相关论文: Protein Lipograms

Multiple logic-based reconstructions of conceptual data modelling languages such as EER, UML Class Diagrams, and ORM exist. They mainly cover various fragments of the languages and none are formalised such that the logic applies…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

Signal processing (SP) techniques convert DNA and protein sequences into information that lead to successful drug discovery. One must, however, be aware about the difference between information and entropy1. Eight other physical properties…

Sparse coding, which is the decomposition of a vector using only a few basis elements, is widely used in machine learning and image processing. The basis set, also called dictionary, is learned to adapt to specific data. This approach has…

In Linguistics, a grapheme is a written unit of a writing system corresponding to a phonological sound. In Natural Language Processing tasks, written language is analysed through two different mediums, word analysis, and character analysis.…

Visual recognition of speech using the lip movement is called Lip-reading. Recent developments in this nascent field uses different neural networks as feature extractors which serve as input to a model which can map the temporal…

Protein circular permutations are crucial for understanding protein evolution and functionality. Traditional detection methods, sequence-based or structure-based, struggle with accuracy and computational efficiency, the latter also limited…

In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…

Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable…

Protein representation learning methods have shown great potential to yield useful representation for many downstream tasks, especially on protein classification. Moreover, a few recent studies have shown great promise in addressing…

Lipreading is understanding speech from observed lip movements. An observed series of lip motions is an ordered sequence of visual lip gestures. These gestures are commonly known, but as yet are not formally defined, as `visemes'. In this…

Although much effort has recently been devoted to training high-quality sentence embeddings, we still have a poor understanding of what they are capturing. "Downstream" tasks, often based on sentence classification, are commonly used to…

Lipton's reduction theory provides an intuitive and simple way for deducing the non-interference properties of concurrent programs, but it is difficult to directly apply the technique to verify linearizability of sophisticated fine-grained…

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

Over the past decade a considerable amount of research has been done to expand logic programming languages to handle incomplete information. One such language is the language of epistemic specifications. As is usual with logic programming…

Recent advances in Protein Language Models (PLMs) have transformed protein engineering, yet unlike their counterparts in Natural Language Processing (NLP), current PLMs exhibit a fundamental limitation: they excel in either Protein Language…

Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…

A new heuristic based on vertex invariants is developed to rapidly distinguish non-isomorphic graphs to a desired level of accuracy. The method is applied to sample subgraphs from an E.coli protein interaction network, and as a probe for…

Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a…

Motivated by old and new applications, we investigate Datalog as a language for sequence databases. We reconsider classical features of Datalog programs, such as negation, recursion, intermediate predicates, and relations of higher arities.…