相关论文: A minimum principle in mRNA editing ?
Machine learning models need to be continually updated or corrected to ensure that the prediction accuracy remains consistently high. In this study, we consider scenarios where developers should be careful to change the prediction results…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Network pruning is a widely-used compression technique that is able to significantly scale down overparameterized models with minimal loss of accuracy. This paper shows that pruning may create or exacerbate disparate impacts. The paper…
We argue that the minimal chiral background for the two-pion exchange nucleon-nucleon interaction has nowadays a rather firm conceptual basis, which entitles it to become a standard ingredient of any modern potential. In order to facilitate…
A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a…
We study the computational problem of computing a fair means clustering of discrete vectors, which admits an equivalent formulation as editing a colored matrix into one with few distinct color-balanced rows by changing at most $k$ values.…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
PCA (Principal Component Analysis) and its variants areubiquitous techniques for matrix dimension reduction and reduced-dimensionlatent-factor extraction. One significant challenge in using PCA, is thechoice of the number of principal…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
A methodology for using random sketching in the context of model order reduction for high-dimensional parameter-dependent systems of equations was introduced in [Balabanov and Nouy 2019, Part I]. Following this framework, we here construct…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
Recent work (Feng et al., 2018) establishes the presence of short, uninterpretable input fragments that yield high confidence and accuracy in neural models. We refer to these as Minimal Prediction Preserving Inputs (MPPIs). In the context…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to lead optimization. Yet a fundamental limitation emerges:…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…