Gradient Vector Fields of Discrete Morse Functions and Watershed-cuts

In this paper, we study a class of discrete Morse functions, coming from Discrete Morse Theory, that are equivalent to a class of simplicial stacks, coming from Mathematical Morphology. We show that, as in Discrete Morse Theory, we can see the gradient vector field of a simplicial stack (seen as a discrete Morse function) as the only relevant information we should consider. Last, but not the least, we also show that the Minimum Spanning Forest of the dual graph of a simplicial stack is induced by the gradient vector field of the initial function. This result allows computing a watershed-cut from a gradient vector field

Unsupervised discovery of Interpretable Visual Concepts

Providing interpretability of deep-learning models to non-experts, while fundamental for a responsible real-world usage, is challenging. Attribution maps from xAI techniques, such as Integrated Gradients, are a typical example of a visualization technique containing a high level of information, but with difficult interpretation. In this paper, we propose two methods, Maximum Activation Groups Extraction (MAGE) and Multiscale Interpretable Visualization (Ms-IV), to explain the model's decision, enhancing global interpretability. MAGE finds, for a given CNN, combinations of features which, globally, form a semantic meaning, that we call concepts. We group these similar feature patterns by clustering in ``concepts'', that we visualize through Ms-IV. This last method is inspired by Occlusion and Sensitivity analysis (incorporating causality), and uses a novel metric, called Class-aware Order Correlation (CaOC), to globally evaluate the most important image regions according to the model's decision space. We compare our approach to xAI methods such as LIME and Integrated Gradients. Experimental results evince the Ms-IV higher localization and faithfulness values. Finally, qualitative evaluation of combined MAGE and Ms-IV demonstrate humans' ability to agree, based on the visualization, on the decision of clusters' concepts; and, to detect, among a given set of networks, the existence of bias

Dynamiques agricoles : trajectoires vs. modèle(s) ? Le cas du Douaisis

Loin des lectures communes opposant agriculture conventionnelle et agriculture biologique et/ou de proximité, il existe une diversité de stratégies non exclusives, répondant à des logiques individuelles, liées non seulement aux spécificités de chaque exploitation, mais aussi aux représentations des agriculteurs. Nous proposons une nouvelle grille de lecture, croisant systèmes de production, itinéraires techniques, modalités de mise en marché et intentions des chefs d’exploitation. Des convergences et des tensions se développent entre les différentes formes d’agriculture reflétant des processus complexes d’hybridation et de disjonction. Nos résultats, en permettant de mieux comprendre les évolutions de l’agriculture et en mettant en évidence les perméabilités entre trajectoires agricoles, pourraient être utilisés pour orienter les politiques publiques en matière d’agriculture et d’alimentation durables.Far from the traditional representations between conventional and organic/local/direct-selling farming, there is a diversity of non-exclusive strategies, responding to individual logics related not only to the farm trajectory, but also to the beliefs of the farmer. We propose a new reading grid crossing different dimensions and leading to the classification of farms according to four profiles. Convergences and tensions are developing between the different “forms” of agriculture, reflecting complex processes of hybridization and disjunction. Our results, by providing a better understanding of the changes in French agriculture and highlighting the permeability between agricultural models, could be used to shape public policies towards sustainable agriculture and food

Strong Euler well-composedness

In this paper, we define a new flavour of well-composedness, called strong Euler well composedness. In the general setting of regular cell complexes, a regular cell complex of dimension n is strongly Euler well-composed if the Euler characteristic of the link of each boundary cell is 1, which is the Euler characteristic of an (n−1)-dimensional ball. Working in the particular setting of cubical complexes canonically associated with nD pictures, we formally prove in this paper that strong Euler well-composedness implies digital well-composedness in any dimension n ≥ 2 and that the converse is not true when n ≥ 4Ministerio de Ciencia, Innovación y Universidades PID2019-107339GB-I00Junta de Andalucía P20_0114

Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation

<p>Abstract</p> <p>Background</p> <p>The industrial chicory, <it>Cichorium intybus</it>, is a member of the <it>Asteraceae </it>family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison.</p> <p>Results</p> <p>Approximately 1,000 Expressed Sequence Tags (EST) were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution.</p> <p>Conclusion</p> <p>This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.</p

Les cartes auto-organisatrices de Kohonen appliquées à l'étude des communautés de micro-algues des cours d'eau

Les cartes auto-organisatrices de Kohonen appliquées à l'étude des communautés de micro-algues des cours d'ea

DC/DC converter 3D assembly for autonomous sensor nodes

This paper reports on the design and the manufacturing of an integrated DCDC converter, which respects the specificity of sensor node network: compactness, high efficiency in acquisition and transmission modes, and compatibility with miniature Lithium batteries. A novel integrated circuit (ASIC) has been designed and manufactured to provide regulated Voltage to the sensor node from miniaturized, thin film Lithium batteries. Then, a 3D integration technique has been used to integrate this ASIC in a 3 layers stack with high efficiency passives components, mixing the wafer level technologies from two different research institutions. Electrical results have demonstrated the feasibility of this integrated system and experiments have shown significant improvements in the case of oscillations in regulated voltage. However, stability of this output voltage toward the input voltage has still to be improved

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors