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.

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 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.

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.

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) 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.