Introducing and assessing the explainable AI (XAI)method: SIDU

Explainable Artificial Intelligence (XAI) has in recent years become a well-suited framework to generate human understandable explanations of black box models. In this paper, we present a novel XAI visual explanation algorithm denoted SIDU that can effectively localize entire object regions responsible for prediction in a full extend. We analyze its robustness and effectiveness through various computational and human subject experiments. In particular, we assess the SIDU algorithm using three different types of evaluations (Application, Human and Functionally-Grounded) to demonstrate its superior performance. The robustness of SIDU is further studied in presence of adversarial attack on black box models to better understand its performance.Comment: Preprint-submitted to Journal of Pattern Recognition (Elsevier

Key plant species and detritivores drive diversity effects on instream leaf litter decomposition more than functional diversity: A microcosm study

Anthropogenic impacts on freshwater ecosystems cause critical losses of biodiversity that can in turn impair key processes such as decomposition and nutrient cycling. Forest streams are mainly subsidized by terrestrial organic detritus, so their functioning and conservation status can be altered by changes in forest biodiversity and composition, particularly if these changes involve the replacement of functional groups or the loss of key species. We examined this issue using a microcosm experiment where we manipulated plant functional diversity (FD) (monocultures and low-FD and high-FD mixtures, resulting from different combinations of deciduous and evergreen Quercus species) and the presence of a key species (Alnus glutinosa), all in presence and absence of detritivores, and assessed effects on litter decomposition, nutrient cycling, and fungal and detritivore biomass. We found (i) positive diversity effects on detritivore-mediated decomposition, litter nutrient losses and detritivore biomass exclusively when A. glutinosa was present; and (ii) negative effects on the same processes when microbially mediated and on fungal biomass. Most positive trends could be explained by the higher litter palatability and litter trait variability obtained with the inclusion of alder leaves in the mixture. Our results support the hypothesis of a consistent slowing down of the decomposition process as a result of plant biodiversity loss, and hence effects on stream ecosystem functioning, especially when a key (N-fixing) species is lost; and underscore the importance of detritivores as drivers of plant diversity effects in the studied ecosystem processes.This study was funded by the 2014–2020 FEDER Operative Program Andalusia (RIOVEGEST project, Ref. FEDER-UAL18 -RNM -B006 – B, to J.J.C). Additional support was provided by the Spanish Ministry for Science, Innovation and Universities and FEDER (BioLoss project, Ref. RTI2018-095023- B-I00, to L.B.). Rubio-Ríos was supported by an FPU grant of the Spanish Ministry of Education, Culture and Sports (reference FPU16/03734)

Predicting serious complications in patients with cancer and pulmonary embolism using decision tree modelling: the EPIPHANY Index

Background: Our objective was to develop a prognostic stratification tool that enables patients with cancer and pulmonary embolism (PE), whether incidental or symptomatic, to be classified according to the risk of serious complications within 15 days. Methods: The sample comprised cases from a national registry of pulmonary thromboembolism in patients with cancer (1075 patients from 14 Spanish centres). Diagnosis was incidental in 53.5% of the events in this registry. The Exhaustive CHAID analysis was applied with 10-fold crossvalidation to predict development of serious complications following PE diagnosis. Results: About 208 patients (19.3%, 95% confidence interval (CI), 17.1-21.8%) developed a serious complication after PE diagnosis. The 15-day mortality rate was 10.1%, (95% CI, 8.4-12.1%). The decision tree detected six explanatory covariates: Hestia-like clinical decision rule (any risk criterion present vs none), Eastern Cooperative Group performance scale (ECOG-PS; = 2), O-2 saturation (= 90%), presence of PE-specific symptoms, tumour response (progression, unknown, or not evaluated vs others), and primary tumour resection. Three risk classes were created (low, intermediate, and high risk). The risk of serious complications within 15 days increases according to the group: 1.6, 9.4, 30.6%; P<0.0001. Fifteen-day mortality rates also rise progressively in low-, intermediate-, and high-risk patients: 0.3, 6.1, and 17.1%; P<0.0001. The cross-validated risk estimate is 0.191 (s.e. = 0.012). The optimism-corrected area under the receiver operating characteristic curve is 0.779 (95% CI, 0.717-0.840). Conclusions: We have developed and internally validated a prognostic index to predict serious complications with the potential to impact decision-making in patients with cancer and PE

The microsporidian parasites Nosema ceranae and Nosema apis are widespread in honeybee (Apis mellifera) colonies across Scotland

Nosema ceranae is spreading into areas where Nosema apis already exists. N. ceranae has been reported to cause an asymptomatic infection that may lead, ultimately, to colony collapse. It is thought that there may be a temperature barrier to its infiltration into countries in colder climates. In this study, 71 colonies from Scottish Beekeeper’s Association members have been screened for the presence of N. apis and N. ceranae across Scotland. We find that only 11 of the 71 colonies tested positive for spores by microscopy. However, 70.4 % of colonies screened by PCR revealed the presence of both N. ceranae and N. apis, with only 4.2 or 7 % having either strain alone and 18.3 % being Nosema free. A range of geographically separated colonies testing positive for N. ceranae were sequenced to confirm their identity. All nine sequences confirmed the presence of N. ceranae and indicated the presence of a single new variant. Furthermore, two of the spore-containing colonies had only N. ceranae present, and these exhibited the presence of smaller spores that could be distinguished from N. apis by the analysis of average spore size. Differential quantification of the PCR product revealed N. ceranae to be the dominant species in all seven samples tested. In conclusion, N. ceranae is widespread in Scotland where it exists in combination with the endemic N. apis. A single variant, identical to that found in France (DQ374655) except for the addition of a single nucleotide polymorphism, is present in Scotland

The Mitochondrial Genome of Toxocara canis

Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secernentean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts

Generalized p value for multivariate Gaussian stochastic processes in continuous time

We construct a Generalized p value for testing statistical hypotheses on the comparison of mean vectors in the sequential observation of two continuous time multidimensional Gaussian processes. The mean vectors depend linearly on two multidimensional parameters and with different conditions about their covariance structures. The invariance of the generalized p value considered is proved under certain linear transformations. We report results of a simulation study showing power and errors probabilities for them. Finally, we apply our results to a real data set