The springing up of large language models(LLMs)has shifted the community from single-task-orientated natural language processing(NLP)research to a holistic end-to-end multi-task learning paradigm.Along this line of re...The springing up of large language models(LLMs)has shifted the community from single-task-orientated natural language processing(NLP)research to a holistic end-to-end multi-task learning paradigm.Along this line of research endeavors in the area,LLM-based prompting methods have attracted much attention,partially due to the technological advantages brought by prompt engineering(PE)as well as the underlying NLP principles disclosed by various prompting methods.Traditional supervised learning usually requires training a model based on labeled data and then making predictions.In contrast,PE methods directly use the powerful capabilities of existing LLMs(e.g.,GPT-3 and GPT-4)via composing appropriate prompts,especially under few-shot or zero-shot scenarios.Facing the abundance of studies related to the prompting and the ever-evolving nature of this field,this article aims to 1)illustrate a novel perspective to review existing PE methods within the well-established communication theory framework,2)facilitate a better/deeper understanding of developing trends of existing PE methods used in three typical tasks,and 3)shed light on promising research directions for future PE methods.展开更多
Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timesc...Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.展开更多
文摘The springing up of large language models(LLMs)has shifted the community from single-task-orientated natural language processing(NLP)research to a holistic end-to-end multi-task learning paradigm.Along this line of research endeavors in the area,LLM-based prompting methods have attracted much attention,partially due to the technological advantages brought by prompt engineering(PE)as well as the underlying NLP principles disclosed by various prompting methods.Traditional supervised learning usually requires training a model based on labeled data and then making predictions.In contrast,PE methods directly use the powerful capabilities of existing LLMs(e.g.,GPT-3 and GPT-4)via composing appropriate prompts,especially under few-shot or zero-shot scenarios.Facing the abundance of studies related to the prompting and the ever-evolving nature of this field,this article aims to 1)illustrate a novel perspective to review existing PE methods within the well-established communication theory framework,2)facilitate a better/deeper understanding of developing trends of existing PE methods used in three typical tasks,and 3)shed light on promising research directions for future PE methods.
基金supported by Shenzhen Science and Technology Innovation Committee(JCYJ20170413173837121)the Hong Kong Research Grant Council(HKUST C6009-15G,14203915,16302214,16304215,16318816,and AoE/P-705/16)+2 种基金King Abdullah University of Science and Technology(KAUST) Office of Sponsored Research(OSR)(OSR-2016-CRG5-3007)Guangzhou Science Technology and Innovation Commission(201704030116)Innovation and Technology Commission(ITCPD/17-9and ITC-CNERC14SC01)
文摘Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.
