Related papers: PhyloFrame: A DataFrame-based Library for Fast, Fl…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
We present FooPar, an extension for highly efficient Parallel Computing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates functional programming features. Our framework FooPar combines…
Random forests are widely used in regression. However, the decision trees used as base learners are poor approximators of linear relationships. To address this limitation we propose RaFFLE (Random Forest Featuring Linear Extensions), a…
Pattern matching is a powerful tool for symbolic computations, based on the well-defined theory of term rewriting systems. Application domains include algebraic expressions, abstract syntax trees, and XML and JSON data. Unfortunately, no…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is…
Deep learning has had remarkable success in robotic perception, but its data-centric nature suffers when it comes to generalizing to ever-changing environments. By contrast, physics-based optimization generalizes better, but it does not…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
With the recent rapid progress in the study of deep generative models (DGMs), there is a need for a framework that can implement them in a simple and generic way. In this research, we focus on two features of DGMs: (1) deep neural networks…
Mathematical models allow us to gain a deeper understanding of real-world dynamical systems. One of the most powerful mathematical frameworks for modeling real-world phenomena are systems of differential equations. In the majority of fields…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
This work introduces ParamRF: a Python library for efficient, parametric modelling of radio frequency (RF) circuits. Built on top of the next-generation computational library JAX, as well as the object-oriented wrapper Equinox, the…
Spatial dataflow accelerators are a promising direction for next-generation computer systems because they can reduce the memory bottlenecks of traditional von Neumann machines such as CPUs and GPUs. They organize computation around…
Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific…
Scientific computing requires handling large linear models, which are often composed of structured matrices. With increasing model size, dense representations quickly become infeasible to compute or store. Matrix-free implementations are…
The emergence of the Next Generation Sequencing increases drastically the volume of transcriptomic data. Although many standalone algorithms and workflows for novel microRNA (miRNA) prediction have been proposed, few are designed for…