14 papers · ranked by Valyu relevance
Carolina Feher da Silva, Todd A. Hare
Distinct model-free and model-based learning processes are thought to drive both typical and dysfunctional behaviors. Data from two-stage decision tasks have seemingly shown that human behavior is driven by both processes operating in parallel. In this study, however, we show that more detailed task instructions lead…
Carolina Feher da Silva, Todd A. Hare
Many studies that aim to detect model-free and model-based influences on behavior employ two-stage behavioral tasks of the type pioneered by Daw and colleagues in 2011. Such studies commonly modify existing two-stage decision paradigms in order to better address a given hypothesis, which is an important means of…
Raúl Luna, Miguel A. Vadillo, David Luque
Human behaviour is driven by two types of processes running in parallel: goal-directed and habitual, each supported by different computational-learning mechanisms, model-free and model-based respectively. In model-free strategies, stimulus-response associations are strengthened when actions are followed by a reward and…
Adele Diederich, Hans Colonius
The issue of how perception and motor planning interact to generate a given choice between actions is a fundamental question in both psychology and neuroscience. Salinas and colleagues have developed a behavioral paradigm, the compelled-response task, where the signal that instructs the subject to make an eye movement…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…
Maren Brand, Nguyen Khoa Tran, Philipp Spohr, Sven Schrinner + 1 more
We consider the homo-edit distance problem, which is the minimum number of homo-deletions or homo-insertions to convert one string into another. A homo-insertion is the insertion of a string of equal characters into another string, while a homo-deletion is the inverse operation. We show how to compute the homo-edit…
Ragnar Groot Koerkamp
We introduce APA2, an exact global pairwise aligner with respect to edit distance. The goal of APA2 is to unify the near-linear runtime of APA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, APA2 uses Ukkonen’s band doubling in combination with Myers’ bitpacking. APA2 1)…
Nara Yoon, Robert Vander Velde, Andriy Marusyk, Jacob G. Scott
Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. To address this issue, researchers have proposed sequential drug therapies with which the resistance developed by a previous drug can be relieved by the next one, a concept called collateral sensitivity. 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…
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…
Ragnar Groot Koerkamp, Pesho Ivanov
Sequence alignment has been at the core of computational biology for half a century. Still, it is an open problem to design a practical algorithm for exact alignment of a pair of related sequences in linear-like time (25). We solve exact global pairwise alignment with respect to edit distance by using the A shortest…
Martin Šošić, Mile Šikić
We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we…
Haojing Shao, Jue Ruan
Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics research. Although classic dynamic-programming algorithms (e.g., Smith-Waterman and Needleman–Wunsch) guarantee to produce the optimal result, their time complexity hinders the application of large-scale sequence alignment.…
Lorién López-Villellas, Cristian Iñiguez, Albert Jiménez-Blanco, Quim Aguado-Puig + 4 more
Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. Existing strategies to reduce…