Related papers: gggenomes: effective and versatile visualizations …
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…
This paper describes structuring data and constructing plots to explore forest classification models interactively. A forest classifier is an example of an ensemble, produced by bagging multiple trees. The process of bagging and combining…
Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the…
Many interesting datasets ubiquitous in machine learning and deep learning can be described via graphs. As the scale and complexity of graph-structured datasets increase, such as in expansive social networks, protein folding, chemical…
Scientific data sets continue to increase in both size and complexity. In the past, dedicated graphics systems at supercomputing centers were required to visualize large data sets, but as the price of commodity graphics hardware has dropped…
Network traffic is difficult to monitor and analyze, especially in high-bandwidth networks. Performance analysis, in particular, presents extreme complexity and scalability challenges. GPU (Graphics Processing Unit) technology has been…
Diabetes is a worldwide health issue affecting millions of people. Machine learning methods have shown promising results in improving diabetes prediction, particularly through the analysis of diverse data types, namely gene expression data.…
Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain…
Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory…
We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional kernel networks to graph-structured data, by representing…
Glioblastoma is a highly aggressive form of brain cancer characterized by rapid progression and poor prognosis. Despite advances in treatment, the underlying genetic mechanisms driving this aggressiveness remain poorly understood. In this…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
In this short article I introduce the knotR package, which creates two dimensional knot diagrams optimized for visual appearance using the R programming language. The knotR package is a systematic R-centric suite of software for the…
Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
An exciting frontier in natural language understanding (NLU) and generation (NLG) calls for (vision-and-) language models that can efficiently access external structured knowledge repositories. However, many existing knowledge bases only…
This letter introduced a new R package 'coexist' which can perform species coexistence simulation and analysis. The package was initially developed for understanding the role of different combinations of varying species growth rates,…
With advanced imaging, sequencing, and profiling technologies, multiple omics data become increasingly available and hold promises for many healthcare applications such as cancer diagnosis and treatment. Multimodal learning for integrative…
The emergence of novel pathogens and zoonotic diseases like the SARS-CoV-2 have underlined the need for developing novel diagnosis and intervention pipelines that can learn rapidly from small amounts of labeled data. Combined with…