相关论文: Weighted genomic distance can hardly impose a boun…
The co-evolution between network structure and functional performance is a fundamental and challenging problem whose complexity emerges from the intrinsic interdependent nature of structure and function. Within this context, we investigate…
Given two labeled data-sets $\mathcal{S}$ and $\mathcal{T}$, we design a simple and efficient greedy algorithm to reweigh the loss function such that the limiting distribution of the neural network weights that result from training on…
We present Junk DNA Hypothesis by adopting a novel task-centric angle for the pre-trained weights of large language models (LLMs). It has been believed that weights in LLMs contain significant redundancy, leading to the conception that a…
The weighted-Hamming metric generalizes the Hamming metric by assigning different weights to blocks of coordinates. It is well-suited for applications such as coding over independent parallel channels, each of which has a different level of…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We develop a general framework for reasoning about distances between transition systems with quantitative information. Taking as starting point an arbitrary distance on system traces, we show how this leads to natural definitions of a…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
The need for tomographic reconstruction from sparse measurements arises when the measurement process is potentially harmful, needs to be rapid, or is uneconomical. In such cases, information from previous longitudinal scans of the same…
In order to take the weight of connection into consideration and to find a natural measurement of weight, we have collected papers in Econophysics and constructed a network of scientific communication to integrate idea transportation among…
Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect…
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…