Related papers: Phylogenetic Tree Inference with Tropical Axial At…
Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of…
This paper introduces Smart-Tree, a supervised method for approximating the medial axes of branch skeletons from a tree point cloud. Smart-Tree uses a sparse voxel convolutional neural network to extract the radius and direction towards the…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Extreme value statistics is the max analogue of classical statistics, while tropical geometry is the max analogue of classical geometry. In this paper, we review recent work where insights from tropical geometry were used to develop new,…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
We propose an algebraic geometric framework to study the expressivity of linear activation neural networks. A particular quantity of neural networks that has been actively studied is the number of linear regions, which gives a…
Knowing the causal structure of a system is of fundamental interest in many areas of science and can aid the design of prediction algorithms that work well under manipulations to the system. The causal structure becomes identifiable from…
Incorporating syntactic information in Neural Machine Translation models is a method to compensate their requirement for a large amount of parallel training text, especially for low-resource language pairs. Previous works on using syntactic…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
Our formulation reveals that the reduction across the sequence axis can be efficiently computed in parallel through a tree reduction. Our algorithm, called Tree Attention, for parallelizing exact attention computation across multiple GPUs…
Program translation is an important tool to migrate legacy code in one language into an ecosystem built in a different language. In this work, we are the first to employ deep neural networks toward tackling this problem. We observe that…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
We report the effects of replacing the scaled dot-product (within softmax) attention with the negative-log of Euclidean distance. This form of attention simplifies to inverse distance weighting interpolation. Used in simple one hidden layer…
In-context learning with attention enables large neural networks to make context-specific predictions by selectively focusing on relevant examples. Here, we adapt this idea to supervised learning procedures such as lasso regression and…
Exponential families are widely used in machine learning; they include many distributions in continuous and discrete domains (e.g., Gaussian, Dirichlet, Poisson, and categorical distributions via the softmax transformation). Distributions…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Attention Residuals replace standard additive residual connections with learned softmax attention over previous layer outputs, enabling selective cross-layer routing. However, standard Attention Residuals still attend over cumulative hidden…
The tropical semiring is an algebraic system with addition ``$\max$'' and multiplication ``$+$''. As well as in conventional algebra, linear programming in the tropical semiring has been developed. In this study, we introduce a new type of…