Min Zeng

Ziwei Ji, Zihan Liu, Nayeon Lee et al.

Dialogue systems can leverage large pre-trained language models and knowledge to generate fluent and informative responses. However, these models are still prone to produce hallucinated responses not supported by the input source, which greatly hinders their application. The heterogeneity between external knowledge and dialogue context challenges representation learning and source integration, and further contributes to unfaithfulness. To handle this challenge and generate more faithful responses, this paper presents RHO ($ρ$) utilizing the representations of linked entities and relation predicates from a knowledge graph (KG). We propose (1) local knowledge grounding to combine textual embeddings with the corresponding KG embeddings; and (2) global knowledge grounding to equip RHO with multi-hop reasoning abilities via the attention mechanism. In addition, we devise a response re-ranking technique based on walks over KG sub-graphs for better conversational reasoning. Experimental results on OpenDialKG show that our approach significantly outperforms state-of-the-art methods on both automatic and human evaluation by a large margin, especially in hallucination reduction (17.54% in FeQA).

Ziwei Ji, Yan Xu, I-Tsun Cheng et al.

In order to offer a customized script tool and inspire professional scriptwriters, we present VScript. It is a controllable pipeline that generates complete scripts, including dialogues and scene descriptions, as well as presents visually using video retrieval. With an interactive interface, our system allows users to select genres and input starting words that control the theme and development of the generated script. We adopt a hierarchical structure, which first generates the plot, then the script and its visual presentation. A novel approach is also introduced to plot-guided dialogue generation by treating it as an inverse dialogue summarization. The experiment results show that our approach outperforms the baselines on both automatic and human evaluations, especially in genre control.

Min Zeng, Wei Xue, Qifeng Liu et al.

Recent advancements in data-driven task-oriented dialogue systems (ToDs) struggle with incremental learning due to computational constraints and time-consuming issues. Continual Learning (CL) attempts to solve this by avoiding intensive pre-training, but it faces the problem of catastrophic forgetting (CF). While generative-based rehearsal CL methods have made significant strides, generating pseudo samples that accurately reflect the underlying task-specific distribution is still a challenge. In this paper, we present Dirichlet Continual Learning (DCL), a novel generative-based rehearsal strategy for CL. Unlike the traditionally used Gaussian latent variable in the Conditional Variational Autoencoder (CVAE), DCL leverages the flexibility and versatility of the Dirichlet distribution to model the latent prior variable. This enables it to efficiently capture sentence-level features of previous tasks and effectively guide the generation of pseudo samples. In addition, we introduce Jensen-Shannon Knowledge Distillation (JSKD), a robust logit-based knowledge distillation method that enhances knowledge transfer during pseudo sample generation. Our experiments confirm the efficacy of our approach in both intent detection and slot-filling tasks, outperforming state-of-the-art methods.

Zaifu Zhan, Min Zeng, Shuang Zhou et al.

Objective: To improve the efficiency of medical question answering (MedQA) with large language models (LLMs) by avoiding unnecessary reasoning while maintaining accuracy. Methods: We propose Selective Chain-of-Thought (Selective CoT), an inference-time strategy that first predicts whether a question requires reasoning and generates a rationale only when needed. Two open-source LLMs (Llama-3.1-8B and Qwen-2.5-7B) were evaluated on four biomedical QA benchmarks-HeadQA, MedQA-USMLE, MedMCQA, and PubMedQA. Metrics included accuracy, total generated tokens, and inference time. Results: Selective CoT reduced inference time by 13-45% and token usage by 8-47% with minimal accuracy loss ($\leq$4\%). In some model-task pairs, it achieved both higher accuracy and greater efficiency than standard CoT. Compared with fixed-length CoT, Selective CoT reached similar or superior accuracy at substantially lower computational cost. Discussion: Selective CoT dynamically balances reasoning depth and efficiency by invoking explicit reasoning only when beneficial, reducing redundancy on recall-type questions while preserving interpretability. Conclusion: Selective CoT provides a simple, model-agnostic, and cost-effective approach for medical QA, aligning reasoning effort with question complexity to enhance real-world deployability of LLM-based clinical systems.

Jing Jin, Xu Liu, Te Gao et al.

Whole Slide Image (WSI) representation is critical for cancer subtyping, cancer recognition and mutation prediction.Training an end-to-end WSI representation model poses significant challenges, as a standard gigapixel slide can contain tens of thousands of image tiles, making it difficult to compute gradients of all tiles in a single mini-batch due to current GPU limitations. To address this challenge, we propose a method of dynamic residual encoding with slide-level contrastive learning (DRE-SLCL) for end-to-end WSI representation. Our approach utilizes a memory bank to store the features of tiles across all WSIs in the dataset. During training, a mini-batch usually contains multiple WSIs. For each WSI in the batch, a subset of tiles is randomly sampled and their features are computed using a tile encoder. Then, additional tile features from the same WSI are selected from the memory bank. The representation of each individual WSI is generated using a residual encoding technique that incorporates both the sampled features and those retrieved from the memory bank. Finally, the slide-level contrastive loss is computed based on the representations and histopathology reports ofthe WSIs within the mini-batch. Experiments conducted over cancer subtyping, cancer recognition, and mutation prediction tasks proved the effectiveness of the proposed DRE-SLCL method.

Shuang Zhou, Kai Yu, Song Wang et al.

Heart diseases remain a leading cause of morbidity and mortality worldwide, necessitating accurate and trustworthy differential diagnosis. However, existing artificial intelligence-based diagnostic methods are often limited by insufficient cardiology knowledge, inadequate support for complex reasoning, and poor interpretability. Here we present HeartAgent, a cardiology-specific agent system designed to support a reliable and explainable differential diagnosis. HeartAgent integrates customized tools and curated data resources and orchestrates multiple specialized sub-agents to perform complex reasoning while generating transparent reasoning trajectories and verifiable supporting references. Evaluated on the MIMIC dataset and a private electronic health records cohort, HeartAgent achieved over 36% and 20% improvements over established comparative methods, in top-3 diagnostic accuracy, respectively. Additionally, clinicians assisted by HeartAgent demonstrated gains of 26.9% in diagnostic accuracy and 22.7% in explanatory quality compared with unaided experts. These results demonstrate that HeartAgent provides reliable, explainable, and clinically actionable decision support for cardiovascular care.

Shuang Zhou, Kai Yu, Zaifu Zhan et al.

Epilepsy and psychogenic non-epileptic seizures often present with similar seizure-like manifestations but require fundamentally different management strategies. Misdiagnosis is common and can lead to prolonged diagnostic delays, unnecessary treatments, and substantial patient morbidity. Although prolonged video-electroencephalography is the diagnostic gold standard, its high cost and limited accessibility hinder timely diagnosis. Here, we developed a low-cost, effective approach, EpiScreen, for early epilepsy detection by utilizing routinely collected clinical notes from electronic health records. Through fine-tuning large language models on labeled notes, EpiScreen achieved an AUC of up to 0.875 on the MIMIC-IV dataset and 0.980 on a private cohort of the University of Minnesota. In a clinician-AI collaboration setting, EpiScreen-assisted neurologists outperformed unaided experts by up to 10.9%. Overall, this study demonstrates that EpiScreen supports early epilepsy detection, facilitating timely and cost-effective screening that may reduce diagnostic delays and avoid unnecessary interventions, particularly in resource-limited regions.

Zaifu Zhan, Yu Hou, Kai Yu et al.

Rare diseases affect over 300 million people worldwide and are characterized by complex care pathways, limited clinical expertise, and substantial unmet communication needs throughout the long patient journey. Recent advances in large language models (LLMs) offer new opportunities to support patient education and communication, yet their application in rare diseases remains unclear. We conducted a scoping review of studies published between January 2022 and March 2026 across major databases, identifying 12 studies on LLM-based rare disease patient education and communication. Data were extracted on study characteristics, application scenarios, model usage, and evaluation methods, and synthesized using descriptive and qualitative analyses. The literature is highly recent and dominated by general-purpose models, particularly ChatGPT. Most studies focus on patient question answering using curated question sets, with limited use of real-world data or longitudinal communication scenarios. Evaluations are primarily centered on accuracy, with limited attention to patient-centered dimensions such as readability, empathy, and communication quality. Multilingual communication is rarely addressed. Overall, the field remains at an early stage. Future research should prioritize patient-centered design, domain-adapted methods, and real-world deployment to support safe, adaptive, and effective communication in rare diseases.

Min Zeng, Shuang Zhou, Zaifu Zhan et al.

Medical language models must be updated as evidence and terminology evolve, yet sequential updating can trigger catastrophic forgetting. Although biomedical NLP has many static benchmarks, no unified, task-diverse benchmark exists for evaluating continual learning under standardized protocols, robustness to task order and compute-aware reporting. We introduce MedCL-Bench, which streams ten biomedical NLP datasets spanning five task families and evaluates eleven continual learning strategies across eight task orders, reporting retention, transfer, and GPU-hour cost. Across backbones and task orders, direct sequential fine-tuning on incoming tasks induces catastrophic forgetting, causing update-induced performance regressions on prior tasks. Continual learning methods occupy distinct retention-compute frontiers: parameter-isolation provides the best retention per GPU-hour, replay offers strong protection at higher cost, and regularization yields limited benefit. Forgetting is task-dependent, with multi-label topic classification most vulnerable and constrained-output tasks more robust. MedCL-Bench provides a reproducible framework for auditing model updates before deployment.

Min Zeng, Caiquan Liu, Shiqi Zhang et al.

In recent years, the use of large language models (LLMs) for text classification has attracted widespread attention. Despite this, the classification accuracy of LLMs has not yet universally surpassed that of smaller models. LLMs can enhance their performance in text classification through fine-tuning. However, existing data quality research based on LLMs is challenging to apply directly to solve text classification problems. To further improve the performance of LLMs in classification tasks, this paper proposes a data quality enhancement (DQE) method for text classification based on LLMs. This method starts by using a greedy algorithm to select data, dividing the dataset into sampled and unsampled subsets, and then performing fine-tuning of the LLMs using the sampled data. Subsequently, this model is used to predict the outcomes for the unsampled data, categorizing incorrectly predicted data into uncovered, difficult, and noisy data. Experimental results demonstrate that our method effectively enhances the performance of LLMs in text classification tasks and significantly improves training efficiency, saving nearly half of the training time. Our method has achieved state-of-the-art performance in several open-source classification tasks.

Rui Jin, Chen Chen, Yin Liu et al.

Accurate diagnosis of Parkinson's disease (PD) from MRI remains challenging due to symptom variability and pathological heterogeneity. Most existing methods rely on conventional magnitude-based MRI modalities, such as T1-weighted images (T1w), which are less sensitive to PD pathology than Quantitative Susceptibility Mapping (QSM), a phase-based MRI technique that quantifies iron deposition in deep gray matter nuclei. In this study, we propose GateFuseNet, an adaptive 3D multimodal fusion network that integrates QSM and T1w images for PD diagnosis. The core innovation lies in a gated fusion module that learns modality-specific attention weights and channel-wise gating vectors for selective feature modulation. This hierarchical gating mechanism enhances ROI-aware features while suppressing irrelevant signals. Experimental results show that our method outperforms three existing state-of-the-art approaches, achieving 85.00% accuracy and 92.06% AUC. Ablation studies further validate the contributions of ROI guidance, multimodal integration, and fusion positioning. Grad-CAM visualizations confirm the model's focus on clinically relevant pathological regions. The source codes and pretrained models can be found at https://github.com/YangGaoUQ/GateFuseNet

Jiahao Tang, Henry Hengyuan Zhao, Lijian Wu et al.

We introduce Chart2Code, a new benchmark for evaluating the chart understanding and code generation capabilities of large multimodal models (LMMs). Chart2Code is explicitly designed from a user-driven perspective, capturing diverse real-world scenarios and progressively increasing task difficulty. It consists of three levels: Level 1 (Chart Reproduction) reproduces charts from a reference figure and user query; Level 2 (Chart Editing) involves complex modifications such as changing chart types or adding elements; and Level 3 (Long-Table to Chart Generation) requires models to transform long, information-dense tables into faithful charts following user instructions. To our knowledge, this is the first hierarchical benchmark that reflects practical chart2code usage while systematically scaling task complexity. In total, Chart2Code contains 2,023 tasks across 22 chart types, paired with multi-level evaluation metrics that assess both code correctness and the visual fidelity of rendered charts. We benchmark 25 state-of-the-art (SoTA) LMMs, including both proprietary and the latest open-source models such as GPT-5, Qwen2.5-VL, InternVL3/3.5, MiMo-VL, and Seed-1.6-VL. Experimental results demonstrate that even the SoTA model GPT-5 averages only 0.57 on code-based evaluation and 0.22 on chart-quality assessment across the editing tasks, underscoring the difficulty of Chart2Code. We anticipate this benchmark will drive advances in multimodal reasoning and foster the development of more robust and general-purpose LMMs. Our code and data are available on Chart2Code.

Min Zeng

Large Language Models (LLMs) have demonstrated remarkable success across a wide range of industries, primarily due to their impressive generative abilities. Yet, their potential in applications requiring cognitive abilities, such as psychological counseling, remains largely untapped. This paper investigates the key question: \textit{Can LLMs be effectively applied to psychological counseling?} To determine whether an LLM can effectively take on the role of a psychological counselor, the first step is to assess whether it meets the qualifications required for such a role, namely the ability to pass the U.S. National Counselor Certification Exam (NCE). This is because, just as a human counselor must pass a certification exam to practice, an LLM must demonstrate sufficient psychological knowledge to meet the standards required for such a role. To address this, we introduce PsychCounsel-Bench, a benchmark grounded in U.S.national counselor examinations, a licensure test for professional counselors that requires about 70\% accuracy to pass. PsychCounsel-Bench comprises approximately 2,252 carefully curated single-choice questions, crafted to require deep understanding and broad enough to cover various sub-disciplines of psychology. This benchmark provides a comprehensive assessment of an LLM's ability to function as a counselor. Our evaluation shows that advanced models such as GPT-4o, Llama3.3-70B, and Gemma3-27B achieve well above the passing threshold, while smaller open-source models (e.g., Qwen2.5-7B, Mistral-7B) remain far below it. These results suggest that only frontier LLMs are currently capable of meeting counseling exam standards, highlighting both the promise and the challenges of developing psychology-oriented LLMs. We release the proposed dataset for public use: https://github.com/cloversjtu/PsychCounsel-Bench

Min Cen, Zhenfeng Zhuang, Yuzhe Zhang et al.

Graph-based Multiple Instance Learning (MIL) is widely used in survival analysis with Hematoxylin and Eosin (H\&E)-stained whole slide images (WSIs) due to its ability to capture topological information. However, variations in staining and scanning can introduce semantic bias, while topological subgraphs that are not relevant to the causal relationships can create noise, resulting in biased slide-level representations. These issues can hinder both the interpretability and generalization of the analysis. To tackle this, we introduce a dual structural causal model as the theoretical foundation and propose a novel and interpretable dual causal graph-based MIL model, C$^2$MIL. C$^2$MIL incorporates a novel cross-scale adaptive feature disentangling module for semantic causal intervention and a new Bernoulli differentiable causal subgraph sampling method for topological causal discovery. A joint optimization strategy combining disentangling supervision and contrastive learning enables simultaneous refinement of both semantic and topological causalities. Experiments demonstrate that C$^2$MIL consistently improves generalization and interpretability over existing methods and can serve as a causal enhancement for diverse MIL baselines. The code is available at https://github.com/mimic0127/C2MIL.

Haojie Zhang, Yixiong Liang, Hulin Kuang et al.

Multimodal Biomedical Image Incremental Learning (MBIIL) is essential for handling diverse tasks and modalities in the biomedical domain, as training separate models for each modality or task significantly increases inference costs. Existing incremental learning methods focus on task expansion within a single modality, whereas MBIIL seeks to train a unified model incrementally across modalities. The MBIIL faces two challenges: I) How to preserve previously learned knowledge during incremental updates? II) How to effectively leverage knowledge acquired from existing modalities to support new modalities? To address these challenges, we propose MSLoRA-CR, a method that fine-tunes Modality-Specific LoRA modules while incorporating Contrastive Regularization to enhance intra-modality knowledge sharing and promote inter-modality knowledge differentiation. Our approach builds upon a large vision-language model (LVLM), keeping the pretrained model frozen while incrementally adapting new LoRA modules for each modality or task. Experiments on the incremental learning of biomedical images demonstrate that MSLoRA-CR outperforms both the state-of-the-art (SOTA) approach of training separate models for each modality and the general incremental learning method (incrementally fine-tuning LoRA). Specifically, MSLoRA-CR achieves a 1.88% improvement in overall performance compared to unconstrained incremental learning methods while maintaining computational efficiency. Our code is publicly available at https://github.com/VentusAislant/MSLoRA_CR.

Yihong Chen, Zhen Fan, Shuai Dong et al.

Stereo image super-resolution (SR) refers to the reconstruction of a high-resolution (HR) image from a pair of low-resolution (LR) images as typically captured by a dual-camera device. To enhance the quality of SR images, most previous studies focused on increasing the number and size of feature maps and introducing complex and computationally intensive structures, resulting in models with high computational complexity. Here, we propose a simple yet efficient stereo image SR model called NAFRSSR, which is modified from the previous state-of-the-art model NAFSSR by introducing recursive connections and lightweighting the constituent modules. Our NAFRSSR model is composed of nonlinear activation free and group convolution-based blocks (NAFGCBlocks) and depth-separated stereo cross attention modules (DSSCAMs). The NAFGCBlock improves feature extraction and reduces number of parameters by removing the simple channel attention mechanism from NAFBlock and using group convolution. The DSSCAM enhances feature fusion and reduces number of parameters by replacing 1x1 pointwise convolution in SCAM with weight-shared 3x3 depthwise convolution. Besides, we propose to incorporate trainable edge detection operator into NAFRSSR to further improve the model performance. Four variants of NAFRSSR with different sizes, namely, NAFRSSR-Mobile (NAFRSSR-M), NAFRSSR-Tiny (NAFRSSR-T), NAFRSSR-Super (NAFRSSR-S) and NAFRSSR-Base (NAFRSSR-B) are designed, and they all exhibit fewer parameters, higher PSNR/SSIM, and faster speed than the previous state-of-the-art models. In particular, to the best of our knowledge, NAFRSSR-M is the lightest (0.28M parameters) and fastest (50 ms inference time) model achieving an average PSNR/SSIM as high as 24.657 dB/0.7622 on the benchmark datasets. Codes and models will be released at https://github.com/JNUChenYiHong/NAFRSSR.

Min Zeng, Haimiao Mo, Zhiming Liang et al.

As the use of robotics becomes more widespread, the huge amount of vision data leads to a dramatic increase in data dimensionality. Although deep learning methods can effectively process these high-dimensional vision data. Due to the limitation of computational resources, some special scenarios still rely on traditional machine learning methods. However, these high-dimensional visual data lead to great challenges for traditional machine learning methods. Therefore, we propose a Lite Fireworks Algorithm with Fractal Dimension constraint for feature selection (LFWA+FD) and use it to solve the feature selection problem driven by robot vision. The "LFWA+FD" focuses on searching the ideal feature subset by simplifying the fireworks algorithm and constraining the dimensionality of selected features by fractal dimensionality, which in turn reduces the approximate features and reduces the noise in the original data to improve the accuracy of the model. The comparative experimental results of two publicly available datasets from UCI show that the proposed method can effectively select a subset of features useful for model inference and remove a large amount of noise noise present in the original data to improve the performance.

Haimiao Mo, Min Zeng

The fireworks algorithm is an optimization algorithm for simulating the explosion phenomenon of fireworks. Because of its fast convergence and high precision, it is widely used in pattern recognition, optimal scheduling, and other fields. However, most of the existing research work on the fireworks algorithm is improved based on its defects, and little consideration is given to reducing the number of parameters of the fireworks algorithm. The original fireworks algorithm has too many parameters, which increases the cost of algorithm adjustment and is not conducive to engineering applications. In addition, in the fireworks population, the unselected individuals are discarded, thus causing a waste of their location information. To reduce the number of parameters of the original Fireworks Algorithm and make full use of the location information of discarded individuals, we propose a simplified version of the Fireworks Algorithm. It reduces the number of algorithm parameters by redesigning the explosion operator of the fireworks algorithm and constructs an adaptive explosion radius by using the historical optimal information to balance the local mining and global exploration capabilities. The comparative experimental results of function optimization show that the overall performance of our proposed LFWA is better than that of comparative algorithms, such as the fireworks algorithm, particle swarm algorithm, and bat algorithm.

Min Zeng, Jiexin Kuang, Mengyang Qiu et al.

The writing examples of English language learners may be different from those of native speakers. Given that there is a significant differences in second language (L2) learners' error types by their proficiency levels, this paper attempts to reduce overcorrection by examining the interaction between LLM's performance and L2 language proficiency. Our method focuses on zero-shot and few-shot prompting and fine-tuning models for GEC for learners of English as a foreign language based on the different proficiency. We investigate GEC results and find that overcorrection happens primarily in advanced language learners' writing (proficiency C) rather than proficiency A (a beginner level) and proficiency B (an intermediate level). Fine-tuned LLMs, and even few-shot prompting with writing examples of English learners, actually tend to exhibit decreased recall measures. To make our claim concrete, we conduct a comprehensive examination of GEC outcomes and their evaluation results based on language proficiency.

Izia Xiaoxiao Wang, Xihan Wu, Edith Coates et al.

The utilization of technology in second language learning and teaching has become ubiquitous. For the assessment of writing specifically, automated writing evaluation (AWE) and grammatical error correction (GEC) have become immensely popular and effective methods for enhancing writing proficiency and delivering instant and individualized feedback to learners. By leveraging the power of natural language processing (NLP) and machine learning algorithms, AWE and GEC systems have been developed separately to provide language learners with automated corrective feedback and more accurate and unbiased scoring that would otherwise be subject to examiners. In this paper, we propose an integrated system for automated writing evaluation with corrective feedback as a means of bridging the gap between AWE and GEC results for second language learners. This system enables language learners to simulate the essay writing tests: a student writes and submits an essay, and the system returns the assessment of the writing along with suggested grammatical error corrections. Given that automated scoring and grammatical correction are more efficient and cost-effective than human grading, this integrated system would also alleviate the burden of manually correcting innumerable essays.

Yu Hou, Zaifu Zhan, Min Zeng et al.

Biomedical literature and clinical narratives pose multifaceted challenges for natural language understanding, from precise entity extraction and document synthesis to multi-step diagnostic reasoning. This study extends a unified benchmark to evaluate GPT-5 and GPT-4o under zero-, one-, and five-shot prompting across five core biomedical NLP tasks: named entity recognition, relation extraction, multi-label document classification, summarization, and simplification, and nine expanded biomedical QA datasets covering factual knowledge, clinical reasoning, and multimodal visual understanding. Using standardized prompts, fixed decoding parameters, and consistent inference pipelines, we assessed model performance, latency, and token-normalized cost under official pricing. GPT-5 consistently outperformed GPT-4o, with the largest gains on reasoning-intensive datasets such as MedXpertQA and DiagnosisArena and stable improvements in multimodal QA. In core tasks, GPT-5 achieved better chemical NER and ChemProt scores but remained below domain-tuned baselines for disease NER and summarization. Despite producing longer outputs, GPT-5 showed comparable latency and 30 to 50 percent lower effective cost per correct prediction. Fine-grained analyses revealed improvements in diagnosis, treatment, and reasoning subtypes, whereas boundary-sensitive extraction and evidence-dense summarization remain challenging. Overall, GPT-5 approaches deployment-ready performance for biomedical QA while offering a favorable balance of accuracy, interpretability, and economic efficiency. The results support a tiered prompting strategy: direct prompting for large-scale or cost-sensitive applications, and chain-of-thought scaffolds for analytically complex or high-stakes scenarios, highlighting the continued need for hybrid solutions where precision and factual fidelity are critical.

Jiawei Mo, Yixuan Chen, Rifen Lin et al.

Despite continuous advancements in deep learning for understanding human motion, existing models often struggle to accurately identify action timing and specific body parts, typically supporting only single-round interaction. Such limitations in capturing fine-grained motion details reduce their effectiveness in motion understanding tasks. In this paper, we propose MoChat, a multimodal large language model capable of spatio-temporal grounding of human motion and understanding multi-turn dialogue context. To achieve these capabilities, we group the spatial information of each skeleton frame based on human anatomical structure and then apply them with Joints-Grouped Skeleton Encoder, whose outputs are combined with LLM embeddings to create spatio-aware and temporal-aware embeddings separately. Additionally, we develop a pipeline for extracting timestamps from skeleton sequences based on textual annotations, and construct multi-turn dialogues for spatially grounding. Finally, various task instructions are generated for jointly training. Experimental results demonstrate that MoChat achieves state-of-the-art performance across multiple metrics in motion understanding tasks, making it as the first model capable of fine-grained spatio-temporal grounding of human motion.

Yifan Wu, Min Zeng, Yang Li et al.

Most current molecular language models transfer the masked language model or image-text generation model from natural language processing to molecular field. However, molecules are not solely characterized by atom/bond symbols; they encapsulate important physical/chemical properties. Moreover, normal language models bring grammar rules that are irrelevant for understanding molecules. In this study, we propose a novel physicochemical knowledge-guided molecular meta language framework MolMetaLM. We design a molecule-specialized meta language paradigm, formatted as multiple <S,P,O> (subject, predicate, object) knowledge triples sharing the same S (i.e., molecule) to enhance learning the semantic relationships between physicochemical knowledge and molecules. By introducing different molecular knowledge and noises, the meta language paradigm generates tens of thousands of pretraining tasks. By recovering the token/sequence/order-level noises, MolMetaLM exhibits proficiency in large-scale benchmark evaluations involving property prediction, molecule generation, conformation inference, and molecular optimization. Through MolMetaLM, we offer a new insight for designing language models.

Min Zeng, Jingfei Sun, Xueyou Luo et al.

In natural language processing tasks, pure reinforcement learning (RL) fine-tuning methods often suffer from inefficient exploration and slow convergence; while supervised fine-tuning (SFT) methods, although efficient in training, have limited performance ceiling and less solid theoretical foundation compared to RL. To address efficiency-capability trade-off, we propose the Guess-Think-Answer (GTA) framework that combines the efficiency of SFT with the capability gains of RL in a unified training paradigm. GTA works by having the model first produce a provisional guess (optimized via cross-entropy loss), then reflect on this guess before generating the final answer, with RL rewards shaping both the final output and the format of the entire GTA structure. This hybrid approach achieves both faster convergence than pure RL and higher performance ceiling than pure SFT. To mitigate gradient conflicts between the two training signals, we employ loss masking and gradient constraints. Empirical results on four text classification benchmarks demonstrate that GTA substantially accelerates convergence while outperforming both standalone SFT and RL baselines.

Zaifu Zhan, Shuang Zhou, Min Zeng et al.

Large language models have demonstrated remarkable capabilities in biomedical natural language processing, yet their rapid growth in size and computational requirements present a major barrier to adoption in healthcare settings where data privacy precludes cloud deployment and resources are limited. In this study, we systematically evaluated the impact of quantization on 12 state-of-the-art large language models, including both general-purpose and biomedical-specific models, across eight benchmark datasets covering four key tasks: named entity recognition, relation extraction, multi-label classification, and question answering. We show that quantization substantially reduces GPU memory requirements-by up to 75%-while preserving model performance across diverse tasks, enabling the deployment of 70B-parameter models on 40GB consumer-grade GPUs. In addition, domain-specific knowledge and responsiveness to advanced prompting methods are largely maintained. These findings provide significant practical and guiding value, highlighting quantization as a practical and effective strategy for enabling the secure, local deployment of large yet high-capacity language models in biomedical contexts, bridging the gap between technical advances in AI and real-world clinical translation.

Holy Lovenia, Bryan Wilie, Willy Chung et al.

Task-adaptive pre-training (TAPT) alleviates the lack of labelled data and provides performance lift by adapting unlabelled data to downstream task. Unfortunately, existing adaptations mainly involve deterministic rules that cannot generalize well. Here, we propose Clozer, a sequence-tagging based cloze answer extraction method used in TAPT that is extendable for adaptation on any cloze-style machine reading comprehension (MRC) downstream tasks. We experiment on multiple-choice cloze-style MRC tasks, and show that Clozer performs significantly better compared to the oracle and state-of-the-art in escalating TAPT effectiveness in lifting model performance, and prove that Clozer is able to recognize the gold answers independently of any heuristics.

Yifan Wu, Min Zeng, Ying Yu et al.

Automatic International Classification of Diseases (ICD) coding is defined as a kind of text multi-label classification problem, which is difficult because the number of labels is very large and the distribution of labels is unbalanced. The label-wise attention mechanism is widely used in automatic ICD coding because it can assign weights to every word in full Electronic Medical Records (EMR) for different ICD codes. However, the label-wise attention mechanism is computational redundant and costly. In this paper, we propose a pseudo label-wise attention mechanism to tackle the problem. Instead of computing different attention modes for different ICD codes, the pseudo label-wise attention mechanism automatically merges similar ICD codes and computes only one attention mode for the similar ICD codes, which greatly compresses the number of attention modes and improves the predicted accuracy. In addition, we apply a more convenient and effective way to obtain the ICD vectors, and thus our model can predict new ICD codes by calculating the similarities between EMR vectors and ICD vectors. Extensive experiments show the superior performance of our model. On the public MIMIC-III dataset and private Xiangya dataset, our model achieves micro f1 of 0.583 and 0.806, respectively, which outperforms other competing models. Furthermore, we verify the ability of our model in predicting new ICD codes. The case study shows how pseudo label-wise attention works, and demonstrates the effectiveness of pseudo label-wise attention mechanism.

Yifan Wu, Min Gao, Min Zeng et al.

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep learning methods extract features only from basic characteristics, such as protein sequences, molecule structures. Others achieve significant improvement by learning from not only sequences/molecules but the protein-protein and drug-drug associations (PPAs and DDAs). The PPAs and DDAs are generally obtained by using computational methods. However, existing computational methods have some limitations, resulting in low-quality PPAs and DDAs that hamper the prediction performance. Therefore, we hope to develop a novel supervised learning method to learn the PPAs and DDAs effectively and thereby improve the prediction performance of the specific task of DPI. Results: In this research, we propose a novel deep learning framework, namely BridgeDPI. BridgeDPI introduces a class of nodes named hyper-nodes, which bridge different proteins/drugs to work as PPAs and DDAs. The hyper-nodes can be supervised learned for the specific task of DPI since the whole process is an end-to-end learning. Consequently, such a model would improve prediction performance of DPI. In three real-world datasets, we further demonstrate that BridgeDPI outperforms state-of-the-art methods. Moreover, ablation studies verify the effectiveness of the hyper-nodes. Last, in an independent verification, BridgeDPI explores the candidate bindings among COVID-19's proteins and various antiviral drugs. And the predictive results accord with the statement of the World Health Organization and Food and Drug Administration, showing the validity and reliability of BridgeDPI.