相关论文: XLMOD: Cross-linking and chromatography derivatiza…

Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…

Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…

Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…

Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…

The capability to generate diverse text is a key challenge facing large language models (LLMs). Thus far, diversity has been studied via metrics such as $n$-gram diversity or diversity of BERT embeddings. However, for these kinds of…

Summary: Mass spectrometry coupled to liquid chromatography (LC-MS/MS) is a powerful technique for the charac-terisation of proteomes. However, the diverse software platforms available for processing the raw proteomics data, each produce…

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…

This study presents a broad perspective of hybrid process modeling and optimization combining the scientific knowledge and data analytics in bioprocessing and chemical engineering with a science-guided machine learning (SGML) approach. We…

Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Cumulant mapping employs a statistical reconstruction of the whole by sampling its parts. The theory developed in this work formalises and extends ad hoc methods of `multi-fold' or `multi-dimensional' covariance mapping. Explicit formulae…

This paper addresses the problem of semi-supervised transfer learning with limited cross-modality data in remote sensing. A large amount of multi-modal earth observation images, such as multispectral imagery (MSI) or synthetic aperture…

With the rapid advancements in multi-modal large language models (MLLMs), connectors play a pivotal role in bridging diverse modalities and enhancing model performance. However, the design and evolution of connectors have not been…

Large Language Models (LLMs) are widely used in both industry and academia for various tasks, yet evaluating the consistency of generated text responses continues to be a challenge. Traditional metrics like ROUGE and BLEU show a weak…

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential…

Motivation: Mass spectrometry-based proteomics is among the most commonly used methods for scrutinizing proteomic profiles in different organs for biological or medical researches. All the proteomic analyses including peptide/protein…

Large language models (LLMs) have been widely applied to assist in finding solutions for diverse questions. Prior work has proposed representing a method as a pair of a question and its corresponding solution, enabling method reuse.…

We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with…

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…