17 papers · ranked by Valyu relevance
Amirmohammad Farzaneh, Mihai-Alin Badiu, Justin P. Coon
—Routing tables in ad hoc and wireless routing protocols can be represented using rooted trees. The constant need for communication and storage of these trees in routing protocols demands an efficient rooted tree coding algorithm. This efficiency is defined in terms of the average code length, and the optimality of the…
Harry Richman, Cheng Zhang, Frederick A. Matsen
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and…
David Harry Richman, Cheng Zhang, Frederick A. Matsen IV
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new “ordered leaf attachment” (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and…
Paolo Bresolin, Fabio Vandin, Vera Pancaldi
A crucial preliminary step to consider when adopting a GNN is the choice of an effective encoding for the nodes of the input graphs. Since we want our model to extract embeddings also for unseen phylogenetic trees, we need an encoding that works for any $T\inT$, with alterations in $M$. However, a first problem is that…
Amirmohammad Farzaneh, Mihai-Alin Badiu, Justin P. Coon
—Measuring the complexity of tree structures can be beneficial in areas that use tree data structures for storage, communication, and processing purposes. This complexity can then be used to compress tree data structures to their informationtheoretic limit. Additionally, the lack of models for random generation of…
Cedric Chauve, Caroline Colijn, Louxin Zhang
Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on $n$ ordered taxa as a vector…
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A. Matsen + 1 more
'Cheng Zhang'] Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they are often sensitive to the choice of distance metric and may lack…
Lukas Hübner, Alexandros Stamatakis
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and – in conjunction with recent advances in ancient DNA sequencing technology – studying human migration patterns over the past few thousand…
Helen L. Smith, Patrick J. Biggs, Nigel P. French, Adam N. H. Smith + 2 more
'Jonathan C. Marshall' 'Muhammad Aleem'] Performance of random forest classification models is often assessed and interpreted using out-of-bag (OOB) samples. Observations which are OOB when a tree is trained may serve as a test set for that tree and predictions from the OOB observations used to calculate OOB error and…
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…
Ryosuke Sugiura, Masaaki Nishino, Norihito Yasuda, Yutaka Kamamoto + 1 more
'Takehiro Moriya'] This paper presents an optimal construction of N-bit-delay almost instantaneous fixed-to-variable-length (AIFV) codes, the general form of binary codes we can make when finite bits of decoding delay are allowed. The presented method enables us to optimize lossless codes among a broader class of codes…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Domenico Cantone, Simone Faro
We present a new variable-length computation-friendly encoding scheme, named SFDC (Succinct Format with Direct aCcesibility), that supports direct and fast accessibility to any element of the compressed sequence and achieves compression ratios often higher than those offered by other solutions in the literature. The…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
Authors not listed
We present a simple yet efficient random (brute-force) algorithm for constructing solvated molecular systems. By placing solvent molecules at random positions and orientations within a simulation box, we circumvent the complexities typically associated with more sophisticated packing algorithms. The main computational…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
'Minjun Kwak' 'Yasa Baig' 'Nicole Moiseyev' 'Shari Tian' 'Alison Zhang' 'Neil Zhenqiang Gong' 'Lingchong You'] Title: Summary Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the…