address these limitations, this work proposes an effective framework for unsupervised fake news detection, which first embeds the knowledge available in four modalities in news records and then proposes a novel noise-robust self-supervised learning technique to identify the veracity of news records from the multi-modal embeddings. Also, we propose a novel technique to construct news datasets minimizing the latent biases in existing news datasets. Following the proposed approach for dataset construction, we produce a Large-scale Unlabelled News Dataset consisting 419,351 news articles related to COVID-19, acronymed as LUND-COVID. We trained the proposed unsupervised framework using LUND-COVID to exploit the potential of large datasets, and evaluate it using a set of existing labelled datasets. Our results show that the proposed unsupervised framework largely outperforms existing unsupervised baselines for different tasks such as multi-modal fake news detection, fake news early detection and few-shot fake news detection, while yielding notable improvements for unseen domains during training.

Amila Silva, Ling Luo, Shanika Karunasekera et al.

With the rapid evolution of social media, fake news has become a significant social problem, which cannot be addressed in a timely manner using manual investigation. This has motivated numerous studies on automating fake news detection. Most studies explore supervised training models with different modalities (e.g., text, images, and propagation networks) of news records to identify fake news. However, the performance of such techniques generally drops if news records are coming from different domains (e.g., politics, entertainment), especially for domains that are unseen or rarely-seen during training. As motivation, we empirically show that news records from different domains have significantly different word usage and propagation patterns. Furthermore, due to the sheer volume of unlabelled news records, it is challenging to select news records for manual labelling so that the domain-coverage of the labelled dataset is maximized. Hence, this work: (1) proposes a novel framework that jointly preserves domain-specific and cross-domain knowledge in news records to detect fake news from different domains; and (2) introduces an unsupervised technique to select a set of unlabelled informative news records for manual labelling, which can be ultimately used to train a fake news detection model that performs well for many domains while minimizing the labelling cost. Our experiments show that the integration of the proposed fake news model and the selective annotation approach achieves state-of-the-art performance for cross-domain news datasets, while yielding notable improvements for rarely-appearing domains in news datasets.

Qingyu Chen, Robert Leaman, Alexis Allot et al.

The COVID-19 pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread. Many of these difficulties are fundamentally information needs; attempts to address these needs have caused an information overload for both researchers and the public. Natural language processing (NLP), the branch of artificial intelligence that interprets human language, can be applied to address many of the information needs made urgent by the COVID-19 pandemic. This review surveys approximately 150 NLP studies and more than 50 systems and datasets addressing the COVID-19 pandemic. We detail work on four core NLP tasks: information retrieval, named entity recognition, literature-based discovery, and question answering. We also describe work that directly addresses aspects of the pandemic through four additional tasks: topic modeling, sentiment and emotion analysis, caseload forecasting, and misinformation detection. We conclude by discussing observable trends and remaining challenges.

Ling Luo, Shankai Yan, Po-Ting Lai et al.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Amila Silva, Shanika Karunasekera, Christopher Leckie et al.

Many learning tasks involve multi-modal data streams, where continuous data from different modes convey a comprehensive description about objects. A major challenge in this context is how to efficiently interpret multi-modal information in complex environments. This has motivated numerous studies on learning unsupervised representations from multi-modal data streams. These studies aim to understand higher-level contextual information (e.g., a Twitter message) by jointly learning embeddings for the lower-level semantic units in different modalities (e.g., text, user, and location of a Twitter message). However, these methods directly associate each low-level semantic unit with a continuous embedding vector, which results in high memory requirements. Hence, deploying and continuously learning such models in low-memory devices (e.g., mobile devices) becomes a problem. To address this problem, we present METEOR, a novel MEmory and Time Efficient Online Representation learning technique, which: (1) learns compact representations for multi-modal data by sharing parameters within semantically meaningful groups and preserves the domain-agnostic semantics; (2) can be accelerated using parallel processes to accommodate different stream rates while capturing the temporal changes of the units; and (3) can be easily extended to capture implicit/explicit external knowledge related to multi-modal data streams. We evaluate METEOR using two types of multi-modal data streams (i.e., social media streams and shopping transaction streams) to demonstrate its ability to adapt to different domains. Our results show that METEOR preserves the quality of the representations while reducing memory usage by around 80% compared to the conventional memory-intensive embeddings.

Amila Silva, Ling Luo, Shanika Karunasekera et al.

Market Basket Analysis (MBA) is a popular technique to identify associations between products, which is crucial for business decision making. Previous studies typically adopt conventional frequent itemset mining algorithms to perform MBA. However, they generally fail to uncover rarely occurring associations among the products at their most granular level. Also, they have limited ability to capture temporal dynamics in associations between products. Hence, we propose OMBA, a novel representation learning technique for Online Market Basket Analysis. OMBA jointly learns representations for products and users such that they preserve the temporal dynamics of product-to-product and user-to-product associations. Subsequently, OMBA proposes a scalable yet effective online method to generate products' associations using their representations. Our extensive experiments on three real-world datasets show that OMBA outperforms state-of-the-art methods by as much as 21%, while emphasizing rarely occurring strong associations and effectively capturing temporal changes in associations.

Jianfeng Liu, Feiyang Pan, Ling Luo

A chatbot that converses like a human should be goal-oriented (i.e., be purposeful in conversation), which is beyond language generation. However, existing dialogue systems often heavily rely on cumbersome hand-crafted rules or costly labelled datasets to reach the goals. In this paper, we propose Goal-oriented Chatbots (GoChat), a framework for end-to-end training chatbots to maximize the longterm return from offline multi-turn dialogue datasets. Our framework utilizes hierarchical reinforcement learning (HRL), where the high-level policy guides the conversation towards the final goal by determining some sub-goals, and the low-level policy fulfills the sub-goals by generating the corresponding utterance for response. In our experiments on a real-world dialogue dataset for anti-fraud in financial, our approach outperforms previous methods on both the quality of response generation as well as the success rate of accomplishing the goal.

Xuhui Fan, Bin Li, Ling Luo et al.

Bayesian nonparametric space partition (BNSP) models provide a variety of strategies for partitioning a $D$-dimensional space into a set of blocks. In this way, the data points lie in the same block would share certain kinds of homogeneity. BNSP models can be applied to various areas, such as regression/classification trees, random feature construction, relational modeling, etc. In this survey, we investigate the current progress of BNSP research through the following three perspectives: models, which review various strategies for generating the partitions in the space and discuss their theoretical foundation `self-consistency'; applications, which cover the current mainstream usages of BNSP models and their potential future practises; and challenges, which identify the current unsolved problems and valuable future research topics. As there are no comprehensive reviews of BNSP literature before, we hope that this survey can induce further exploration and exploitation on this topic.

Ling Luo, Dingyu Xue, Xinglong Feng

A large number of retinal vessel analysis methods based on image segmentation have emerged in recent years. However, existing methods depend on cumbersome backbones, such as VGG16 and ResNet-50, benefiting from their powerful feature extraction capabilities but suffering from high computational costs. In this paper, we propose a novel neural network (HybridNetSeg) dedicated to solving this drawback while further improving overall performance. Considering deformable convolution can extract complex and variable structural information, and larger kernel in mixed depthwise convolution makes contribution to higher accuracy. We have integrated these two modules and propose a Hybrid Convolution Block (HCB) using the idea of heuristic learning. Inspired by the U-Net, we use HCB to replace a part of the common convolution of the U-Net encoder, drastically reducing the parameter count to 0.71M while accelerating the inference process. Not only that, we also propose a multi-scale mixed loss mechanism. Extensive experiments on three major benchmark datasets demonstrate the effectiveness of our proposed method

Amila Silva, Shanika Karunasekera, Christopher Leckie et al.

Building spatiotemporal activity models for people's activities in urban spaces is important for understanding the ever-increasing complexity of urban dynamics. With the emergence of Geo-Tagged Social Media (GTSM) records, previous studies demonstrate the potential of GTSM records for spatiotemporal activity modeling. State-of-the-art methods for this task embed different modalities (location, time, and text) of GTSM records into a single embedding space. However, they ignore Non-GeoTagged Social Media (NGTSM) records, which generally account for the majority of posts (e.g., more than 95\% in Twitter), and could represent a great source of information to alleviate the sparsity of GTSM records. Furthermore, in the current spatiotemporal embedding techniques, less focus has been given to the users, who exhibit spatially motivated behaviors. To bridge this research gap, this work proposes USTAR, a novel online learning method for User-guided SpatioTemporal Activity Representation, which (1) embeds locations, time, and text along with users into the same embedding space to capture their correlations; (2) uses a novel collaborative filtering approach based on two different empirically studied user behaviors to incorporate both NGTSM and GTSM records in learning; and (3) introduces a novel sampling technique to learn spatiotemporal representations in an online fashion to accommodate recent information into the embedding space, while avoiding overfitting to recent records and frequently appearing units in social media streams. Our results show that USTAR substantially improves the state-of-the-art for region retrieval and keyword retrieval and its potential to be applied to other downstream applications such as local event detection.