Explaining deep neural networks through knowledge extraction and graph analysis

Explainable Artificial Intelligence (XAI) has recently become an active research field due to the need for transparency and accountability when deploying AI models for high-stake decision making. Despite the success of Deep Neural Networks (DNNs), understanding their decision processes is still a known challenge. The research direction presented in this thesis stems from the idea that combining knowledge with deep representations can be the key to more transparent decision making. Specifically, we have focused on Computer Vision tasks and Convolutional Neural Networks (CNNs) and we have proposed a graph representation, called co-activation graph, that serves as an intermediate representation between knowledge encoded within a CNN and the semantics contained in external knowledge bases. Given a trained CNN, we first show how a co-activation graph can be created and exploited to generate global insights for the model’s inner-workings. Then, we propose a taxonomy extraction method that captures how symbolic class concepts and their hypernyms in a given domain are hierarchically organised in the model’s subsymbolic representation. We then illustrate how background knowledge can be connected to the graph in order to generate textual local factual and counterfactual explanations. Our results indicate that graph analysis approaches applied to co-activation graphs can reveal important insights into how CNNs work and enable both global and local semantic explanations. Despite focusing on CNN architectures, we believe that our approach can be adapted to other architectures which would make it possible to apply the same methodology in other domains such as Natural Language Processing. At the end of the thesis we will discuss interesting research directions that are being investigated in the area of using knowledge graphs and graph analysis for explainability of deep learning models, and we outline opportunities for the development of this research are

O desafio do envelhecimento populacional na perspectiva sistêmica da saúde

Bibliografia: p. 119-124O envelhecimento da população é uma tendência razoavelmente previsível, permitindo que as sociedades se planejem e moldem o futuro levando-a em consideração. O artigo tem como objetivo discutir as tendências gerais de necessidades de saúde da população no contexto do envelhecimento, com ênfase no caso brasileiro. Para isso, são levantados os principais motivos que fazem da área de saúde um campo privilegiado para a promoção do desenvolvimento econômico e social. Também são debatidos, com base em dados da Organização das nações unidas (ONU), da organização Mundial da Saúde (OMS), do Instituto Brasileiro de Geografia e Estatística (IBGE) e da Fundação Oswaldo Cruz (Fiocruz), os fundamentos históricos e demográficos do fenômeno em questão. Por fim, discutem-se as diretrizes a serem observadas pelos sistemas de saúde para que se adaptem-se à realidade demográfica descrita. Argumenta-se que a visão sistêmica da saúde pode ser a chave para transformar os desafios gerados pelo envelhecimento populacional em oportunidades para o desenvolvimento do complexo econômico e industrial da saúde (Ceis)

AVALIAÇÃO DE A1C E GLICOSE POR DRIFTS: UMA NOVA ABORDAGEM ANALÍTICA PARA DIAGNÓSTICO DE DIABETES MELLITUS

O diabetes mellitus (DM) inclui um grupo de doenças metabólicas resultante de disfunção na secreção e/ou ação da insulina. O diagnóstico de DM é definido com base na avaliação da glicemia de jejum(GJ) e hemoglobina glicada (A1C) que também informa a persistência da hiperglicemia. Entretanto novas tecnologias analíticas estão sempre sob constante investigação. A espectroscopia de absorção molecular no infravermelho com Transformada de Fourier (FT-IR) associada à análise multivariada tem surgido como uma alternativa nesse contexto. O presente estudo buscou avaliar a FT-IR, através da técnica de reflectância difusa, para quantificar glicose e A1C em um grupo de indivíduos adultos. O estudo foi composto por 46 pacientes de 32 a 59 anos, com valores GJ de 71,67 a 135 mg/dL e de A1C de 5,3 a 7,2 %. O modelo PLS-DRIFTS para GJ o apresentou RMSECV=1,37 mg/dL e R²=0,995 e para A1C, RMSECV=0,06% R²=0,993 sem exclusão de amostras e usando a faixa de 4000-2401, 2300-600 cm-1. Dessa forma foi possível concluir que FT-IR associada a análise multivariada se mostrou adequado para predizer os parâmetros bioquímicos de glicose e A1C de jejum com um erro mínimo, atendendo os requisitos analíticos da ANVISA para quantificação destes parâmetros

Brazilian health system: governance, institutions and finance

Bibliografia: p. 70-77O artigo sistematiza o histórico, o retrato atual e os principais desafios do sistema de saúde brasileiro. São apresentados os princípios constitucionais que orientam o Sistema Único de Saúde (SUS) e os desafios de sua implementação. Discute-se o financiamento à saúde, destacando-se os mecanismos de pagamento por serviços e sua relação com a eficiência das despesas e geração de incentivos. São resumidos e sistematizados, ainda, os arranjos organizacionais que pautam a ação dos prestadores de serviços, discutindo questões como autonomia e efetividade. Ao fim, são apresentados desafios do SUS, em especial a incompleta integração com a saúde suplementar e os avanços recentes na expansão da atenção primária à saúde como eixo organizador do sistema.The article systematizes the history, the current status and main challenges of the Brazilian health care system. First, the constitutional principles in the light of its historical and theoretical context are presented. Then, the challenges of health financing are discussed, highlighting payment mechanisms and their relation with incentives and efficiency. The main organizational arrangements of the services providers are also ummarized, discussing budget autonomy and comparative effectiveness. Finally, some of the Brazil’s healthcare challenges, such as public-private integration and the recent advances of primary health care diffusion strategy, are also addressed

Blooms of bryozoans and epibenthic diatoms in an urbanized sandy Beach (Balneário Camboriú - SC - Brazil): dynamics, possible causes and biomass characterization

Balneário Camboriú (SC - Brasil) é uma cidade turística, onde o crescimento desordenado da população urbana e a implementação de obras costeiras sem uma avaliação adequada tem gerado impactos ambientais e afetado severamenteou a qualidade sanitária da água e do sedimento do rio Camboriú e da área marinha adjacente. Um dos fenômenos mais recentes e alarmantes observados são as florações de briozoários invasivos (Arboscuspis bellula e Membraniporopsis tubigera) associados com as diatomáceas epibênticas (Amphitetras antediluviana e Biddulphia biddulphiana). Vários indícios associam esses fenômenos, iniciados em 2003, com o excesso de nutrientes e matéria orgânica na enseada Camboriú e com grandes obras costeiras locais, como dragagem, aterro e construção de molhes, levando a mudanças na estrutura ecológica bêntica. Sendo um problema de estético e ambiental, a preocupação da comunidade e órgãos governamentais gerou uma intensificação nos estudos, uma vez que as ocorrências se tornaram mais frequentes e persistentes. O presente trabalho aborda este problema através de estudos ambientais e experimentais. A coleta de material bêntico com embarcação e mergulhos e monitoramento florações junto a praia compuseram a abordagem ambiental. Os trabalhos de laboratório incluíram o isolamento e a cultura de algas e brioozários, bem como a avalição do crescimento desses organismos, além da análise e avaliação química biomassa. Os dados de monitoramento mostraram uma tendência sazonal nas florações, com eventos mais evidentes nos meses mais quentes. Diatomáceas aumentaram em abundância nos meses mais frios e briozoários nos mais quentes. A diatomácea A. antediluviana, predominante nas florações, cresceu de forma satisfatória em cultivo laboratorial, mostrando um melhor crescimento em meios com concentrações mais elevadas de silicato e fosfato. Os briozoários mostraram crescimento lento em condições de laboratório. O material depositado no ambiente mostrou baixas concentrações de ácidos graxos, predominantemente saturados, mas a elevada biomassa sugere um possível uso para a produção de biocombustíveis. Amostras de biomassa dominadas por briozoários apresentaram atividade antimicrobiana moderada contra Klebsiella pneumoniae. A explicação para a ocorrência destes eventos ainda são inconclusivas, mas há evidências consideráveis de que há um efeito sinérgico entre a alta concentração de bactérias e detritos orgânicos na água, relacionada com a poluição local, e a eliminação de competidores naturais pelos impactos das obras costeiras.Balneário Camboriu (SC - Brazil) is a touristic city where the disordered growth of the urban population and the implementation of coastal works without proper evaluation generated environmental impacts and affected the sanitary quality of water and sediment of Camboriu River and marine adjacent area. One of the most recent and alarming phenomena observed are the blooms of invasive bryozoans (Arboscuspis bellula and Membraniporopsis tubigera) associated with epibenthic diatoms (Amphitetras antediluviana and Biddulphia biddulphiana). Several clues associate these phenomena, started in 2003, with the excess of nutrients and organic matter in the Camboriú cove and large coastal works such as dredging, landfills and construction of jetties, leading to changes in benthic ecological structure. Being an aesthetic and environmental health problem, the concern of the scientific community and government agencies intensified as the occurrences become more frequent and persistent. This research addresses this issue through environmental and experimental studies. Samplings of the benthic material collected by boat and diving, and blooms monitoring were the environmental approach. The laboratory work included the algal isolation and culture, in addition to growth conditions assessment and chemical biomass analysis. Monitoring data showed a seasonal trend in the blooms, with more conspicuous events in warmer months. Diatoms increase in abundance in colder months and bryozoans in the warmer ones. The diatom A. antediluviana, predominant in the blooms, grew satisfactorily in laboratory cultivation, showing better growth in media with higher concentrations of silicate and phosphate. Bryozoans showed slow growth in laboratory conditions. The deposited material collected in the environment showed low concentrations of saturated fatty acids, but the high biomass suggest a possible use for biofuels production. Biomass samples dominated by bryozoans showed moderate antimicrobial activity against Klebsiella pneumoniae. The explanation for the occurrence of these blooms are still inconclusive, but there is considerable evidence that it is a synergistic effect between the high concentration of bacteria and organic debris in the water related to local pollution and the elimination of natural competitors by coastal works

Poor Immune Reconstitution in HIV-Infected Patients Associates with High Percentage of Regulatory CD4(+) T Cells

CD4(+) regulatory T cells (Tregs) are essential for the maintenance of the immune system's equilibrium, by dampening the activation of potential auto-reactive T cells and avoiding excessive immune activation. To correctly perform their function, Tregs must be maintained at the right proportion with respect to effector T cells. Since this equilibrium is frequently disrupted in individuals infected with the human immunodeficiency virus (HIV), we hypothesize that its deregulation could hamper immune reconstitution in patients with poor CD4(+) T cell recovery under highly active antiretroviral therapy (HAART). We analysed Tregs percentages amongst CD4(+) T cells in 53 HIV-infected patients under HAART, with suppression of viral replication and distinct levels of immune reconstitution. As controls, 51 healthy individuals were also analysed. We observed that amongst the patients with Nadir values (the lowest CD4(+) T cell counts achieved) = 10% of total CD4(+) T cells) had the worse CD4(+) T cell reconstitution. In accordance, the well-described direct correlation between the Nadir value and CD4(+) T cell reconstitution is clearly more evident in individuals with high Tregs proportions. Furthermore, we observed a strong negative correlation between Tregs percentages and CD4(+) T cell recovery among immunological non-responder HIV+ individuals. All together, this work shows that high Tregs frequency is an important factor associated with sub-optimal CD4(+) T cell recovery. This is particularly relevant for immunological non-responders with low Nadir values. Our results suggest that the Tregs proportion might be of clinical relevance to define cut-offs for HAART initiation

Violacein-Induced Chaperone System Collapse Underlies Multistage Antiplasmodial Activity

Antimalarial drugs with novel modes of action and wide therapeutic potential are needed to pave the way for malaria eradication. Violacein is a natural compound known for its biological activity against cancer cells and several pathogens, including the malaria parasite, Plasmodium falciparum (Pf). Herein, using chemical genomic profiling (CGP), we found that violacein affects protein homeostasis. Mechanistically, violacein binds Pf chaperones, PfHsp90 and PfHsp70-1, compromising the latter's ATPase and chaperone activities. Additionally, violacein-treated parasites exhibited increased protein unfolding and proteasomal degradation. The uncoupling of the parasite stress response reflects the multistage growth inhibitory effect promoted by violacein. Despite evidence of proteotoxic stress, violacein did not inhibit global protein synthesis via UPR activation - a process that is highly dependent on chaperones, in agreement with the notion of a violacein-induced proteostasis collapse. Our data highlight the importance of a functioning chaperone-proteasome system for parasite development and differentiation. Thus, a violacein-like small molecule might provide a good scaffold for development of a novel probe for examining the molecular chaperone network and/or antiplasmodial drug design.publishersversionpublishe

Knowledge Graphs Evolution and Preservation -- A Technical Report from ISWS 2019

One of the grand challenges discussed during the Dagstuhl Seminar "Knowledge Graphs: New Directions for Knowledge Representation on the Semantic Web" and described in its report is that of a: "Public FAIR Knowledge Graph of Everything: We increasingly see the creation of knowledge graphs that capture information about the entirety of a class of entities. [...] This grand challenge extends this further by asking if we can create a knowledge graph of "everything" ranging from common sense concepts to location based entities. This knowledge graph should be "open to the public" in a FAIR manner democratizing this mass amount of knowledge." Although linked open data (LOD) is one knowledge graph, it is the closest realisation (and probably the only one) to a public FAIR Knowledge Graph (KG) of everything. Surely, LOD provides a unique testbed for experimenting and evaluating research hypotheses on open and FAIR KG. One of the most neglected FAIR issues about KGs is their ongoing evolution and long term preservation. We want to investigate this problem, that is to understand what preserving and supporting the evolution of KGs means and how these problems can be addressed. Clearly, the problem can be approached from different perspectives and may require the development of different approaches, including new theories, ontologies, metrics, strategies, procedures, etc. This document reports a collaborative effort performed by 9 teams of students, each guided by a senior researcher as their mentor, attending the International Semantic Web Research School (ISWS 2019). Each team provides a different perspective to the problem of knowledge graph evolution substantiated by a set of research questions as the main subject of their investigation. In addition, they provide their working definition for KG preservation and evolution

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio