Search Results - "Kari, Lila"

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes by Solis-Reyes, Stephen, Avino, Mariano, Poon, Art, Kari, Lila

“…For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification…”
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MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes by Li, Wanxin, Kari, Lila, Yu, Yaoliang, Hug, Laura A

“…We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of…”
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Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study by Randhawa, Gurjit S, Soltysiak, Maximillian P M, El Roz, Hadi, de Souza, Camila P E, Hill, Kathleen A, Kari, Lila

“…The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed…”
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ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels by Randhawa, Gurjit S, Hill, Kathleen A, Kari, Lila

“…Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains…”
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DeLUCS: Deep learning for unsupervised clustering of DNA sequences by Millán Arias, Pablo, Alipour, Fatemeh, Hill, Kathleen A, Kari, Lila

“…We present a novel Deep Learning method for the Unsupervised Clustering of DNA Sequences (DeLUCS) that does not require sequence alignment, sequence homology,…”
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Simplifying the role of signals in tile self-assembly by Kari, Lila, Simjour, Amirhossein

“…Sending signals through DNA-based structures is one of the methods used to enhance the capabilities of DNA self-assembly systems. Signal Tile Assembly Models…”
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Additive methods for genomic signatures by Karamichalis, Rallis, Kari, Lila, Konstantinidis, Stavros, Kopecki, Steffen, Solis-Reyes, Stephen

“…Studies exploring the potential of Chaos Game Representations (CGR) of genomic sequences to act as "genomic signatures" (to be species- and genome-specific)…”
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An investigation into inter- and intragenomic variations of graphic genomic signatures by Karamichalis, Rallis, Kari, Lila, Konstantinidis, Stavros, Kopecki, Steffen

“…Motivated by the general need to identify and classify species based on molecular evidence, genome comparisons have been proposed that are based on measuring…”
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Environment and taxonomy shape the genomic signature of prokaryotic extremophiles by Arias, Pablo Millán, Butler, Joseph, Randhawa, Gurjit S., Soltysiak, Maximillian P. M., Hill, Kathleen A., Kari, Lila

“…This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental…”
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As good as it gets: a scaling comparison of DNA computing, network biocomputing, and electronic computing approaches to an NP-complete problem by Sudalaiyadum Perumal, Ayyappasamy, Wang, Zihao, Ippoliti, Giulia, van Delft, Falco C M J M, Kari, Lila, Nicolau, Dan V

“…Abstract All known algorithms to solve nondeterministic polynomial (NP) complete problems, relevant to many real-life applications, require the exploration of…”
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Conjugate word blending: formal model and experimental implementation by XPCR by Bellamoli, Francesco, Franco, Giuditta, Kari, Lila, Lampis, Silvia, Ng, Timothy, Wang, Zihao

“…This paper introduces conjugate word blending as a formal model of molecular processes that occur during a DNA experimental protocol called cross-pairing…”
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Leveraging machine learning for taxonomic classification of emerging astroviruses by Alipour, Fatemeh, Holmes, Connor, Lu, Yang Young, Hill, Kathleen A, Kari, Lila

“…Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens…”
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Mapping the space of genomic signatures by Kari, Lila, Hill, Kathleen A, Sayem, Abu S, Karamichalis, Rallis, Bryans, Nathaniel, Davis, Katelyn, Dattani, Nikesh S

“…We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of…”
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Efficient Algorithms for Computing the Inner Edit Distance of a Regular Language via Transducers by Kari, Lila, Konstantinidis, Stavros, Kopecki, Steffen, Yang, Meng

“…The concept of edit distance and its variants has applications in many areas such as computational linguistics, bioinformatics, and synchronization error…”
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Binary Pattern Tile Set Synthesis Is NP-Hard by Kari, Lila, Kopecki, Steffen, Meunier, Pierre-Étienne, Patitz, Matthew J., Seki, Shinnosuke

“…We solve an open problem, stated in 2008, about the feasibility of designing efficient algorithmic self-assembling systems which produce 2-dimensional colored…”
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Editorial by Kari, Lila

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Editorial by Kari, Lila

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Editorial by Kari, Lila

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Editorial by Kari, Lila

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On the weight of universal insertion grammars by Kari, Lila, Sosík, Petr

“…We study the computational power of pure insertion grammars. We show that pure insertion grammars of weight 3 can characterize all recursively enumerable…”
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