在采矿基因相互作用和途径知识中对大型语言模型的全面评估
Muhammad Azam1,2, Yibo Chen1,2,3, Micheal Olaolu Arowolo1,2
1Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
bioRxiv : the preprint server for biology
|February 8, 2024
概括
大型语言模型 (LLM) 显示出分析基因网络和生物通路的前景. 基于API的模型,如ChatGPT-4,优于开源选项,凸显了生物医学研究中需要仔细选择LLM的需要.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 生物通路的自动文本挖掘对于了解疾病机制和药物开发至关重要.
- 手册文学策划很难跟上科学出版物的快速增长.
- 大型语言模型 (LLM) 由于其广泛的培训数据,为有效的路径分析提供了潜力.
研究的目的:
- 评估21个大型语言模型 (LLM) 在分析生物通路中的有效性.
- 为了比较基于API和开源的LLM在基因调节关系和KEGG路径识别任务上的性能.
主要方法:
- 评估了21个LLM,包括基于API和开源模型.
- 专注于预测基因调节关系 (激活,抑制,酸化) 和识别KEGG通路组件.
- 使用了性能指标,如精度,回忆,F1分数和Jaccard相似度指数.
主要成果:
- 基于API的模型,特别是ChatGPT-4和Claude-Pro,在基因调节关系预测和KEGG通路识别方面都表现出卓越的性能.
- 开源模型通常落后于基于API的模型,猎-180b-chat和 llama1-7b在他们的类别中表现出最高的性能.
- 在评估的LLMs中观察到显著的绩效差异.
结论:
- 在生物医学研究中,LLM是基因网络分析和路径映射的宝贵工具.
- 由于有效性各不相同,必须仔细选择LLM.
- 这项研究提供了使用LLM作为生物途径数据的知识图的见解.
相关概念视频
Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Higher Mental Functions of the Brain: Language
Language is a system of communication that allows the expression of thoughts, ideas, and feelings. The brain processes language in both hemispheres.
Language formation and comprehension take place in the dominant hemisphere. The dominant hemisphere is responsible for understanding the meaning of spoken, written, or sign language, as well as the ability to communicate. For most people, the left hemisphere is the dominant one. The right hemisphere, then, gives tone and emotional context to the...
Language formation and comprehension take place in the dominant hemisphere. The dominant hemisphere is responsible for understanding the meaning of spoken, written, or sign language, as well as the ability to communicate. For most people, the left hemisphere is the dominant one. The right hemisphere, then, gives tone and emotional context to the...
Components of Language
Language, whether spoken, signed, or written, consists of specific components: lexicon and grammar. The lexicon is the vocabulary of a language, comprising its words. Grammar is the set of rules used to convey meaning through the lexicon. For example, English grammar adds “-ed” to most verbs to indicate past tense. Words are formed by combining phonemes, which are the basic sound units of a language. Different languages have different sets of phonemes (e.g., “ah” vs. “eh”). Phonemes combine to...
Language Development
Children master language quickly and with relative ease, supported by both biological predisposition and reinforcement. B. F. Skinner (1957) proposed that language is learned through reinforcement, while Noam Chomsky (1965) argued that language acquisition mechanisms are biologically determined.
The critical period for language acquisition suggests that the ability to acquire language is at its peak early in life. As people age, this proficiency decreases. Language development begins very...
The critical period for language acquisition suggests that the ability to acquire language is at its peak early in life. As people age, this proficiency decreases. Language development begins very...
Language and Cognition
Language serves as a bridge between ideas and communication, influencing how individuals perceive and interact with the world. Psychologists have long debated whether language shapes thought or vice versa. This discussion gained grip with Edward Sapir and Benjamin Lee Whorf in the 1940s, who proposed that language determines thought, a concept known as linguistic determinism. They suggested that the vocabulary and structure of a language influence how its speakers think and perceive reality.


