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.

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.

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.

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.

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.

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.

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.