scholarly journals Fine-grained annotation and classification of de novo predicted LTR retrotransposons

2009 ◽  
Vol 37 (21) ◽  
pp. 7002-7013 ◽  
Author(s):  
Sascha Steinbiss ◽  
Ute Willhoeft ◽  
Gordon Gremme ◽  
Stefan Kurtz
Keyword(s):  
De Novo ◽  
Ltr Retrotransposons ◽  
Fine Grained

scholarly journals A Machine Vision Approach for Bioreactor Foam Sensing

2021 ◽  
pp. 247263032110088
Author(s):  
Jonas Austerjost ◽  
Robert Söldner ◽  
Christoffer Edlund ◽  
Johan Trygg ◽  
David Pollard ◽  
...  
Keyword(s):  
Machine Learning ◽  
Machine Vision ◽  
State Of The Art ◽  
Low Cost ◽  
High Accuracy ◽  
Consumer Electronics ◽  
Learning System ◽  
Automotive Applications ◽  
Fine Grained

Machine vision is a powerful technology that has become increasingly popular and accurate during the last decade due to rapid advances in the field of machine learning. The majority of machine vision applications are currently found in consumer electronics, automotive applications, and quality control, yet the potential for bioprocessing applications is tremendous. For instance, detecting and controlling foam emergence is important for all upstream bioprocesses, but the lack of robust foam sensing often leads to batch failures from foam-outs or overaddition of antifoam agents. Here, we report a new low-cost, flexible, and reliable foam sensor concept for bioreactor applications. The concept applies convolutional neural networks (CNNs), a state-of-the-art machine learning system for image processing. The implemented method shows high accuracy for both binary foam detection (foam/no foam) and fine-grained classification of foam levels.

scholarly journals Datives with psych nouns and adjectives in Basque

2020 ◽  
Vol 54 (3) ◽  
pp. 647-696
Author(s):  
Beatriz Fernández ◽  
Fernando Zúñiga ◽  
Ane Berro
Keyword(s):  
Natural Language ◽  
Linguistic Theory ◽  
Psychological State ◽  
Formal Expression ◽  
Fine Grained ◽  
Psych Verbs ◽  
Other Regarding ◽  
Psychological Verbs

Abstract This paper explores the formal expression of two Basque dative argument types in combination with psych nouns and adjectives, in intransitive and transitive clauses: (i) those that express the experiencer, and (ii) those that express the stimulus of the psychological state denoted by the psych noun and adjective. In the intransitive structure involving a dative experiencer (DatExpIS), the stimulus is in the absolutive case, and the intransitive copula izan ‘be’ shows both dative and absolutive agreement. This construction basically corresponds to those built upon the piacere type of psychological verbs typified in (Belletti, Adriana & Luigi Rizzi. 1988. Psych-verbs and θ-theory. Natural Language and Linguistic Theory 6. 291–352) three-way classification of Italian psych verbs. In the intransitive structure involving a dative stimulus (DatStimIS), the experiencer is marked by absolutive case, and the same intransitive copula shows both absolutive and dative agreement (with the latter corresponding to the dative stimulus and not to the experiencer). We show that the behavior of the dative argument in the two constructions is just the opposite of each other regarding a number of morphosyntactic tests, including agreement, constituency, hierarchy and selection. Additionally, we explore two parallel transitive constructions that involve either a dative experiencer and an ergative stimulus (DatExpTS) or a dative stimulus and an ergative experiencer (DatStimTS), which employ the transitive copula *edun ‘have’. Considering these configurations, we propose an extended and more fine-grained typology of psych predicates.

Change Taxonomy: A Fine-Grained Classification of Software Change

2018 ◽  
Vol 20 (4) ◽  
pp. 28-36 ◽  
Author(s):  
Mohamed Elkholy ◽  
Ahmed Elfatatry
Keyword(s):  
Fine Grained ◽  
Software Change

scholarly journals Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dennie te Molder ◽  
Wasin Poncheewin ◽  
Peter J. Schaap ◽  
Jasper J. Koehorst
Keyword(s):  
Machine Learning ◽  
Plant Pathogens ◽  
De Novo ◽  
Classification Algorithms ◽  
Learning Approaches ◽  
Enabling Factors ◽  
Essential Step ◽  
The World ◽  
Genome Content

Abstract Background The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. Results Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. Conclusion The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.

scholarly journals Experimental analysis on the optimal excitation wavelength for fine-grained identification of refined oil pollutants on water surface based on laser-induced fluorescence

2021 ◽  
Author(s):  
Ming Xie ◽  
Yunpeng Jia ◽  
Ying Li ◽  
Xiaohua Cai ◽  
Kai Cao
Keyword(s):  
Oil Spill ◽  
Theoretical Basis ◽  
Water Surface ◽  
Laser Induced Fluorescence ◽  
Excitation Wavelength ◽  
Refined Oil ◽  
Fine Grained ◽  
Optimal Excitation ◽  
Oil Spill Identification

Abstract Laser-induced fluorescence (LIF) is an effective, all-weather oil spill identification method that has been widely applied for oil spill monitoring. However, the distinguishability on oil types is seldom considered while selecting excitation wavelength. This study is intended to find the optimal excitation wavelength for fine-grained classification of refined oil pollutants using LIF by comparing the distinguishability of fluorometric spectra under various excitation wavelengths on some typical types of refined-oil samples. The results show that the fluorometric spectra of oil samples significantly vary under different excitation wavelengths, and the four types of oil applied in this study are most likely to be distinguished under the excitation wavelengths of 395 nm and 420 nm. This study is expected to improve the ability of oil types identification using LIF method without increasing time or other cost, and also provides theoretical basis for the development of portable LIF devices for oil spill identification.

scholarly journals What else is in an evolved name? Exploring evolvable specificity with SignalGP

2018 ◽  
Author(s):  
Alexander Lalejini ◽  
Charles Ofria
Keyword(s):  
Adaptive Evolution ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
De Novo ◽  
Direct Access ◽  
Evolutionary Transitions ◽  
Fine Grained ◽  
Flexible Mechanism ◽  
Gene Regulatory ◽  
Program Modules

Tags are evolvable labels that provide genetic programs a flexible mechanism for specification. Tags are used to label and refer to programmatic elements, such as functions or jump targets. However, tags differ from traditional, more rigid methods for handling labeling because they allow for inexact references; that is, a referring tag need not exactly match its referent. Here, we explore how adjusting the threshold for how what qualifies as a match affects adaptive evolution. Further, we propose broadened applications of tags in the context of a genetic programming (GP) technique called SignalGP. SignalGP gives evolution direct access to the event-driven paradigm. Program modules in SignalGP are tagged and can be triggered by signals (with matching tags) from the environment, from other agents, or due to internal regulation. Specifically, we propose to extend this tag based system to: (1) provide more fine-grained control over module execution and regulation (e.g., promotion and repression) akin to natural gene regulatory networks, (2) employ a mosaic of GP representations within a single program, and (3) facilitate major evolutionary transitions in individuality (i.e., allow hierarchical program organization to evolve de novo).

Sign in / Sign up

Export Citation Format

Share Document