Model customization requires high-quality and diverse datasets, but acquiring such data remains challenging and costly. Although large language models (LLMs) can synthesize training data, current approaches are constrained by limited seed data, model bias and insufficient control over the generation process, resulting in limited diversity and biased distribution with the increase of data scales. To tackle this challenge, we present TreeSynth, a tree-guided subspace-based data synthesis framework that recursively partitions the entire data space into hierar-chical subspaces, enabling comprehensive and diverse scaling of data synthesis. Briefly, given a task-specific description, we construct a data space partitioning tree by iteratively executing criteria determination and subspace coverage steps. This hierarchically divides the whole space (i.e., root node) into mutually exclusive and complementary atomic subspaces (i.e., leaf nodes). By collecting synthesized data according to the attributes of each leaf node, we obtain a diverse dataset that fully covers the data space. Empirically, our extensive experiments demonstrate that TreeSynth surpasses both human-designed datasets and the state-of-the-art data synthesis baselines, achieving maximum improvements of 45.2% in data diversity and 17.6% in downstream task performance across various models and tasks. Hopefully, TreeSynth provides a scalable solution to synthesize diverse and comprehensive datasets from scratch without human intervention.

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis and synthesis, attracting widespread attention from academics and medicine. In this paper, we systematically investigate the application of prompt-based methods with LLMs to biological sequences, including DNA, RNA, proteins, and drug discovery tasks. Specifically, we focus on how prompt engineering enables LLMs to tackle domain-specific problems, such as promoter sequence prediction, protein structure modeling, and drug-target binding affinity prediction, often with limited labeled data. Furthermore, our discussion highlights the transformative potential of prompting in bioinformatics while addressing key challenges such as data scarcity, multimodal fusion, and computational resource limitations. Our aim is for this paper to function both as a foundational primer for newcomers and a catalyst for continued innovation within this dynamic field of study.

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 language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of these LLMs. However, current benchmarks can hardly evaluate the performance of these models across diverse tasks effectively. In this paper, we introduce a comprehensive prompting-based benchmarking framework, termed Bio-benchmark, which includes 30 key bioinformatics tasks covering areas such as proteins, RNA, drugs, electronic health records, and traditional Chinese medicine. Using this benchmark, we evaluate six mainstream LLMs, including GPT-4o and Llama-3.1-70b, etc., using 0-shot and few-shot Chain-of-Thought (CoT) settings without fine-tuning to reveal their intrinsic capabilities. To improve the efficiency of our evaluations, we demonstrate BioFinder, a new tool for extracting answers from LLM responses, which increases extraction accuracy by round 30% compared to existing methods. Our benchmark results show the biological tasks suitable for current LLMs and identify specific areas requiring enhancement. Furthermore, we propose targeted prompt engineering strategies for optimizing LLM performance in these contexts. Based on these findings, we provide recommendations for the development of more robust LLMs tailored for various biological applications. This work offers a comprehensive evaluation framework and robust tools to support the application of LLMs in bioinformatics.

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.

The rapid scaling of large language models necessitates more lightweight finetuning methods to reduce the explosive GPU memory overhead when numerous customized models are served simultaneously. Targeting more parameter-efficient low-rank adaptation (LoRA), parameter sharing presents a promising solution. Empirically, our research into high-level sharing principles highlights the indispensable role of differentiation in reversing the detrimental effects of pure sharing. Guided by this finding, we propose Mixture of Shards (MoS), incorporating both inter-layer and intra-layer sharing schemes, and integrating four nearly cost-free differentiation strategies, namely subset selection, pair dissociation, vector sharding, and shard privatization. Briefly, it selects a designated number of shards from global pools with a Mixture-of-Experts (MoE)-like routing mechanism before sequentially concatenating them to low-rank matrices. Hence, it retains all the advantages of LoRA while offering enhanced parameter efficiency, and effectively circumvents the drawbacks of peer parameter-sharing methods. Our empirical experiments demonstrate approximately 8x parameter savings in a standard LoRA setting. The ablation study confirms the significance of each component. Our insights into parameter sharing and MoS method may illuminate future developments of more parameter-efficient finetuning methods.

Existing dialogue data augmentation (DA) techniques predominantly focus on augmenting utterance-level dialogues, which makes it difficult to take dialogue contextual information into account. The advent of large language models (LLMs) has simplified the implementation of multi-turn dialogues. Due to absence of professional understanding and knowledge, it remains challenging to deliver satisfactory performance in low-resource domain, like psychological dialogue dialogue. DA involves creating new training or prompting data based on the existing data, which help the model better understand and generate psychology-related responses. In this paper, we aim to address the issue of multi-turn dialogue data augmentation for boosted performance in the psychology domain. We propose a knowledge-driven progressive thought prompting method to guide LLM to generate multi-turn psychology-related dialogue. This method integrates a progressive thought generator, a psychology knowledge generator, and a multi-turn dialogue generator. The thought generated by the progressive thought generator serves as a prompt to prevent the generated dialogue from having significant semantic deviations, while the psychology knowledge generator produces psychological knowledge to serve as the dialogue history for the LLM, guiding the dialogue generator to create multi-turn psychological dialogue. To ensure the precision of multi-turn psychological dialogue generation by LLM, a meticulous professional evaluation is required. Extensive experiments conducted on three datasets related to psychological dialogue verify the effectiveness of the proposed method.

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

With the remarkable capabilities, large language models (LLMs) have emerged as essential elements in numerous NLP applications, while parameter-efficient finetuning, especially LoRA, has gained popularity as a lightweight approach for model customization. Meanwhile, various dropout methods, initially designed for full finetuning with all the parameters updated, alleviates overfitting associated with excessive parameter redundancy. Hence, a possible contradiction arises from negligible trainable parameters of LoRA and the effectiveness of previous dropout methods, which has been largely overlooked. To fill this gap, we first confirm that parameter-efficient LoRA is also overfitting-prone. We then revisit transformer-specific dropout methods, and establish their equivalence and distinctions mathematically and empirically. Building upon this comparative analysis, we introduce a unified framework for a comprehensive investigation, which instantiates these methods based on dropping position, structural pattern and compensation measure. Through this framework, we reveal the new preferences and performance comparisons of them when involved with limited trainable parameters. This framework also allows us to amalgamate the most favorable aspects into a novel dropout method named HiddenKey. Extensive experiments verify the remarkable superiority and sufficiency of HiddenKey across multiple models and tasks, which highlights it as the preferred approach for 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 CS 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 CS 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 CS principle and emotional support strategy of the target response. Then a decoder interacts with the perceived CS 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.