Trepan Reloaded: A Knowledge-driven Approach to Explaining Artificial Neural Networks

Explainability in Artificial Intelligence has been revived as a topic of active research by the need of conveying safety and trust to users in the `how' and `why' of automated decision-making. Whilst a plethora of approaches have been developed for post-hoc explainability, only a few focus on how to use domain knowledge, and how this influences the understandability of global explanations from the users' perspective. In this paper, we show how ontologies help the understandability of global post-hoc explanations, presented in the form of symbolic models. In particular, we build on Trepan, an algorithm that explains artificial neural networks by means of decision trees, and we extend it to include ontologies modeling domain knowledge in the process of generating explanations. We present the results of a user study that measures the understandability of decision trees using a syntactic complexity measure, and through time and accuracy of responses as well as reported user confidence and understandability. The user study considers domains where explanations are critical, namely, in finance and medicine. The results show that decision trees generated with our algorithm, taking into account domain knowledge, are more understandable than those generated by standard Trepan without the use of ontologies

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

AimWetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific environmental space and historical stability.LocationSouth America.TaxonRodentia.MethodsUsing complementary analyses (Mantel tests, dbRDA, Procrustes, covariance structure of allele frequencies and environmental niche models [ENMs]) with 8,000–32,000 SNPs per species, we quantified the association between genomic variation and geographic and/or environmental differences.ResultsSignificant association between genetic variation and geography was identified for all species. Similarity in the strength of the association suggests connectivity patterns dictated by shared species‐traits predominate at the biome scale. However, substantial amounts of genetic variation are not explained by geography. Focusing on this portion of the variance, we demonstrate a significant quantitative association between genetic variation and the environmental space of a biome, and a qualitative association with varying regional stability. Specifically, historically stable areas estimated from ecological niche models are correlated with local levels of geographic structuring, suggesting that local biome‐specific histories affect population isolation/connectivity.Main conclusionsThese tests show that although species exhibit similar patterns of genetic variation that are consistent with shared natural histories, irrespective of inhabiting different wetland biomes, local biome‐specific properties (i.e. varying environmental conditions and historical stability) contribute to departures from equilibrium patterns of genetic variation expected by isolation by geographic distance. The reflection of these biome‐specific properties in the genetic structure of the marsh rats provides a window into the differences among South American wetlands with evolutionary consequences for their respective constituent assemblages.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149336/1/jbi13529.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149336/2/jbi13529_am.pd

The Offline Software Framework of the Pierre Auger Observatory

The Pierre Auger Observatory is designed to unveil the nature and the origins of the highest energy cosmic rays. The large and geographically dispersed collaboration of physicists and the wide-ranging collection of simulation and reconstruction tasks pose some special challenges for the offline analysis software. We have designed and implemented a general purpose framework which allows collaborators to contribute algorithms and sequencing instructions to build up the variety of applications they require. The framework includes machinery to manage these user codes, to organize the abundance of user-contributed configuration files, to facilitate multi-format file handling, and to provide access to event and time-dependent detector information which can reside in various data sources. A number of utilities are also provided, including a novel geometry package which allows manipulation of abstract geometrical objects independent of coordinate system choice. The framework is implemented in C++, and takes advantage of object oriented design and common open source tools, while keeping the user side simple enough for C++ novices to learn in a reasonable time. The distribution system incorporates unit and acceptance testing in order to support rapid development of both the core framework and contributed user code.Comment: 4 pages, 2 figures, presented at IEEE NSS/MIC, 23-29 October 2005, Puerto Ric

Utilização do Diagrama V em Atividades Experimentais de Física em Sala de Aula de Ensino Médio Vitória

O presente trabalho relata a utilização do Vê epistemológico de Gowin, chamado nesse trabalho de Diagrama V em atividades experimentais de Física em sala de aula em uma escola da rede pública estadual do Estado do Espírito Santo. A escola onde realizou-se o trabalho é a Escola Estadual de Ensino Fundamental e Médio Clovis Borges Miguel localizada no município de Serra, região metropolitana da Grande Vitória. Foram trabalhadas três atividades experimentais de Física com uma turma do 3º ano do Ensino Médio, estudantes com idade, em média, de 17 anos. Foram realizadas duas atividades de Eletrodinâmica e uma atividade de Magnetismo tendo o Diagrama V sido utilizado como instrumento de orientação, coletas de dados e avaliação em todo o processo. Para a segunda atividade experimental, sobre circuitos elétricos, ainda foi aplicada uma prova sobre o tema trabalhado e feito uma comparação com outra turma que realizou a mesma atividade, mas sem utilizar o Diagrama V. Foram feitas análises conceituais e análises baseadas nos critérios de Gowin e Alvarez (2005). Os resultados revelaram que os estudantes foram capazes de adquirir independência na realização das atividades experimentais propostas, estabelecer relação entre os conceitos abordados e a atividade propriamente dita, Pensar sobre as atividades experimentais proposta antes, durante e após a realização das mesmas, e organizar de forma estruturada os dados coletados. Foi também observado que os estudantes apresentaram dificuldade em definir o objetivo da atividade experimental e em organizar e interpretar os dados coletados. Na avaliação geral da metodologia com o Diagrama V, os estudantes mostraram favoráveis à sua utilização

Opportunities for reducing environmental emissions from forage-based dairy farms

Modern dairy production is inevitably associated with impacts to the environment and the challenge for the industry today is to increase production to meet growing global demand while minimising emissions to the environment. Negative environmental impacts include gaseous emissions to the atmosphere, of ammonia from livestock manure and fertiliser use, of methane from enteric fermentation and manure management, and of nitrous oxide from nitrogen applications to soils and from manure management. Emissions to water include nitrate, ammonium, phosphorus, sediment, pathogens and organic matter, deriving from nutrient applications to forage crops and/or the management of grazing livestock. This paper reviews the sources and impacts of such emissions in the context of a forage-based dairy farm and considers a number of potential mitigation strategies, giving some examples using the farm-scale model SIMSDAIRY. Most of the mitigation measures discussed are associated with systemic improvements in the efficiency of production in dairy systems. Important examples of mitigations include: improvements to dairy herd fertility, that can reduce methane and ammonia emissions by up to 24 and 17%, respectively; diet modification such as the use of high sugar grasses for grazing, which are associated with reductions in cattle N excretion of up to 20% (and therefore lower N losses to the environment) and potentially lower methane emissions, or reducing the crude protein content of the dairy cow diet through use of maize silage to reduce N excretion and methane emissions; the use of nitrification inhibitors with fertiliser and slurry applications to reduce nitrous oxide emissions and nitrate leaching by up to 50%. Much can also be achieved through attention to the quantity, timing and method of application of nutrients to forage crops and utilising advances made through genetic improvements

Relação de indicadores biológicos de qualidade de solos com Fusarium spp., Rhizoctonia solani e Trichoderma spp. em uma área sob integração lavoura-pecuária.

O objetivo deste trabalho foi verificar a relação de populações dos patógenos Fusarium solani, Rhizoctonia solani, dos antagonistas Trichoderma spp. e de formas saprófitas de F. oxysporum, com alguns indicadores biológicos de qualidade do solo

On the random neighbor Olami-Feder-Christensen slip-stick model

We reconsider the treatment of Lise and Jensen (Phys. Rev. Lett. 76, 2326 (1996)) on the random neighbor Olami-Feder-Christensen stik-slip model, and examine the strong dependence of the results on the approximations used for the distribution of states p(E).Comment: 6pages, 3 figures. To be published in PRE as a brief repor

Dispersal of human and plant pathogens biofilms via nitric oxide donors at 4°C

Recent studies suggest that nitric oxide donors capable of manipulating nitric oxide-mediated signaling in bacteria could induce dispersal of biofilms. Encased in extracellular polymeric substances, human and plant pathogens within biofilms are significantly more resistant to sanitizers. This is particularly a problem in refrigerated environments where food is processed. In an exercise aimed to study the potential of nitric oxide donors as biofilm dispersal in refrigerated conditions, we compared the ability of different nitric oxide donors (SNAP, NO-aspirin and Noc-5) to dislodge biofilms formed by foodborne, human and plant pathogens treated at 4 °C. The donors SNAP and Noc-5 were efficient in dispersing biofilms formed by Salmonella enterica, pathogenic Escherichia coli and Listeria innocua. The biomasses were decreased up to 30 % when compared with the untreated controls. When the plant pathogens Pectobacterium sp. and Xanthomonas sp. were tested the dispersion was mainly limited to Pectobacterium carotovorum biofilms, decreasing up to 15 % after exposure to molsidomine. Finally, the association of selected nitric oxide donors with sanitizers (DiQuat, H2O2, peracetic acid and PhenoTek II) was effective in dispersing biofilms. The best dispersal was achieved by pre-treating P. carotovorum with molsidomine and then peracetic acid. The synergistic effect was estimated up to ~35 % in dispersal when compared with peracetic acid alone. The association of nitric oxide donors with sanitizers could provide a foundation for an improved sanitization procedure for cleaning refrigerate environments