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Genchain: A blockchain based genetic disease prediction system
No full textGenetic testing can be used to learn about the genetic disorders a person may have based on their family history; however, they are overpriced and out of reach for many. We propose Genchain, which is a secure, private consortium blockchain system that calculates the probability of genetic diseases. Our system stores the information of the genetic diseases a user and their family have in a blockchain, and when requested, calculates the possible genetic disease percentages. The solution involves sending genetic disease data from all hospitals registered in the private system to Genchain, along with the family numbers of the patients taken from a trusted authority. Genchain uses the Paillier cryptosystem, a probabilistic asymmetric method for public key cryptography, which has the property of homomorphism, which we will use in our encryption scheme to protect the confidentiality and privacy of the system
Diffusion policies for out-of-distribution generalization in offline reinforcement learning
No full textOffline Reinforcement Learning (RL) methods leverage previous experiences to learn better policies than the behavior policy used for data collection. However, they face challenges handling distribution shifts due to the lack of online interaction during training. To this end, we propose a novel method named State Reconstruction for Diffusion Policies (SRDP) that incorporates state reconstruction feature learning in the recent class of diffusion policies to address the problem of out-of-distribution (OOD) generalization. Our method promotes learning of generalizable state representation to alleviate the distribution shift caused by OOD states. To illustrate the OOD generalization and faster convergence of SRDP, we design a novel 2D Multimodal Contextual Bandit environment and realize it on a 6-DoF real-world UR10 robot, as well as in simulation, and compare its performance with prior algorithms. In particular, we show the importance of the proposed state reconstruction via ablation studies. In addition, we assess the performance of our model on standard continuous control benchmarks (D4RL), namely the navigation of an 8-DoF ant and forward locomotion of half-cheetah, hopper, and walker2d, achieving state-of-the-art results. Finally, we demonstrate that our method can achieve 167% improvement over the competing baseline on a sparse continuous control navigation task where various regions of the state space are removed from the offline RL dataset, including the region encapsulating the goal.Japan Society for the Promotion of Science (JSPS) KAKENHI ; New Energy and Industrial Technology Development Organization (NEDO) ; INVERSE ; TÜBİTA
Modeling crosstalk coefficients in orbital angular momentum-multiplexed fso channels under gaussian pointing errors
No full textCrosstalk coefficients induced by pointing errors pose a significant challenge in orbital angular momentum (OAM)-multiplexed free space optical (FSO) communication systems. This paper presents a detailed investigation into the impact of Gaussian pointing errors on crosstalk coefficients within OAM-multiplexed FSO channels. Unlike previous studies which primarily focused on fixed strength of pointing error, our analysis encompasses a range of pointing error strengths. We propose closed-form expressions for the probability distribution function (PDF) governing the crosstalk coefficient, accommodating varying pointing error strengths. This analytical framework provides valuable insights into the behavior of crosstalk under different environmental conditions, facilitating the design and optimization of robust OAM-based FSO communication systems.TÜBİTA
Capacitated mobile facility location problem with mobile demand: Efficient relief aid provision to en route refugees
No full textAs a humanity crisis, the tragedy of forced displacement entails relief aid distribution efforts among en route refugees to alleviate their migration hardships. This study aims to assist humanitarian organizations in cost-efficiently optimizing the logistics of capacitated mobile facilities utilized to deliver relief aid to transiting refugees in a multi-period setting. The problem is referred to as the Capacitated Mobile Facility Location Problem with Mobile Demands (CMFLP-MD). In CMFLP-MD, refugee groups follow specific paths, and meanwhile, they receive relief aid at least once every fixed number of consecutive periods, maintaining continuity of service. To this end, the overall costs associated with capacitated mobile facilities, including fixed, service provision, and relocation costs, are minimized. We formulate a mixed integer linear programming (MILP) model and propose two solution methods to solve this complex problem: an accelerated Benders decomposition approach as an exact solution method and a matheuristic algorithm that relies on an enhanced fix-and-optimize agenda. We evaluate our methodologies by designing realistic instances based on the Honduras migration crisis that commenced in 2018. Our numerical results reveal that the accelerated Benders decomposition excels MILP with a 46% run time improvement on average while acquiring solutions at least as good as the MILP across all instances. Moreover, our matheuristic acquires high-quality solutions with a 2.4% average gap compared to best-incumbents rapidly. An in-depth exploration of the solution properties underscores the robustness of our relief distribution plans under varying migration circumstances. Across several metrics, our sensitivity analyses also highlight the managerial advantages of implementing CMFLP-MD solutions.TÜBİTA
Corrigendum to “Unveiling placental development in circadian rhythm-disrupted mice: A photo-acoustic imaging study on unstained tissue”
No full textKnowledge production in refugee studies from the south: Theorization of refugee labour in the literature on Turkey
No full textThis article explores the case of the migration studies industry in Turkey, which has flourished over the past decade, through an examination of knowledge production on refugee labour. Focusing on research about Syrian refugees' labour and employment in Turkey between 2012 and 2018, the article discusses the ways in which refugee labour is articulated and studied to provide ground for a wider critique of migration-related knowledge production. This study aims to reflexively question academic outputs by (1) exploring the conceptual frames used broadly in research on refugee labour, and (2) developing an overview of the literature on Turkey with a focus on this topic. Through the case of the literature on refugee labour in Turkey, we explore the underlying political economy premises of migration research. This case serves as an example to argue that knowledge produced in a Southern context is mainly incorporated as case studies despite attempts to advance theoretical discussions, highlighting a North-South hierarchization of knowledge.Publisher versio
Optimal reconstruction of graph evolution dynamics for duplication-based models
No full textThe research on biological network evolution and graph growth models, such as the Duplication-Mutation with Random Mutation (DMR) model, enable us to characterize the protein interaction network's evolutionary dynamics founded on duplication and divergence via mutation in a principled way. The existing approaches to reconstruct historical ancestral graphs for DMR model mainly focus on greedy approaches and results in suboptimal solutions. In this study, we come up with ILP-DMR, a novel Integer Linear Programming (ILP)-based formulation, to reconstruct historical PPI graphs by likelihood maximization over DMR model. We assess the effectiveness of our approach in reconstructing the history of synthetic as well as optimal history of the proteins from the families of bZIP transcription factors. In comparison to the existing techniques, solutions returned by our ILP-DMR have a higher likelihood and are more robust to model mismatch and noise in the data. Solutions extracted by ILP-DMR have a higher likelihood than the existing methods, and our solutions better agree with the biological findings of different studies. Our datasets and code are available at https://github.com/seferlab/dmrhistory
Art zamanlı kentsel morfoloji: Ait Ben Haddou'nun oluşum süreci, Fas.
No full textThis study focuses on the Ksar (Ighrem) Ait Ben Haddou as an outstanding example of a well-preserved earth settlement in southern Morocco. The fortified town is located in a semi-desert basin within the Draa region and stands on the side of a hill constructed primarily of rammed earth. The site was inscribed on the UNESCO World Heritage List in 1987, indicating that the oldest constructions do not date before the 17th century. However, the fortified town conveys ancient construction materials and techniques. Interestingly, Al-Wazzan [1, p. 194], mentions the existence of fortified castles along the Drâa valley in the 15th century. In this respect, the research explores the formation process of Ait Benhaddou by comparing available fragmentary historical data through geographers' and travelers' records and oral history with the results of the typo-morphological analysis based on the Caniggian school of thought. The application of the Caniggian theoretical framework demonstrates the role of urban attractors in forging the urban tissue and the urban grid, and the results reveal that the village originated from the hilltop and gradually expanded downhill from east to west (valley). The typo-morphological study explains a transformation of the urban pattern assisted by the development of building types following the growth direction while maintaining the notion of enclosure. Furthermore, the inspection of social, religious, economic, and commercial local attributes offered valuable insights into the logic of urban growth and the building form as an outcome of local contextual factors that characterize the village in its territory.Bu çalışma, Güney Fas'ta iyi korunmuş bir toprak yerleşiminin olağanüstü bir örneği olarak Ksar (Ighrem) Ait Ben Haddou'ya odaklanmaktadır. Müstahkem kasaba, Draa bölgesindeki yarı çöl bir havzada yer alır ve sıkıştırılmış topraktan inşa edilmiş bir tepenin kenarında durur. Alan, 1987'de UNESCO Dünya Mirası Listesi'ne kaydedildi, bu da en eski yapıların 17. yüzyıldan önce tarihlenmediğini gösteriyor. Ancak müstahkem kasaba kadim inşaat malzemelerini ve tekniklerini taşıyor. İlginçtir ki, Al-Wazzan, 15. yüzyılda Drâa vadisi boyunca müstahkem kalelerin varlığından bahsediyor [1, p. 194]. Bu bağlamda araştırma, Ait Benhaddou'nun oluşum sürecini, coğrafyacıların ve gezginlerin kayıtları ve sözlü tarih aracılığıyla mevcut parçalı tarihsel verileri Caniggian düşünce okuluna dayalı tipo-morfolojik analizin sonuçlarıyla karşılaştırarak araştırıyor. Caniggian teorik çerçevesinin uygulanması, kentsel dokuyu ve kentselleşme ağının yapımında kentsel çekicilerinin rolünü gösteriyor. Sonuçlar, köyün tepesinden kaynaklandığını ve yavaş yavaş yokuş aşağı doğudan batıya (vadi) genişlediğini ortaya koyuyor. Tipo-morfolojik çalışma, kentsel modelin değişimini, bina türlerinin büyüme yönünü izlerken, kapsama kavramını koruyarak gelişmesi yardımıyla açıklanmıştır. Ayrıca, sosyal, dini, ekonomik ve ticari yerel özelliklerin incelenmesi, bölgeyi karakterize eden yerel bağlam faktörlerinin bir sonucu olarak kentsel büyümenin mantığı ve bina şekli hakkında değerli fikirler sundu
Deep learning-based optimization of underwater QKD systems with time-gated SPADs
No full textIn this paper, we consider underwater quantum key distribution (QKD) systems with time-gated single photon avalanche photodiodes (SPADs) and present a comprehensive performance analysis and optimization. We utilize a deep learning model for the system optimization. We first perform Monte Carlo simulations for a subset of possible scenarios and train the deep learning model on them. Then, we use this model to instantly extract the optimum values for possible underwater scenarios. Our study provides critical insights on determining the optimal bit time, field of view (FoV), and gate time in underwater QKD. Through a meticulous analysis of the propagation delay and angle of arrival results, we determine the bit time and FoV, respectively, by striking a balance between the average number of received photons and background noise. Afterwards, using the proper bit time and FoV from the previous steps, we determine the optimal gate times in the sense of minimizing the quantum bit error rate (QBER). Our findings reveal that the proposed method significantly improves QBER, with enhancements reaching up to two orders of magnitude across different link lengths.Publisher versio
Reference-free inferring of transcriptomic events in cancer cells on single-cell data
No full textBackground Cancerous cells' identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus, bulk RNA-seq and more recent single-cell RNA-seq data (scRNA-seq) are important to identify pathogenic differences. In this case, we rely on k-mer decomposition of sequences to identify pathogenic variations in detail which does not need a reference, so it outperforms more traditional Next-Generation Sequencing (NGS) analysis techniques depending on the alignment of the sequences to a reference.Results Via our alignment-free analysis, over esophageal and glioblastoma cancer patients, high-frequency variations over multiple different locations (repeats, intergenic regions, exons, introns) as well as multiple different forms (fusion, polyadenylation, splicing, etc.) could be discovered. Additionally, we have analyzed the importance of less-focused events systematically in a classic transcriptome analysis pipeline where these events are considered as indicators for tumor prognosis, tumor prediction, tumor neoantigen inference, as well as their connection with respect to the immune microenvironment.Conclusions Our results suggest that esophageal cancer (ESCA) and glioblastoma processes can be explained via pathogenic microbial RNA, repeated sequences, novel splicing variants, and long intergenic non-coding RNAs (lincRNAs). We expect our application of reference-free process and analysis to be helpful in tumor and normal samples differential scRNA-seq analysis, which in turn offers a more comprehensive scheme for major cancer-associated events.TÜBİTAKPublisher versio