Related papers: Design Proteins Using Large Language Models: Enhan…

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective…

Language models have steadily increased in size over the past few years. They achieve a high level of performance on various natural language processing (NLP) tasks such as question answering and summarization. Large language models (LLMs)…

Integrating free-text explanations to in-context learning of large language models (LLM) is shown to elicit strong reasoning capabilities along with reasonable explanations. In this paper, we consider the problem of leveraging the…

Predictive analysis is a cornerstone of modern decision-making, with applications in various domains. Large Language Models (LLMs) have emerged as powerful tools in enabling nuanced, knowledge-intensive conversations, thus aiding in complex…

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a…

The popularity of LLaMA (Touvron et al., 2023a;b) and other recently emerged moderate-sized large language models (LLMs) highlights the potential of building smaller yet powerful LLMs. Regardless, the cost of training such models from…

Despite the impressive performance of large language models (LLMs), they often lag behind specialized models in various tasks. LLMs only use a fraction of the existing training data for in-context learning, while task-specific models…

We present MeshLLM, a novel framework that leverages large language models (LLMs) to understand and generate text-serialized 3D meshes. Our approach addresses key limitations in existing methods, including the limited dataset scale when…

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in…

Protein language models (pLMs) produce per-residue representations that capture evolutionary and structural information, yet their mean-pooled sequence embeddings are not explicitly trained to reflect functional, evolutionary or structural…

The impact of Transformer-based language models has been unprecedented in Natural Language Processing (NLP). The success of such models has also led to their adoption in other fields including bioinformatics. Taking this into account, this…

Recently, decoder-only pre-trained large language models (LLMs), with several tens of billion parameters, have significantly impacted a wide range of natural language processing (NLP) tasks. While encoder-only or encoder-decoder pre-trained…

User profile modeling plays a key role in personalized systems, as it requires building accurate profiles and updating them with new information. In this paper, we present two high-quality open-source user profile datasets: one for profile…

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…

The rapid advancement of large language models has opened new avenues for automating complex problem-solving tasks such as algorithmic coding and competitive programming. This paper introduces a novel evaluation technique, LLM-ProS, to…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

The creation of Business Process Model and Notation (BPMN) models is a complex and time-consuming task requiring both domain knowledge and proficiency in modeling conventions. Recent advances in large language models (LLMs) have…

Although Large Language Models (LLMs) have established pre-dominance in automated code generation, they are not devoid of shortcomings. The pertinent issues primarily relate to the absence of execution guarantees for generated code, a lack…

Large language models (LLMs) achieve strong performance across diverse tasks, largely driven by high-quality web data used in pre-training. However, recent studies indicate this data source is rapidly depleting. Synthetic data emerges as a…

Evaluating Large Language Models (LLMs) in open-ended scenarios is challenging because existing benchmarks and metrics can not measure them comprehensively. To address this problem, we propose to fine-tune LLMs as scalable judges (JudgeLM)…