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Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…

其他定量生物学 · 定量生物学 2025-01-29 Wang Liang

Large Language Models have demonstrated remarkable progress in general-purpose capabilities and can achieve strong performance in specific domains through fine-tuning on domain-specific data. However, acquiring high-quality data for target…

人工智能 · 计算机科学 2026-05-29 Tong Ye , Hang Yu , Tengfei Ma , Xuhong Zhang , Jianguo Li , Peng Di , Peiyu Liu , Jianwei Yin , Wenhai Wang

DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…

基因组学 · 定量生物学 2026-05-21 Taewon Kim , Jihwan Shin , Hyomin Kim , Youngmok Jung , Jonghoon Lee , Won-Chul Lee , Sungsoo Ahn , Insu Han

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…

Large Language Models (LLMs) have the unique capability to understand and generate human-like text from input queries. When fine-tuned, these models show enhanced performance on domain-specific queries. OpenAI highlights the process of…

计算与语言 · 计算机科学 2024-07-02 Scott Barnett , Zac Brannelly , Stefanus Kurniawan , Sheng Wong

Fine-tuning large language models (LLMs) with limited data poses a practical challenge in low-resource languages, specialized domains, and constrained deployment settings. While pre-trained LLMs provide strong foundations, effective…

计算与语言 · 计算机科学 2025-10-29 Marton Szep , Daniel Rueckert , Rüdiger von Eisenhart-Rothe , Florian Hinterwimmer

Large language models (LLMs) excel in general tasks but struggle with domain-specific ones, requiring fine-tuning with specific data. With many open-source LLMs available, selecting the best model for fine-tuning downstream tasks is…

计算与语言 · 计算机科学 2025-09-05 Wei Huang , Huang Wei , Yinggui Wang

The current standard approach for fine-tuning transformer-based language models includes a fixed number of training epochs and a linear learning rate schedule. In order to obtain a near-optimal model for the given downstream task, a search…

计算与语言 · 计算机科学 2022-02-08 Felix Stollenwerk

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…

计算与语言 · 计算机科学 2024-04-24 Yang Tan , Mingchen Li , Bingxin Zhou , Bozitao Zhong , Lirong Zheng , Pan Tan , Ziyi Zhou , Huiqun Yu , Guisheng Fan , Liang Hong

Foundation language models learn from their finetuning input context in different ways. In this paper, we reformulate inputs during finetuning for challenging translation tasks, leveraging model strengths from pretraining in novel ways to…

计算与语言 · 计算机科学 2026-01-05 Brian Yu , Hansen Lillemark , Kurt Keutzer

The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…

基因组学 · 定量生物学 2024-09-25 Qihang Zhao , Chi Zhang , Weixiong Zhang

The rapid advancement of foundation modelslarge-scale neural networks trained on diverse, extensive datasetshas revolutionized artificial intelligence, enabling unprecedented advancements across domains such as natural language processing,…

We propose a new finetuning method to provide pre-trained large language models (LMs) the ability to scale test-time compute through the diffusion framework. By increasing the number of diffusion steps, we show our finetuned models achieve…

计算与语言 · 计算机科学 2025-06-04 Edoardo Cetin , Tianyu Zhao , Yujin Tang

Pretraining DNA language models (DNALMs) on the full human genome is resource-intensive, yet often considered necessary for strong downstream performance. Inspired by recent findings in NLP and long-context modeling, we explore an…

基因组学 · 定量生物学 2025-06-24 Sohan Mupparapu , Parameswari Krishnamurthy , Ratish Puduppully

This paper presents SOLOMON, a novel Neuro-inspired Large Language Model (LLM) Reasoning Network architecture that enhances the adaptability of foundation models for domain-specific applications. Through a case study in semiconductor layout…

计算与语言 · 计算机科学 2025-02-10 Bo Wen , Xin Zhang

Fine-tuning of Large Language Models (LLMs) for downstream tasks, performed on domain-specific data has shown significant promise. However, commercial use of such LLMs is limited by the high computational cost required for their deployment…

计算与语言 · 计算机科学 2025-03-06 Boris Nazarov , Darya Frolova , Yackov Lubarsky , Alexei Gaissinski , Pavel Kisilev

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…

基因组学 · 定量生物学 2024-09-24 Gonzalo Benegas , Chengzhong Ye , Carlos Albors , Jianan Canal Li , Yun S. Song

Learning from Text-Attributed Graphs (TAGs) has attracted significant attention due to its wide range of real-world applications. The rapid evolution of language models (LMs) has revolutionized the way we process textual data, which…

机器学习 · 计算机科学 2024-10-25 Rui Xue , Xipeng Shen , Ruozhou Yu , Xiaorui Liu

Large Language Models (LLMs) have become a cornerstone in Natural Language Processing (NLP), achieving impressive performance in text generation. Their token-level representations capture rich, human-aligned semantics. However, pooling…

计算与语言 · 计算机科学 2025-09-25 Benedikt Roth , Stephan Rappensperger , Tianming Qiu , Hamza Imamović , Julian Wörmann , Hao Shen

Nowadays, billions of people engage in communication and express their opinions on the internet daily. Unfortunately, not all of these expressions are friendly or compliant, making content moderation an indispensable task. A common approach…

机器学习 · 计算机科学 2024-03-08 Huan Ma , Changqing Zhang , Huazhu Fu , Peilin Zhao , Bingzhe Wu
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