13 papers · ranked by Valyu relevance
Dmitry Kobak, George C. Linderman
One of the most ubiquitous analysis tools employed in single-cell transcriptomics and cytometry is t-distributed stochastic neighbor embedding (t-SNE) [1], used to visualize individual cells as points on a 2D scatter plot such that similar cells are positioned close together. Recently, a related algorithm, called…
Marius Pachitariu, Lin Zhong, Alexa Gracias, Amanda Minisi + 2 more
Artificial neural networks learn faster if they are initialized well. Good initializations can generate high-dimensional macroscopic dynamics with long timescales. It is not known if biological neural networks have similar properties. Here we show that the eigenvalue spectrum and dynamical properties of large-scale…
Abiy Tasissa, Rongjie Lai, Chunyu Wang
The problem of finding the configuration of points given partial information on pairwise inter-point distances, the Euclidean distance geometry problem, appears in multiple applications. In this paper, we propose an approach that integrates homology modeling and a nonconvex distance geometry algorithm for the protein…
Tomáš Flouri, Kassian Kobert, Torbjørn Rognes, Alexandros Stamatakis
Pairwise sequence alignment is perhaps the most fundamental bioinformatics operation. An optimal global alignment algorithm was described in 1970 by Needleman and Wunsch. In 1982 Gotoh presented an improved algorithm with lower time complexity. Gotoh’s algorithm is frequently cited (1447 citations, Google Scholar, May…
Neha Vinayak, Shandar Ahmad
A multi-layer perceptron (MLP) consists of a number of forward-connected weights (W_ijk_) from each feeding layer node (n_ij_) to the many initially equivalent nodes (n_i+1,k_) in the next layer. Exact a priori order and search space of these weights (W_ijk_) is random and prone to redundancy, irreproducibility and…
Abdol Aziz Ould Ismail, Drew Parker, Moises Hernandez-Fernandez, Ronald Wolf + 6 more
Characterization of healthy versus pathological tissue is a key concern when modeling tissue microstructure in the peritumoral area, confounded by the presence of free water (e.g., edema). Most methods that model tissue microstructure are either based on advanced acquisition schemes not readily available in the clinic…
Mohammed Baragilly, Brian H Willis
Meta-analysis may be used to summarise a test’s accuracy. Often the sensitivity and specificity are the measures of interest and as these are correlated a bivariate random effects model is commonly used to fit the data. This model has five parameters and it may be optimised using a Newton-Raphson based algorithm…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
Omer Sabary, Alexander Yucovich, Guy Shapira, Eitan Yaakobi
In the trace reconstruction problem a length-n string x yields a collection of noisy copies, called traces, y_1_, …, y_t_ where each y_i_ is independently obtained from x by passing through a deletion channel, which deletes every symbol with some fixed probability. The main goal under this paradigm is to determine the…
Koichi Miyamoto, Naoki Yamamoto, Yasubumi Sakakibara
We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The…
Kazunori D Yamada
In the deep learning era, a gradient descent method is the most common method to optimize parameters of neural networks. Among various mathematical optimization methods, a gradient descent method is the most naive method. Although controlling a learning rate of the method is necessary for quick convergence, the…
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp + 3 more
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by…
Arne Kutzner, Pok-Son Kim, Markus Schmidt
Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, max. spanning seeds). The former strategy benefits from fast index building and fast seed computation, while the latter one…