A Partial-Closure Canonicity Test to Increase the Efficiency of CbO-Type Algorithms

Computing formal concepts is a fundamental part of Formal Concept Analysis and the design of increasingly efficient algorithms to carry out this task is a continuing strand of FCA research. Most approaches suffer from the repeated computation of the same formal concepts and, initially, algorithms concentrated on efficient searches through already computed results to detect these repeats, until the so-called canonicity test was introduced. The canonicity test meant that it was sufficient to examine the attributes of a computed concept to determine its newness: searching through previously computed concepts was no longer necessary. The employment of this test in Close-by-One type algorithms has proved to be highly effective. The typical CbO approach is to compute a concept and then test its canonicity. This paper describes a more efficient approach, whereby a concept need only be partially computed in order to carry out the test. Only if it passes the test does the computation of the concept need to be completed. This paper presents this ‘partial-closure’ canonicity test in the In-Close algorithm and compares it to a traditional CbO algorithm to demonstrate the increase in efficiency

A reference-grade wild soybean genome

Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci

A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs

Phytochrome-mediated growth inhibition of seminal roots in rice seedlings

In rice (Oryza sativa) seedlings, continuous white-light irradiation inhibited the growth of seminal roots but promoted the growth of crown roots. Here, we examined the mechanisms of photoinhibition of seminal root growth. Photoinhibition occurred in the absence of nitrogen, but increased with increasing nitrogen concentrations. In the presence of nitrogen, photoinhibition was correlated with coiling of the root tips. The seminal roots were most photosensitive 48-72 h after germination during the 7-d period after germination. White-light irradiation for at least 6 h was required for photoinhibition, and the Bunsen-Roscoe law of reciprocity was not observed. Experiments with phytochrome mutants showed that far-red light was perceived exclusively by phyA, that red light was perceived by both phyA and phyB, and phyC had little or no role in growth inhibition or coiling of the seminal roots. Fluence-response curve analyses also showed that phyA and phyB control very low fluence response and low fluence response, respectively, in the seminal roots. This was essentially the same as the growth inhibition previously observed at the late stage of coleoptile development (80 h after germination). These results also suggest that other blue-light photoreceptors are involved in growth inhibition of the seminal roots. The photoperceptive site for the root growth inhibition appeared to be the roots themselves. All three phytochrome species of rice were detected immunochemically in roots

Book Reviews

This paper presents a program, called In-Close2, that is a high performance realisation of the Close-by-One (CbO) algorithm. The design of In-Close2 is discussed and some new optimisation and data preprocessing techniques are presented. The performance of In-Close2 is favourably compared with another contemporary CbO variant called FCbO. An application of In-Close2 is given, using minimum support to reduce the size and complexity of a large formal context. Based on this application, an analysis of gene expression data is presented. In-Close2 can be downloaded from Sourceforge

CLASSIFICATION OF STRAWBERRY FRUIT SHAPE BY MACHINE LEARNING

Shape is one of the most important traits of agricultural products due to its relationships with the quality, quantity, and value of the products. For strawberries, the nine types of fruit shape were defined and classified by humans based on the sampler patterns of the nine types. In this study, we tested the classification of strawberry shapes by machine learning in order to increase the accuracy of the classification, and we introduce the concept of computerization into this field. Four types of descriptors were extracted from the digital images of strawberries: (1) the Measured Values (MVs) including the length of the contour line, the area, the fruit length and width, and the fruit width/length ratio; (2) the Ellipse Similarity Index (ESI); (3) Elliptic Fourier Descriptors (EFDs), and (4) Chain Code Subtraction (CCS). We used these descriptors for the classification test along with the random forest approach, and eight of the nine shape types were classified with combinations of MVs + CCS + EFDs. CCS is a descriptor that adds human knowledge to the chain codes, and it showed higher robustness in classification than the other descriptors. Our results suggest machine learning's high ability to classify fruit shapes accurately. We will attempt to increase the classification accuracy and apply the machine learning methods to other plant species