Recommending medications from electronic health records (EHRs) is a safety-critical task that demands therapeutic coverage, explicit safety constraints, traceable justification, and continual adaptivity. Supervised neural models freeze at deployment and cannot reason about new phenotypes, while existing LLM pipelines are single-pass and lack a cross-case improvement loop. We propose **SEMPA**, a training-free agentic framework that couples a Proposer with a Critic in multi-round adversarial deliberation, grounds candidates with molecular-aware retrieval, contrastively evolves both agents’ natural-language policies under a semantic-anchor constraint, and enforces rule-based DDI and contraindication checks. On 100 MIMIC-IV encounters, SEMPA reaches 0.3116 Jaccard, 0.7295 F1, and a 0.0172 DDI rate, improving F1 by 57.7% and cutting DDI by 77.5% over the strongest supervised baseline. Two LLM judges rank SEMPA highest, and six-backbone studies confirm that gains derive from the framework rather than a specific model.

Vision-language models (VLMs) often answer new questions about recurring visual content, where reusing the key-value (KV) cache can avoid re-encoding expensive visual prefixes. Exact-prefix reuse, however, fails when the same visual content appears under a changed prefix. Selective recomputation can recover quality under a small visual-token budget, but only when the right stale tokens are refreshed. Raw-attention selection can waste budget on high-attention tokens with small value-norm proxy scores and on query-irrelevant images. To address these failure modes, we propose CONDUIT, a training-free refresh policy that unifies single- and multi-image reuse as residual-stream restoration. Building on norm-weighted attention, CONDUIT ranks cached visual tokens using cached-key query attention and an accessible pre-output cached-value-norm proxy, then applies empirical image-level relevance amplification before one global selection. With one image, the coefficient is one and the rule reduces to intra-image token selection. The method preserves model architecture and weights, adding only a single query-conditioned scoring pass at inference. At a 10% refresh budget, CONDUIT achieves 97.0%–99.5% of the corresponding full-prefill five-dataset average across three VLM backbones and leads budgeted methods on average; on the MMLongBench-Doc latency subset, it uses 13.5% of full-prefill FLOPs and achieves a 2.99× time-to-first-token speedup.

RNA’s conformational flexibility enables diverse biological functions but makes structure-guided design difficult. Although precise control of 3D structure is essential, existing methods often overlook the molecular surface, which critically shapes intermolecular interactions and functional outcomes. To address this, we propose gRFold, a multimodal framework that incorporates molecular surface information as a core design constraint. gRFold employs two geometric encoders: a Frame-Averaged Geometric Surface Encoder (FA-GSE) to learn E(3)-invariant surface features, and an Equivariant Backbone Graph Perceptron (EBGP) to capture backbone topology. The structural representations are integrated via hierarchical cross-attention to guide autoregressive generation; at inference, candidates are re-ranked by agreement between their predicted folds and the target base-pairing pattern. Across three RNA inverse-folding benchmarks covering RNA-protein complexes, monomeric RNAs and independently curated RNA-Puzzles targets, gRFold achieves strong sequence recovery and structural fidelity under both secondary-structure and 3D refolding evaluations, and ablations show that the surface and backbone branches contribute complementary gains. These results highlight the potential of surface-aware geometric modeling for structure-guided RNA design.

The rapid evolution of large language models (LLMs) has transformed the competitive landscape in natural language processing (NLP), particularly for English and other data-rich languages. However, underrepresented languages like Cantonese, spoken by over 85 million people, face significant development gaps, which is particularly concerning given the economic significance of the Guangdong-Hong Kong-Macau Greater Bay Area, and in substantial Cantonese-speaking populations in places like Singapore and North America. Despite its wide use, Cantonese has scant representation in NLP research, especially compared to other languages from similarly developed regions. To bridge these gaps, we outline current Cantonese NLP methods and introduce new benchmarks designed to evaluate LLM performance in factual generation, mathematical logic, complex reasoning, and general knowledge in Cantonese, which aim to advance open-source Cantonese LLM technology. We also propose future research directions and recommended models to enhance Cantonese LLM development.

Proteins are critical for various molecular functions, relying on their precise tertiary structures. This structure-sequence relationship is complex and degenerate, meaning multiple sequences can fold into a similar structure. The challenges in protein prediction, design, and modification increase with sequence complexity, while research on RNA-protein interactions, especially RNA-binding proteins (RBPs), is gaining importance. Large-scale pre-trained language models (LLMs) have shown promising results in handling biological sequences by treating them as natural language, though integrating spatial structures remains complex due to the need for specialized visual and 3D modeling approaches. We introduce a method to integrate protein 3D structural data within a sequence processing framework, converting 3D coordinates into discrete structure tokens using a VQ-VAE-like network. This simplifies the handling of 3D data, avoiding complex pipelines and facilitating a unified sequence-to-sequence processing model. Our approach demonstrates strong performance across a range of tasks, achieving high sequence recovery in inverse folding and protein-conditioned RNA design. These outstanding results demonstrate significant potential for application in complex biological systems research.

High-quality data resources play a crucial role in learning large language models (LLMs), particularly for low-resource languages like Cantonese. Despite having more than 85 million native speakers, Cantonese is still considered a low-resource language in the field of natural language processing (NLP) due to factors such as the dominance of Mandarin, lack of cohesion within the Cantonese-speaking community, diversity in character encoding and input methods, and the tendency of overseas Cantonese speakers to prefer using English. In addition, rich colloquial vocabulary of Cantonese, English loanwords, and code-switching characteristics add to the complexity of corpus collection and processing. To address these challenges, we collect Cantonese texts from a variety of sources, including open source corpora, Hong Kong-specific forums, Wikipedia, and Common Crawl data. We conduct rigorous data processing through language filtering, quality filtering, content filtering, and de-duplication steps, successfully constructing a high-quality Cantonese corpus of over 2 billion tokens for training large language models. We further refined the model through supervised fine-tuning (SFT) on curated Cantonese tasks, enhancing its ability to handle specific applications. Upon completion of the training, the model achieves state-of-the-art (SOTA) performance on four Cantonese benchmarks. After training on our dataset, the model also exhibits improved performance on other mainstream language tasks.

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling, RNA structure prediction, protein function inference, and single-cell transcriptomics. Meanwhile, we also discuss several key challenges, including data scarcity, computational complexity, and cross-omics integration, and explore future directions such as multimodal learning, hybrid AI models, and clinical applications. By offering a comprehensive perspective, this paper underscores the transformative potential of LLMs in driving innovations in bioinformatics and precision medicine.

Large vision-language models (LVLMs) have witnessed significant progress on visual understanding tasks. However, they often prioritize language knowledge over image information on visual reasoning tasks, incurring performance degradation. To tackle this issue, we first identify the drawbacks of existing solutions (i.e., limited multi-modal reasoning capacities, and insufficient and irrelevant visual descriptions). We then decompose visual reasoning process into two stages: proactive visual perception (i.e., eyesight) and textual reasoning (i.e., wisdom), and introduce a novel visual reasoning framework named ProReason. This framework features decoupled vision-reasoning capabilities and multi-run proactive perception. Briefly, given a multi-modal question, ProReason iterates proactive information collection and reasoning until the answer can be concluded with necessary and sufficient visual descriptions. Notably, the disassociation of capabilities allows seamless integration of existing large language models (LLMs) to compensate for the reasoning deficits of LVLMs. Our extensive experiments demonstrate that ProReason outperforms existing multi-step reasoning frameworks on various benchmarks for both open-source and closed-source models, with the average performance gain reaching 13.2%. Besides, the integration of LLMs allows ProReason to produce high-quality visual reasoning data, which empowers ProReason-distilled models (i.e., ProReason-VL and ProReason-Q3) to achieve superior performance in downstream tasks. Our insights into existing solutions and the decoupled perspective for feasible integration of LLMs illuminate future research on visual reasoning techniques, especially LLM-assisted ones. The code is available at https://github.com/lian-tian-mo-zun/Pro_Reason.

RNA-binding proteins (RBPs) play essential roles in post-transcriptional gene regulation via recognizing specific RNA molecules as well as modulating several key physiological processes in cellulo, represented by alternative splicing and RNA degradation. Despite extensive research, most existing approaches still rely on superficial sequence features or coarse structural representations, limiting their ability to capture the intricate nature of RBP-RNA interactions. The recent surge in large language models (LLMs), combined with advances in geometric deep learning for extracting three-dimensional representations, enables the integration of multi-modal, multi-scale biological data for precise modeling and biologically informed de novo RNA design. In this work, we curate and extend RPI15223 into a multi-resolution, structure-level RBP-RNA dataset, and introduce RBPtool, a multi-task, multi-resolution framework that combines a geometric vector perception (GVP) module together with a deep language model encoder to fuse sequence and structural information. Our tool achieves state-of-the-art performance on public benchmarks and the RPI15223 dataset, while also supporting fine-grained level predictions and enabling de novo RNA design through a generative module conditioned on protein, cell-type, and specified species. RBPtool provides a fast and versatile platform for both fundamental RBP-RNA research and practical RNA drug design, delivering enhanced predictive accuracy and fine-grained structural insights.

With the remarkable capabilities, large language models (LLMs) have emergedas essential elements in numerous NLP applications, while parameter-efficientfinetuning, especially LoRA, has gained popularity as a lightweight approachfor model customization. Meanwhile, various dropout methods, initially designedfor full finetuning with all the parameters updated, alleviates overfittingassociated with excessive parameter redundancy. Hence, a possible contradictionarises from negligible trainable parameters of LoRA and the effectiveness ofprevious dropout methods, which has been largely overlooked. To fill this gap,we first confirm that parameter-efficient LoRA is also overfitting-prone. Wethen revisit transformer-specific dropout methods, and establish theirequivalence and distinctions mathematically and empirically. Building upon thiscomparative analysis, we introduce a unified framework for a comprehensiveinvestigation, which instantiates these methods based on dropping position,structural pattern and compensation measure. Through this framework, we revealthe new preferences and performance comparisons of them when involved withlimited trainable parameters. This framework also allows us to amalgamate themost favorable aspects into a novel dropout method named HiddenKey. Extensiveexperiments verify the remarkable superiority and sufficiency of HiddenKeyacross multiple models and tasks, which highlights it as the preferred approachfor high-performance and parameter-efficient finetuning of LLMs.

With the rapid scaling of large language models (LLMs), serving numerouslow-rank adaptations (LoRAs) concurrently has become increasingly impractical,leading to unaffordable costs and necessitating more parameter-efficientfinetuning methods. In this work, we introduce Partially Rotation-enhanced Low-Rank Adaptation (PRoLoRA), an intra-layer sharing mechanism comprising fouressential components: broadcast reduction, rotation enhancement,partially-sharing refinement, and rectified initialization strategy. As asuperset of LoRA, PRoLoRA retains its advantages, and effectively circumventthe drawbacks of peer parameter-sharing methods with superior model capacity,practical feasibility, and broad applicability. Empirical experimentsdemonstrate the remarkably higher parameter efficiency of PRoLoRA in bothspecific parameter budget and performance target scenarios, and its scalabilityto larger LLMs. Notably, with one time less trainable parameters, PRoLoRA stilloutperforms LoRA on multiple instruction tuning datasets. Subsequently, anablation study is conducted to validate the necessity of individual componentsand highlight the superiority of PRoLoRA over three potential variants.Hopefully, the conspicuously higher parameter efficiency can establish PRoLoRAas a resource-friendly alternative to LoRA.

When communicating with elders with cognitive impairment, cognitive stimulation (CS) help to maintain the cognitive health of elders. Data sparsity is the main challenge in building CS-based dialogue systems, particularly in the Chinese language. To fill this gap, we construct a Chinese CS conversation (CSConv) dataset, which contains about 2.6K groups of dialogues with therapy principles and emotional support strategy labels. Making chit chat while providing emotional support is overlooked by the majority of existing cognitive dialogue systems. In this paper, we propose a multi-source knowledge fusion method for CS dialogue (CSD), to generate open-ended responses guided by the therapy principle and emotional support strategy. We first use a progressive mask method based on external knowledge to learn encoders as effective classifiers, which is the prerequisite to predict the therapy principle and emotional support strategy of the target response. Then a decoder interacts with the perceived therapy principle and emotional support strategy to generate responses. Extensive experiments conducted on the CSConv dataset demonstrate the effectiveness of the proposed method, while there is still a large space for improvement compared to human performance.