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.

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.

The softmax function is crucial in Transformer attention, which normalizes each row of the attention scores with summation to one. **Usually, tokens with larger attention scores are important for the final prediction.However, the softmax function can face a gradient vanishing issue for such important tokens (e.g., probabilities close to one), leading to optimization difficulties for the important tokens so that the performance may not be better.**In this paper, we propose Self-Adjust Softmax (SA-Softmax) to address this issue by modifying softmax(z) to z ⋅ softmax(z) and its normalized variant ^{(z - min(z_min,0))}⁄_{max(0,zmax)-min(zmin,0)} ⋅ softmax(z).We theoretically show that SA-Softmax provides enhanced gradient properties compared to the vanilla softmax function.Moreover, Attention can be seamlessly integrated into existing Transformer models to their attention mechanisms with minor adjustments.We conducted experiments to evaluate the empirical performance of Transformer models using compared to the vanilla softmax function. These experiments, involving models with up to 2.7 billion parameters, are conducted across diverse datasets, language tasks, and positional encoding methods.

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.

The attention mechanism is a fundamental component of the Transformer model, contributing to interactions among distinct tokens. In general, the attention scores are determined simply by the key-query products. However, this work’s occasional trial (combining DAPE and NoPE) of including additional MLPs on attention scores without position encoding indicates that the classical key-query multiplication may limit the performance of Transformers. In this work, we conceptualize attention as a feature map and apply the convolution operator (for neighboring attention scores across different heads) to mimic the processing methods in computer vision. Specifically, the main contribution of this paper is identifying and interpreting the Transformer length extrapolation problem as a result of the limited expressiveness of the naive query and key dot product, and we successfully translate the length extrapolation issue into a well-understood feature map processing problem, which is called Convolutional Data-Adaptive Position Encoding (CDAPE).The novel insight, which can be adapted to various attention-related models, reveals that the current Transformer architecture has the potential for further evolution. Extensive experiments demonstrate that treating attention as a feature map and applying convolution as a processing method significantly enhances Transformer performance.

Large Language Models (LLMs) have shown great potential in the biomedical domain with the advancement of retrieval-augmented generation (RAG). However, existing retrieval-augmented approaches face challenges in addressing diverse queries and documents, particularly for medical knowledge queries, resulting in sub-optimal performance. To address these limitations, we propose a novel plug-and-play LLM-based retrieval method called Self-Rewarding Tree Search (SeRTS) based on Monte Carlo Tree Search (MCTS) and a self-rewarding paradigm. By combining the reasoning capabilities of LLMs with the effectiveness of tree search, SeRTS boosts the zero-shot performance of retrieving high-quality and informative results for RAG. We further enhance retrieval performance by fine-tuning LLMs with Proximal Policy Optimization (PPO) objectives using the trajectories collected by SeRTS as feedback. Controlled experiments using the BioASQ-QA dataset with GPT-3.5-Turbo and LLama2-7b demonstrate that our method significantly improves the performance of the BM25 retriever and surpasses the strong baseline of self-reflection in both efficiency and scalability. Moreover, SeRTS generates higher-quality feedback for PPO training than self-reflection. Our proposed method effectively adapts LLMs to document retrieval tasks, enhancing their ability to retrieve highly relevant documents for RAG in the context of medical knowledge queries. This work presents a significant step forward in leveraging LLMs for accurate and comprehensive biomedical question answering.