Finding counterfactual explanations through constraint relaxations

Interactive constraint systems often suffer from infeasibility (no solution) due to conflicting user constraints. A common approach to recover infeasibility is to eliminate the constraints that cause the conflicts in the system. This approach allows the system to provide an explanation as: "if the user is willing to drop out some of their constraints, there exists a solution". However, one can criticise this form of explanation as not being very informative. A counterfactual explanation is a type of explanation that can provide a basis for the user to recover feasibility by helping them understand which changes can be applied to their existing constraints rather than removing them. This approach has been extensively studied in the machine learning field, but requires a more thorough investigation in the context of constraint satisfaction. We propose an iterative method based on conflict detection and maximal relaxations in over-constrained constraint satisfaction problems to help compute a counterfactual explanation

Automated layout of process description maps drawn in systems biology graphical notation = Systems biology graphical notation kullanılarak çizilen proses diyagramlarının otomatik yerleştirilmesi

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2014.Thesis (Master's) -- Bilkent University, 2014.Includes bibliographical references leaves 74-78.Evolving technology has increased the focus on genomics. The combination of today’s advanced studies with decades of molecular biology research yield in huge amount of pathway data. These models can be used to improve high-throughput data analysis by linking correlation to the causation, shedding light on many complex diseases. In order to prevent ambiguity and ensure regularity of the research, a need for using a standard notation has emerged. Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modellers and computer scientists with the intention of enabling scientists to represent networks, including models of cellular processes, in a standard, unambiguous way. SBGN is formed of three languages: process, entity relationship and activity flow. This research is focused on its process diagram branch. Automated layout is commonly used to clearly visualize the information represented by graphs. Considering the fact that, biological pathways includes nested structures (e.g., nucleoplasms), we have made use of a force-directed automatic layout algorithm called Compound Spring Embedder (CoSE), which supports the compound graph structures. On top of this layout structure, we have developed a specialized layout algorithm called SBGN-PD layout. SBGN-PD layout enhancements mainly include properly tiling of complex members and disconnected molecules, placement of product and substrate edges on the opposite sides of a process node without disturbing the force-directed structure of the algorithm.Genç, BegümM.S

A Collection of Constraint Programming Models for the Three-Dimensional Stable Matching Problem with Cyclic Preferences

We introduce five constraint models for the 3-dimensional stable matching problem with cyclic preferences and study their relative performances under diverse configurations. While several constraint models have been proposed for variants of the two-dimensional stable matching problem, we are the first to present constraint models for a higher number of dimensions. We show for all five models how to capture two different stability notions, namely weak and strong stability. Additionally, we translate some well-known fairness notions (i.e. sex-equal, minimum regret, egalitarian) into 3-dimensional matchings, and present how to capture them in each model. Our tests cover dozens of problem sizes and four different instance generation methods. We explore two levels of commitment in our models: one where we have an individual variable for each agent (individual commitment), and another one where the determination of a variable involves pairing the three agents at once (group commitment). Our experiments show that the suitability of the commitment depends on the type of stability we are dealing with. Our experiments not only led us to discover dependencies between the type of stability and the instance generation method, but also brought light to the role that learning and restarts can play in solving this kind of problems

Orthognathic Surgery after Mandibular Large-Volume Osteoma Treatment

Osteoma is a benign asymptomatic osseous tumor. Characterization of osteoma is the proliferation of cancellous or compact bone that increases in size by continuous formation of bone. It can be seen in any craniofacial structures, usually in paranasal sinuses and jaws. In this study, we present a 17-year-old male patient with a giant osteoma in the mandibular condyle. Posttreatment post-op follow-up, post-ortho, and orthognathic surgery after dental implantation are described

1953’ten günümüze Pancar Kooperatifleri Bankası : Şekerbank’ın Türkiye tarımı üzerindeki etkileri

Ankara : İhsan Doğramacı Bilkent Üniversitesi İktisadi, İdari ve Sosyal Bilimler Fakültesi, Tarih Bölümü, 2015.This work is a student project of the The Department of History, Faculty of Economics, Administrative and Social Sciences, İhsan Doğramacı Bilkent University.by Öztürk, İbrahim Mert

Molecular characterization of Ditylenchus dipsaci on Onion in Turkey

WOS:000428804400013Ditylenchus dipsaci is a species complex including diploid and polyploid individuals. The onion race of D. dipsaci is a sensu stricto group and has a wide range of host spectrum. Identification of the D. dipsaci onion race is difficult using morphological and morphometrical methods. Species specific primers are mostly used in molecular approaches for identification of D. dipsaci populations. Fifty one morphologically selected Ditylenchus spp. populations from onion production areas in Turkey were subjected to molecular identification using four D. dipsaci species specific primer sets (PF1-PR1, PF2-PR2, DdpS1-rDNA2, DitNF1- rDNA2, H05-H06) targeting 5.8S and 18S rDNA, ITS1 and flanking ITS regions. Thirty nine percent of the nematode samples were positive with four primers tested, while four of the nematode samples gave specific bands with H05-H06 primers. Ditylenchus dipsaci sensu stricto was identified with specific primer sets in Adana, Hatay, Tekirdag, Bursa, Aksaray, Karaman, Eskisehir and Ankara provinces in Mediterranean, Trace, Aegean and Central Regions in Turkey.Turkish Scientific and Technical Research Council (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [215O468]This research has been financially supported by Turkish Scientific and Technical Research Council (TUBITAK) (Project No: 215O468)

Molecular characterization of Ditylenchus dipsaci on garlic in Turkey

WOS:000492175100001Garlic plant, which has an important place in the world economy as well as in human nutrition, is grown extensively in Turkey. The stem and bulb nematode, Ditylenchus dipsaci (Kuhn) is one of the most important biotic stresses and is under quarantine as it significantly interrupts garlic production wherever it emerges. Thus, being up to date regarding the distribution and population of the stem and bulb nematode, which is locally found in garlic cultivation areas, identification of the races found on the garlic plant at the molecular level and knowing the host spectrum of the races found at the region are of great importance. The objective of this study is to perform species diagnosis using the species-specific molecular markers at ITS-rDNA regions of the stem and bulb nematode isolates collected from the garlic cultivation areas in Turkey in 2016 and 2017. In the study, molecular screening data of the nematodes isolated from the plant and soil samples were analyzed phylogenetically. In this study, upon molecular screening using 9 different species-specific SSR and SCAR primers, it was found that 34 nematode samples of 53 are D. dipsaci. Nematode samples were from the garlic fields in Kastamonu, Amasya, Aksaray, Tekirdag, Tokat, Balikesir, Bursa, Hatay, Gaziantep, Kahramanmaras, Adiyaman, and Kirklareli provinces. Identification of stem and bulb nematodes found in the areas of garlic cultivation with this study will be useful for conscious and efficient control applications to this nematode.Turkish Scientific and Technical Research Council (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [215O468]This research was funded by Turkish Scientific and Technical Research Council (TUBITAK) (Project No.: 215O468)