Related papers: Haplotype Assembly: An Information Theoretic View
Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…
Most graph neural networks follow the message passing mechanism. However, it faces the over-smoothing problem when multiple times of message passing is applied to a graph, causing indistinguishable node representations and prevents the…
In this paper we develop a novel mathematical formalism for the modeling of neural information networks endowed with additional structure in the form of assignments of resources, either computational or metabolic or informational. The…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
An assembly is a large population of neurons whose synchronous firing is hypothesized to represent a memory, concept, word, and other cognitive categories. Assemblies are believed to provide a bridge between high-level cognitive phenomena…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
We consider the following problem for a fixed graph H: given a graph G and two H-colorings of G, i.e. homomorphisms from G to H, can one be transformed (reconfigured) into the other by changing one color at a time, maintaining an H-coloring…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
Correspondence homomorphisms are both a generalization of standard homomorphisms and a generalization of correspondence colourings. For a fixed target graph $H$, the problem is to decide whether an input graph $G$, with each edge labeled by…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Multi-hop machine reading comprehension is a challenging task in natural language processing as it requires more reasoning ability across multiple documents. Spectral models based on graph convolutional networks have shown good inferring…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…