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Large Language Models for Bioinformatics

arXiv.org Artificial Intelligence

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.


AgoraSpeech: A multi-annotated comprehensive dataset of political discourse through the lens of humans and AI

arXiv.org Artificial Intelligence

Political discourse datasets are important for gaining political insights, analyzing communication strategies or social science phenomena. Although numerous political discourse corpora exist, comprehensive, high-quality, annotated datasets are scarce. This is largely due to the substantial manual effort, multidisciplinarity, and expertise required for the nuanced annotation of rhetorical strategies and ideological contexts. In this paper, we present AgoraSpeech, a meticulously curated, high-quality dataset of 171 political speeches from six parties during the Greek national elections in 2023. The dataset includes annotations (per paragraph) for six natural language processing (NLP) tasks: text classification, topic identification, sentiment analysis, named entity recognition, polarization and populism detection. A two-step annotation was employed, starting with ChatGPT-generated annotations and followed by exhaustive human-in-the-loop validation. The dataset was initially used in a case study to provide insights during the pre-election period. However, it has general applicability by serving as a rich source of information for political and social scientists, journalists, or data scientists, while it can be used for benchmarking and fine-tuning NLP and large language models (LLMs).


What Matters for In-Context Learning: A Balancing Act of Look-up and In-Weight Learning

arXiv.org Artificial Intelligence

Large Language Models (LLMs) have demonstrated impressive performance in various tasks, including In-Context Learning (ICL), where the model performs new tasks by conditioning solely on the examples provided in the context, without updating the model's weights. While prior research has explored the roles of pretraining data and model architecture, the key mechanism behind ICL remains unclear. In this work, we systematically uncover properties present in LLMs that support the emergence of ICL. To disambiguate these factors, we conduct a study with a controlled dataset and data sequences using a deep autoregressive model. We show that conceptual repetitions in the data sequences are crucial for ICL, more so than previously indicated training data properties like burstiness or long-tail distribution. Conceptual repetitions could refer to $n$-gram repetitions in textual data or exact image copies in image sequence data. Such repetitions also offer other previously overlooked benefits such as reduced transiency in ICL performance. Furthermore, we show that the emergence of ICL depends on balancing the in-weight learning objective with the in-context solving ability during training.


Multiagent Finetuning: Self Improvement with Diverse Reasoning Chains

arXiv.org Artificial Intelligence

Large language models (LLMs) have achieved remarkable performance in recent years but are fundamentally limited by the underlying training data. To improve models beyond the training data, recent works have explored how LLMs can be used to generate synthetic data for autonomous self-improvement. However, successive steps of self-improvement can reach a point of diminishing returns. In this work, we propose a complementary approach towards self-improvement where finetuning is applied to a multiagent society of language models. A group of language models, all starting from the same base model, are independently specialized by updating each one using data generated through multiagent interactions among the models. By training each model on independent sets of data, we illustrate how this approach enables specialization across models and diversification over the set of models. As a result, our overall system is able to preserve diverse reasoning chains and autonomously improve over many more rounds of fine-tuning than single-agent self-improvement methods. We quantitatively illustrate the efficacy of the approach across a wide suite of reasoning tasks.


Cascaded Self-Evaluation Augmented Training for Efficient Multimodal Large Language Models

arXiv.org Artificial Intelligence

Efficient Multimodal Large Language Models (EMLLMs) have rapidly advanced recently. Incorporating Chain-of-Thought (CoT) reasoning and step-by-step self-evaluation has improved their performance. However, limited parameters often hinder EMLLMs from effectively using self-evaluation during inference. Key challenges include synthesizing evaluation data, determining its quantity, optimizing training and inference strategies, and selecting appropriate prompts. To address these issues, we introduce Self-Evaluation Augmented Training (SEAT). SEAT uses more powerful EMLLMs for CoT reasoning, data selection, and evaluation generation, then trains EMLLMs with the synthesized data. However, handling long prompts and maintaining CoT reasoning quality are problematic. Therefore, we propose Cascaded Self-Evaluation Augmented Training (Cas-SEAT), which breaks down lengthy prompts into shorter, task-specific cascaded prompts and reduces costs for resource-limited settings. During data synthesis, we employ open-source 7B-parameter EMLLMs and annotate a small dataset with short prompts. Experiments demonstrate that Cas-SEAT significantly boosts EMLLMs' self-evaluation abilities, improving performance by 19.68%, 55.57%, and 46.79% on the MathVista, Math-V, and We-Math datasets, respectively. Additionally, our Cas-SEAT Dataset serves as a valuable resource for future research in enhancing EMLLM self-evaluation.


Collaboration of Large Language Models and Small Recommendation Models for Device-Cloud Recommendation

arXiv.org Artificial Intelligence

Large Language Models (LLMs) for Recommendation (LLM4Rec) is a promising research direction that has demonstrated exceptional performance in this field. However, its inability to capture real-time user preferences greatly limits the practical application of LLM4Rec because (i) LLMs are costly to train and infer frequently, and (ii) LLMs struggle to access real-time data (its large number of parameters poses an obstacle to deployment on devices). Fortunately, small recommendation models (SRMs) can effectively supplement these shortcomings of LLM4Rec diagrams by consuming minimal resources for frequent training and inference, and by conveniently accessing real-time data on devices. In light of this, we designed the Device-Cloud LLM-SRM Collaborative Recommendation Framework (LSC4Rec) under a device-cloud collaboration setting. LSC4Rec aims to integrate the advantages of both LLMs and SRMs, as well as the benefits of cloud and edge computing, achieving a complementary synergy. We enhance the practicability of LSC4Rec by designing three strategies: collaborative training, collaborative inference, and intelligent request. During training, LLM generates candidate lists to enhance the ranking ability of SRM in collaborative scenarios and enables SRM to update adaptively to capture real-time user interests. During inference, LLM and SRM are deployed on the cloud and on the device, respectively. LLM generates candidate lists and initial ranking results based on user behavior, and SRM get reranking results based on the candidate list, with final results integrating both LLM's and SRM's scores. The device determines whether a new candidate list is needed by comparing the consistency of the LLM's and SRM's sorted lists. Our comprehensive and extensive experimental analysis validates the effectiveness of each strategy in LSC4Rec.


Iconicity in Large Language Models

arXiv.org Artificial Intelligence

Lexical iconicity, a direct relation between a word's meaning and its form, is an important aspect of every natural language, most commonly manifesting through sound-meaning associations. Since Large language models' (LLMs') access to both meaning and sound of text is only mediated (meaning through textual context, sound through written representation, further complicated by tokenization), we might expect that the encoding of iconicity in LLMs would be either insufficient or significantly different from human processing. This study addresses this hypothesis by having GPT-4 generate highly iconic pseudowords in artificial languages. To verify that these words actually carry iconicity, we had their meanings guessed by Czech and German participants (n=672) and subsequently by LLM-based participants (generated by GPT-4 and Claude 3.5 Sonnet). The results revealed that humans can guess the meanings of pseudowords in the generated iconic language more accurately than words in distant natural languages and that LLM-based participants are even more successful than humans in this task. This core finding is accompanied by several additional analyses concerning the universality of the generated language and the cues that both human and LLM-based participants utilize.


Exploring Large Language Models for Translating Romanian Computational Problems into English

arXiv.org Artificial Intelligence

Recent studies have suggested that large language models (LLMs) underperform on mathematical and computer science tasks when these problems are translated from Romanian into English, compared to their original Romanian format. Accurate translation is critical for applications ranging from automatic translations in programming competitions to the creation of high-quality educational materials, as well as minimizing errors or fraud in human translations. This study shows that robust large language models (LLMs) can maintain or even enhance their performance in translating less common languages when given well-structured prompts. Our findings suggest that LLMs, with appropriate supervision, can be reliably used for the automatic translation of IOI (International Olympiad in Informatics)-style tasks. We evaluate several translation methods across multiple LLMs, including OpenRoLLM, Llama 3.1 8B, Llama 3.2 3B and GPT-4o, assessing their translation accuracy and performance stability through repeated runs. Additionally, we augment the OJI (Romanian County-Level Informatics Olympiad) Romanian dataset with accurate English translations, enhancing its utility for future LLM training and evaluation. Through detailed syntactic and semantic analyses, we confirm that with human oversight, LLMs can serve as a viable solution for multilingual problem-solving. We also compare the translation quality of LLMs against human translators, as evaluated by a certified expert, underscoring the potential of LLMs in realworld scenarios.


Vision-Language Models for Autonomous Driving: CLIP-Based Dynamic Scene Understanding

arXiv.org Artificial Intelligence

Scene understanding is essential for enhancing driver safety, generating human-centric explanations for Automated Vehicle (AV) decisions, and leveraging Artificial Intelligence (AI) for retrospective driving video analysis. This study developed a dynamic scene retrieval system using Contrastive Language-Image Pretraining (CLIP) models, which can be optimized for real-time deployment on edge devices. The proposed system outperforms state-of-the-art in-context learning methods, including the zero-shot capabilities of GPT-4o, particularly in complex scenarios. By conducting frame-level analysis on the Honda Scenes Dataset, which contains a collection of about 80 hours of annotated driving videos capturing diverse real-world road and weather conditions, our study highlights the robustness of CLIP models in learning visual concepts from natural language supervision. Results also showed that fine-tuning the CLIP models, such as ViT-L/14 and ViT-B/32, significantly improved scene classification, achieving a top F1 score of 91.1%. These results demonstrate the ability of the system to deliver rapid and precise scene recognition, which can be used to meet the critical requirements of Advanced Driver Assistance Systems (ADAS). This study shows the potential of CLIP models to provide scalable and efficient frameworks for dynamic scene understanding and classification. Furthermore, this work lays the groundwork for advanced autonomous vehicle technologies by fostering a deeper understanding of driver behavior, road conditions, and safety-critical scenarios, marking a significant step toward smarter, safer, and more context-aware autonomous driving systems.


LLMQuoter: Enhancing RAG Capabilities Through Efficient Quote Extraction From Large Contexts

arXiv.org Artificial Intelligence

We introduce LLMQuoter, a lightweight, distillation-based model designed to enhance Retrieval Augmented Generation (RAG) by extracting the most relevant textual evidence for downstream reasoning tasks. Built on the LLaMA-3B architecture and fine-tuned with Low-Rank Adaptation (LoRA) on a 15,000-sample subset of HotpotQA, LLMQuoter adopts a "quote-first-then-answer" strategy, efficiently identifying key quotes before passing curated snippets to reasoning models. This workflow reduces cognitive overhead and outperforms full-context approaches like Retrieval-Augmented Fine-Tuning (RAFT), achieving over 20-point accuracy gains across both small and large language models. By leveraging knowledge distillation from a high-performing teacher model, LLMQuoter achieves competitive results in a resource-efficient fine-tuning setup. It democratizes advanced RAG capabilities, delivering significant performance improvements without requiring extensive model retraining. Our results highlight the potential of distilled quote-based reasoning to streamline complex workflows, offering a scalable and practical solution for researchers and practitioners alike.