Cluster-based active learning for compact image classification

In this paper, we consider active sampling to label pixels grouped with hierarchical clustering. The objective of the method is to match the data relationships discovered by the clustering algorithm with the user's desired class semantics. The first is represented as a complete tree to be pruned and the second is iteratively provided by the user. The active learning algorithm proposed searches the pruning of the tree that best matches the labels of the sampled points. By choosing the part of the tree to sample from according to current pruning's uncertainty, sampling is focused on most uncertain clusters. This way, large clusters for which the class membership is already fixed are no longer queried and sampling is focused on division of clusters showing mixed labels. The model is tested on a VHR image in a multiclass classification setting. The method clearly outperforms random sampling in a transductive setting, but cannot generalize to unseen data, since it aims at optimizing the classification of a given cluster structure.

A game theoretical approach to the algebraic counterpart of the Wagner hierarchy

La hiérarchie de Wagner constitue à ce jour la plus fine classification des langages ω-réguliers. Par ailleurs, l'approche algébrique de la théorie de langages formels montre que ces ensembles ω-réguliers correspondent précisément aux langages reconnaissables par des ω-semigroupes finis pointés. Ce travail s'inscrit dans ce contexte en fournissant une description complète de la contrepartie algébrique de la hiérarchie de Wagner, et ce par le biais de la théorie descriptive des jeux de Wadge. Plus précisément, nous montrons d'abord que le degré de Wagner d'un langage ω-régulier est effectivement un invariant syntaxique. Nous définissons ensuite une relation de réduction entre ω-semigroupes pointés par le biais d'un jeu infini de type Wadge. La collection de ces structures algébriques ordonnée par cette relation apparaît alors comme étant isomorphe à la hiérarchie de Wagner, soit un quasi bon ordre décidable de largeur 2 et de hauteur ω. Nous exposons par la suite une procédure de décidabilité de cette hiérarchie algébrique : on décrit une représentation graphique des ω-semigroupes finis pointés, puis un algorithme sur ces structures graphiques qui calcule le degré de Wagner de n'importe quel élément. Ainsi le degré de Wagner de tout langage ω-régulier peut être calculé de manière effective directement sur son image syntaxique. Nous montrons ensuite comment construire directement et inductivement une structure de n''importe quel degré. Nous terminons par une description détaillée des invariants algébriques qui caractérisent tous les degrés de cette hiérarchie. Abstract The Wagner hierarchy is known so far to be the most refined topological classification of ω-rational languages. Also, the algebraic study of formal languages shows that these ω-rational sets correspond precisely to the languages recognizable by finite pointed ω-semigroups. Within this framework, we provide a construction of the algebraic counterpart of the Wagner hierarchy. We adopt a hierarchical game approach, by translating the Wadge theory from the ω-rational language to the ω-semigroup context. More precisely, we first show that the Wagner degree is indeed a syntactic invariant. We then define a reduction relation on finite pointed ω-semigroups by means of a Wadge-like infinite two-player game. The collection of these algebraic structures ordered by this reduction is then proven to be isomorphic to the Wagner hierarchy, namely a well-founded and decidable partial ordering of width 2 and height $\omega^\omega$. We also describe a decidability procedure of this hierarchy: we introduce a graph representation of finite pointed ω-semigroups allowing to compute their precise Wagner degrees. The Wagner degree of every ω-rational language can therefore be computed directly on its syntactic image. We then show how to build a finite pointed ω-semigroup of any given Wagner degree. We finally describe the algebraic invariants characterizing every Wagner degree of this hierarchy.

Evidence-based provisional clinical classification criteria for autoinflammatory periodic fevers.

The objective of this work was to develop and validate a set of clinical criteria for the classification of patients affected by periodic fevers. Patients with inherited periodic fevers (familial Mediterranean fever (FMF); mevalonate kinase deficiency (MKD); tumour necrosis factor receptor-associated periodic fever syndrome (TRAPS); cryopyrin-associated periodic syndromes (CAPS)) enrolled in the Eurofever Registry up until March 2013 were evaluated. Patients with periodic fever, aphthosis, pharyngitis and adenitis (PFAPA) syndrome were used as negative controls. For each genetic disease, patients were considered to be 'gold standard' on the basis of the presence of a confirmatory genetic analysis. Clinical criteria were formulated on the basis of univariate and multivariate analysis in an initial group of patients (training set) and validated in an independent set of patients (validation set). A total of 1215 consecutive patients with periodic fevers were identified, and 518 gold standard patients (291 FMF, 74 MKD, 86 TRAPS, 67 CAPS) and 199 patients with PFAPA as disease controls were evaluated. The univariate and multivariate analyses identified a number of clinical variables that correlated independently with each disease, and four provisional classification scores were created. Cut-off values of the classification scores were chosen using receiver operating characteristic curve analysis as those giving the highest sensitivity and specificity. The classification scores were then tested in an independent set of patients (validation set) with an area under the curve of 0.98 for FMF, 0.95 for TRAPS, 0.96 for MKD, and 0.99 for CAPS. In conclusion, evidence-based provisional clinical criteria with high sensitivity and specificity for the clinical classification of patients with inherited periodic fevers have been developed.

A founder CEP120 mutation in Jeune asphyxiating thoracic dystrophy expands the role of centriolar proteins in skeletal ciliopathies.

Jeune asphyxiating thoracic dystrophy (JATD) is a skeletal dysplasia characterized by a small thoracic cage and a range of skeletal and extra-skeletal anomalies. JATD is genetically heterogeneous with at least nine genes identified, all encoding ciliary proteins, hence the classification of JATD as a skeletal ciliopathy. Consistent with the observation that the heterogeneous molecular basis of JATD has not been fully determined yet, we have identified two consanguineous Saudi families segregating JATD who share a single identical ancestral homozygous haplotype among the affected members. Whole-exome sequencing revealed a single novel variant within the disease haplotype in CEP120, which encodes a core centriolar protein. Subsequent targeted sequencing of CEP120 in Saudi and European JATD cohorts identified two additional families with the same missense mutation. Combining the four families in linkage analysis confirmed a significant genome-wide linkage signal at the CEP120 locus. This missense change alters a highly conserved amino acid within CEP120 (p.Ala199Pro). In addition, we show marked reduction of cilia and abnormal number of centrioles in fibroblasts from one affected individual. Inhibition of the CEP120 ortholog in zebrafish produced pleiotropic phenotypes characteristic of cilia defects including abnormal body curvature, hydrocephalus, otolith defects and abnormal renal, head and craniofacial development. We also demonstrate that in CEP120 morphants, cilia are shortened in the neural tube and disorganized in the pronephros. These results are consistent with aberrant CEP120 being implicated in the pathogenesis of JATD and expand the role of centriolar proteins in skeletal ciliopathies.

Taxogenomics of the order Chlamydiales.

Bacterial classification is a long-standing problem for taxonomists and species definition itself is constantly debated among specialists. The classification of strict intracellular bacteria such as members of the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences and are difficult to culture. The availability of full genome sequences allows the comparison of the performance of conserved protein sequences to reconstruct Chlamydiales phylogeny. This approach permits the identification of markers that maximize the phylogenetic signal and the robustness of the inferred tree. In this study, a set of 424 core proteins was identified and concatenated to reconstruct a reference species tree. Although individual protein trees present variable topologies, we detected only few cases of incongruence with the reference species tree, which were due to horizontal gene transfers. Detailed analysis of the phylogenetic information of individual protein sequences (i) showed that phylogenies based on single randomly chosen core proteins are not reliable and (ii) led to the identification of twenty taxonomically highly reliable proteins, allowing the reconstruction of a robust tree close to the reference species tree. We recommend using these protein sequences to precisely classify newly discovered isolates at the family, genus and species levels.

May increasing incidence of breast cancer be related to overdiagnosis? : a population-based study

Background: Breast cancer is the first cause of cancer in women in Switzerland. While breast cancer mortality has sharply decreased in the two last decades in Switzerland, the incidence of breast cancer has increased during the same period. Various reasons for this increase have been hypothesized, such as the increase in the prevalence of obesity, the use of postmenauposal hormone replacement therapy, or a later age for having a first child. Overdiagnosis secondary to screening and any other forms of early detection procedures could be also involved. Analyses of breast cancer by stage can help evaluate if overdiagnosis could have contributed to the increase in the incidence of breast cancer. Methods: We used data from the Valais cancer registry at the Observatoire valaisan de la santé (www.ovs.ch). This population based registry collects data on all new (incident) cases of cancer diagnosed in women living in one canton of Switzerland, Valais. Cancers are coded according to the International Classification of Diseases for Oncology (ICD-O-3) and the stages are coded according to the TNM classification. Information on breast cancer stage (in situ: 0; invasive: I, II, III, IV) was available for all cases recorded between 1993 and 2011 (N=4246). Standardized rates of breast cancer were computed (direct standardization on European population).

Disease profiles of detainees in the Canton of Vaud in Switzerland: gender and age differences in substance abuse, mental health and chronic health conditions.

BACKGROUND: Literature on the disease profile of prisoners that differentiates by age and gender remains sparse. This study aimed to describe the health of correctional inmates in terms of substance abuse problems and mental and somatic health conditions, and compare it by gender and age. METHODS: This study examined cross-sectional data from the Canton of Vaud in Switzerland on the health conditions of detainees who were in prison on January 1, 2011 or entered prison in 2011. Health conditions validated by physician examination were reported using the International Classification of Diseases (ICD) version 10. The analyses were descriptive by groups of prisoners: the entire sample (All), Men, Older adults and Women. RESULTS: A total of 1,664 individuals were included in the analysis. Men comprised 91.5 % of the sample and had a mean age of 33 years. The other 8.5 % were women and had an average age of 39. Older adults (i.e., age 50 and older) represented 7 % of the total sample. Overall, 80 % of inmates were non-Swiss citizens, but the proportion of Swiss prisoners was higher among the older adults (51 %) and women (29 %). Overall, 41 % of inmates self-reported substance abuse problems. Of those, 27 % were being treated by psychiatrists for behavioral disorders related to substance abuse. Chronic infectious diseases were found in 9 % of the prison population. In addition, 27 % of detainees suffered from serious mental health conditions. Gender and age had an influence on the disease profile of this sample: compared to the entire prison population, the older inmates were less likely to misuse illegal drugs and to suffer from communicable infections but exhibited more problems with alcohol and a higher burden of chronic health conditions. Female prisoners were more disposed to mental health problems (including drug abuse) and infectious diseases. In terms of chronic diseases, women suffered from the same conditions as men, but the diseases were more prevalent in women. CONCLUSION: It is important to understand the different disease profiles of prisoners by gender and age, as it helps identify the needs of different groups and tailor age-and gender-specific interventions.

Improved predictive mapping of indoor radon concentrations using ensemble regression trees based on automatic clustering of geological units.

PURPOSE: According to estimations around 230 people die as a result of radon exposure in Switzerland. This public health concern makes reliable indoor radon prediction and mapping methods necessary in order to improve risk communication to the public. The aim of this study was to develop an automated method to classify lithological units according to their radon characteristics and to develop mapping and predictive tools in order to improve local radon prediction. METHOD: About 240 000 indoor radon concentration (IRC) measurements in about 150 000 buildings were available for our analysis. The automated classification of lithological units was based on k-medoids clustering via pair-wise Kolmogorov distances between IRC distributions of lithological units. For IRC mapping and prediction we used random forests and Bayesian additive regression trees (BART). RESULTS: The automated classification groups lithological units well in terms of their IRC characteristics. Especially the IRC differences in metamorphic rocks like gneiss are well revealed by this method. The maps produced by random forests soundly represent the regional difference of IRCs in Switzerland and improve the spatial detail compared to existing approaches. We could explain 33% of the variations in IRC data with random forests. Additionally, the influence of a variable evaluated by random forests shows that building characteristics are less important predictors for IRCs than spatial/geological influences. BART could explain 29% of IRC variability and produced maps that indicate the prediction uncertainty. CONCLUSION: Ensemble regression trees are a powerful tool to model and understand the multidimensional influences on IRCs. Automatic clustering of lithological units complements this method by facilitating the interpretation of radon properties of rock types. This study provides an important element for radon risk communication. Future approaches should consider taking into account further variables like soil gas radon measurements as well as more detailed geological information.

Managing the Sick Child in the Era of Declining Malaria Transmission: Development of ALMANACH, an Electronic Algorithm for Appropriate Use of Antimicrobials.

OBJECTIVE: To review the available knowledge on epidemiology and diagnoses of acute infections in children aged 2 to 59 months in primary care setting and develop an electronic algorithm for the Integrated Management of Childhood Illness to reach optimal clinical outcome and rational use of medicines. METHODS: A structured literature review in Medline, Embase and the Cochrane Database of Systematic Review (CDRS) looked for available estimations of diseases prevalence in outpatients aged 2-59 months, and for available evidence on i) accuracy of clinical predictors, and ii) performance of point-of-care tests for targeted diseases. A new algorithm for the management of childhood illness (ALMANACH) was designed based on evidence retrieved and results of a study on etiologies of fever in Tanzanian children outpatients. FINDINGS: The major changes in ALMANACH compared to IMCI (2008 version) are the following: i) assessment of 10 danger signs, ii) classification of non-severe children into febrile and non-febrile illness, the latter receiving no antibiotics, iii) classification of pneumonia based on a respiratory rate threshold of 50 assessed twice for febrile children 12-59 months; iv) malaria rapid diagnostic test performed for all febrile children. In the absence of identified source of fever at the end of the assessment, v) urine dipstick performed for febrile children <2 years to consider urinary tract infection, vi) classification of 'possible typhoid' for febrile children >2 years with abdominal tenderness; and lastly vii) classification of 'likely viral infection' in case of negative results. CONCLUSION: This smartphone-run algorithm based on new evidence and two point-of-care tests should improve the quality of care of <5 year children and lead to more rational use of antimicrobials.

Severity and burden of partial-onset seizures in a phase III trial of eslicarbazepine acetate.

OBJECTIVE: The objective of this study was to compare posttreatment seizure severity in a phase III clinical trial of eslicarbazepine acetate (ESL) as adjunctive treatment of refractory partial-onset seizures. METHODS: The Seizure Severity Questionnaire (SSQ) was administered at baseline and posttreatment. The SSQ total score (TS) and component scores (frequency and helpfulness of warning signs before seizures [BS]; severity and bothersomeness of ictal movement and altered consciousness during seizures [DS]; cognitive, emotional, and physical aspects of postictal recovery after seizures [AS]; and overall severity and bothersomeness [SB]) were calculated for the per-protocol population. Analysis of covariance, adjusted for baseline scores, estimated differences in posttreatment least square means between treatment arms. RESULTS: Out of 547 per-protocol patients, 441 had valid SSQ TS both at baseline and posttreatment. Mean posttreatment TS for ESL 1200mg/day was significantly lower than that for placebo (2.68 vs 3.20, p<0.001), exceeding the minimal clinically important difference (MCID: 0.48). Mean DS, AS, and SB were also significantly lower with ESL 1200mg/day; differences in AS and SB exceeded the MCIDs. The TS, DS, AS, and SB were lower for ESL 800mg/day than for placebo; only SB was significant (p=0.013). For both ESL arms combined versus placebo, mean scores differed significantly for TS (p=0.006), DS (p=0.031), and SB (p=0.001). CONCLUSIONS: Therapeutic ESL doses led to clinically meaningful, dose-dependent reductions in seizure severity, as measured by SSQ scores. CLASSIFICATION OF EVIDENCE: This study presents Class I evidence that adjunctive ESL (800 and 1200mg/day) led to clinically meaningful, dose-dependent seizure severity reductions, measured by the SSQ.

Classification supervisée multi-étiquette en actes de dialogue: analyse discriminante et transformations de Schoenberg

Abstract This work studies the multi-label classification of turns in simple English Wikipedia talk pages into dialog acts. The treated dataset was created and multi-labeled by (Ferschke et al., 2012). The first part analyses dependences between labels, in order to examine the annotation coherence and to determine a classification method. Then, a multi-label classification is computed, after transforming the problem into binary relevance. Regarding features, whereas (Ferschke et al., 2012) use features such as uni-, bi-, and trigrams, time distance between turns or the indentation level of the turn, other features are considered here: lemmas, part-of-speech tags and the meaning of verbs (according to WordNet). The dataset authors applied approaches such as Naive Bayes or Support Vector Machines. The present paper proposes, as an alternative, to use Schoenberg transformations which, following the example of kernel methods, transform original Euclidean distances into other Euclidean distances, in a space of high dimensionality. Résumé Ce travail étudie la classification supervisée multi-étiquette en actes de dialogue des tours de parole des contributeurs aux pages de discussion de Simple English Wikipedia (Wikipédia en anglais simple). Le jeu de données considéré a été créé et multi-étiqueté par (Ferschke et al., 2012). Une première partie analyse les relations entre les étiquettes pour examiner la cohérence des annotations et pour déterminer une méthode de classification. Ensuite, une classification supervisée multi-étiquette est effectuée, après recodage binaire des étiquettes. Concernant les variables, alors que (Ferschke et al., 2012) utilisent des caractéristiques telles que les uni-, bi- et trigrammes, le temps entre les tours de parole ou l'indentation d'un tour de parole, d'autres descripteurs sont considérés ici : les lemmes, les catégories morphosyntaxiques et le sens des verbes (selon WordNet). Les auteurs du jeu de données ont employé des approches telles que le Naive Bayes ou les Séparateurs à Vastes Marges (SVM) pour la classification. Cet article propose, de façon alternative, d'utiliser et d'étendre l'analyse discriminante linéaire aux transformations de Schoenberg qui, à l'instar des méthodes à noyau, transforment les distances euclidiennes originales en d'autres distances euclidiennes, dans un espace de haute dimensionnalité.

The High Prevalence and Diversity of Chlamydiales DNA within Ixodes ricinus Ticks Suggest a Role for Ticks as Reservoirs and Vectors of Chlamydia-Related Bacteria.

The Chlamydiales order is composed of nine families of strictly intracellular bacteria. Among them, Chlamydia trachomatis, C. pneumoniae, and C. psittaci are established human pathogens, whereas Waddlia chondrophila and Parachlamydia acanthamoebae have emerged as new pathogens in humans. However, despite their medical importance, their biodiversity and ecology remain to be studied. Even if arthropods and, particularly, ticks are well known to be vectors of numerous infectious agents such as viruses and bacteria, virtually nothing is known about ticks and chlamydia. This study investigated the prevalence of Chlamydiae in ticks. Specifically, 62,889 Ixodes ricinus ticks, consolidated into 8,534 pools, were sampled in 172 collection sites throughout Switzerland and were investigated using pan-Chlamydiales quantitative PCR (qPCR) for the presence of Chlamydiales DNA. Among the pools, 543 (6.4%) gave positive results and the estimated prevalence in individual ticks was 0.89%. Among those pools with positive results, we obtained 16S rRNA sequences for 359 samples, allowing classification of Chlamydiales DNA at the family level. A high level of biodiversity was observed, since six of the nine families belonging to the Chlamydiales order were detected. Those most common were Parachlamydiaceae (33.1%) and Rhabdochlamydiaceae (29.2%). "Unclassified Chlamydiales" (31.8%) were also often detected. Thanks to the huge amount of Chlamydiales DNA recovered from ticks, this report opens up new perspectives on further work focusing on whole-genome sequencing to increase our knowledge about Chlamydiales biodiversity. This report of an epidemiological study also demonstrates the presence of Chlamydia-related bacteria within Ixodes ricinus ticks and suggests a role for ticks in the transmission of and as a reservoir for these emerging pathogenic Chlamydia-related bacteria.

Development of a systematic computer vision-based method to analyse and compare images of false identity documents for forensic intelligence purposes-Part I: acquisition, calibration and validation issues

Following their detection and seizure by police and border guard authorities, false identity and travel documents are usually scanned, producing digital images. This research investigates the potential of these images to classify false identity documents, highlight links between documents produced by a same modus operandi or same source, and thus support forensic intelligence efforts. Inspired by previous research work about digital images of Ecstasy tablets, a systematic and complete method has been developed to acquire, collect, process and compare images of false identity documents. This first part of the article highlights the critical steps of the method and the development of a prototype that processes regions of interest extracted from images. Acquisition conditions have been fine-tuned in order to optimise reproducibility and comparability of images. Different filters and comparison metrics have been evaluated and the performance of the method has been assessed using two calibration and validation sets of documents, made up of 101 Italian driving licenses and 96 Portuguese passports seized in Switzerland, among which some were known to come from common sources. Results indicate that the use of Hue and Edge filters or their combination to extract profiles from images, and then the comparison of profiles with a Canberra distance-based metric provides the most accurate classification of documents. The method appears also to be quick, efficient and inexpensive. It can be easily operated from remote locations and shared amongst different organisations, which makes it very convenient for future operational applications. The method could serve as a first fast triage method that may help target more resource-intensive profiling methods (based on a visual, physical or chemical examination of documents for instance). Its contribution to forensic intelligence and its application to several sets of false identity documents seized by police and border guards will be developed in a forthcoming article (part II).

Prevalence of sleep apnoea syndrome in the middle to old age general population.

On the basis of a large populationbased sample who underwent full polysomnography at home (HypnoLaus cohort), we recently reported that 49·7% of men and 23·4% of women aged 40 years or older had an apnoea-hypopnoea index of 15 events per h or more1 according to the American Academy of Sleep Medicine (AASM) 2013 scoring criteria. When excessive daytime sleepiness (ie, Epworth score >10 [maximum score 24]) was included in the definition with an apnoea-hypopnoea index of 5 events per h or more, the prevalence was 12·5% in men and 5·9% in women. This high prevalence of sleep disordered breathing reinforced the idea that the treatment decision should not only be based the apnoeahypopnoea index, but should also take into account associated symptoms and cardiovascular and metabolic comorbidities. After this Article was published, several readers contacted us to ask for the prevalence of sleep apnoea syndrome in our sample according to the International Classification of Sleep Disorders (ICSD-3) criteria. These criteria include either the presence of an apnoea-hypopnoea index of 5 events per h or more associated with obstructive sleep apnoearelated symptoms or cardiovascular and metabolic comorbidities, or an apnoea-hypopnoea index of 15 events per h or more (figure).

Image guided critical screw placement precision in the cervical spine : important or incidental? : results of a series of 91 consecutive cases using OVEM

Study design: A retrospective study of image guided cervical implant placement precision. Objective: To describe a simple and precise classification of cervical critical screw placement. Summary of Background Data: "Critical" screw placement is defined as implant insertion into a bone corridor which is surrounded circumferentially by neurovascular structures. While the use of image guidance has improved accuracy, there is currently no classification which provides sufficient precision to assess the navigation success of critical cervical screw placement. Methods: Based on postoperative clinical evaluation and CT imaging, the orthogonal view evaluation method (OVEM) is used to classify screw accuracy into grade I (no cortical breach), grade la (screw thread cortical breach), grade II (internal diameter cortical breach) and grade III (major cortical breach causing neural or vascular injury). Grades II and III are considered to be navigation failures, after accounting for bone corridor / screw mismatch (minimal diameter of targeted bone corridor being smaller than an outer screw diameter). Results: A total of 276 screws from 91 patients were classified into grade I (64.9%), grade la (18.1%), and grade II (17.0%). No grade III screw was observed. The overall rate of navigation failure was 13%. Multiple logistic regression indicated that navigational failure was significantly associated with the level of instrumentation and the navigation system used. Navigational failure was rare (1.6%) when the margin around the screw in the bone corridor was larger than 1.5 mm. Conclusions: OVEM evaluation appears to be a useful tool to assess the precision of critical screw placement in the cervical spine. The OVEM validity and reliability need to be addressed. Further correlation with clinical outcomes will be addressed in future studies.