相关论文: Protein Lipograms
The impact of Transformer-based language models has been unprecedented in Natural Language Processing (NLP). The success of such models has also led to their adoption in other fields including bioinformatics. Taking this into account, this…
A theory is developed which uses "networks" (directed acyclic graphs with some extra structure) as a formalism for expressions in multilinear algebra. It is shown that this formalism is valid for arbitrary PROPs (short for 'PROducts and…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Several methods have recently been proposed to analyze speech and automatically infer the personality of the speaker. These methods often rely on prosodic and other hand crafted speech processing features extracted with off-the-shelf…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
The use of subword-level information (e.g., characters, character n-grams, morphemes) has become ubiquitous in modern word representation learning. Its importance is attested especially for morphologically rich languages which generate a…
The Categorical Compositional Distributional (DisCoCat) Model is a powerful mathematical model for composing the meaning of sentences in natural languages. Since we can think of biological sequences as the "language of life", it is…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…
Proteinoids are solidified gels made from poly(amino acids) based polymers that exhibit oscillatory electrical activity. It has been proposed that proteinoids are capable of performing analog computing as their electrical activity can be…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
In this article, we present a fresh perspective on language, combining ideas from various sources, but mixed in a new synthesis. As in the minimalist program, the question is whether we can formulate an elegant formalism, a universal…
Probing the multilingual knowledge of linguistic structure in LLMs, often characterized as sequence labeling, faces challenges with maintaining output templates in current text-to-text prompting strategies. To solve this, we introduce a…
When looking at the structure of natural language, "phrases" and "words" are central notions. We consider the problem of identifying such "meaningful subparts" of language of any length and underlying composition principles in a completely…
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemical databases. However, misidentifications may result due to…
Descriptive grammars are highly valuable, but writing them is time-consuming and difficult. Furthermore, while linguists typically use corpora to create them, grammar descriptions often lack quantitative data. As for formal grammars, they…