A probabilistic tree-based representation for non-convex minimum cost flow problems

Network flow optimisation has many real-world applications. The minimum cost flow problem (MCFP) is one of the most common network flow problems. Mathematical programming methods often assume the linearity and convexity of the underlying cost function, which is not realistic in many real-world situations. Solving large-sized MCFPs with nonlinear non-convex cost functions poses a much harder problem. In this paper, we propose a new representation scheme for solving non-convex MCFPs using genetic algorithms (GAs). The most common representation scheme for solving the MCFP in the literature using a GA is priority-based encoding, but it has some serious limitations including restricting the search space to a small part of the feasible set. We introduce a probabilistic tree-based representation scheme (PTbR) that is far superior compared to the priority-based encoding. Our extensive experimental investigations show the advantage of our encoding compared to previous methods for a variety of cost functions

Optimising a nonlinear utility function in multi-objective integer programming

In this paper we develop an algorithm to optimise a nonlinear utility function of multiple objectives over the integer efficient set. Our approach is based on identifying and updating bounds on the individual objectives as well as the optimal utility value. This is done using already known solutions, linear programming relaxations, utility function inversion, and integer programming. We develop a general optimisation algorithm for use with k objectives, and we illustrate our approach using a tri-objective integer programming problem.Comment: 11 pages, 2 tables; v3: minor revisions, to appear in Journal of Global Optimizatio

MicroRNA expression profiles in pediatric dysembryoplastic neuroepithelial tumors.

© Springer Science+Business Media New York 2015Among noncoding RNAs, microRNAs (miRNAs) have been most extensively studied, and their biology has repeatedly been proven critical for central nervous system pathological conditions. The diagnostic value of several miRNAs was appraised in pediatric dysembryoplastic neuroepithelial tumors (DNETs) using miRNA microarrays and receiving operating characteristic curves analyses. Overall, five pediatric DNETs were studied. As controls, 17 samples were used: the FirstChoice Human Brain Reference RNA and 16 samples from deceased children who underwent autopsy and were not present with any brain malignancy. The miRNA extraction was carried out using the mirVANA miRNA Isolation Kit, while the experimental approach included miRNA microarrays covering 1211 miRNAs. Quantitative real-time polymerase chain reaction was performed to validate the expression profiles of miR-1909* and miR-3138 in all samples initially screened with miRNA microarrays. Our findings indicated that miR-3138 might act as a tumor suppressor gene when down-regulated and miR-1909* as a putative oncogenic molecule when up-regulated in pediatric DNETs compared to the control cohort. Subsequently, both miRNA signatures might serve as putative diagnostic biomarkers for pediatric DNETs.Peer reviewedFinal Accepted Versio

A resampling-based meta-analysis for detection of differential gene expression in breast cancer

<p>Abstract</p> <p>Background</p> <p>Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures.</p> <p>Methods</p> <p>A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC) samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis.</p> <p>Results</p> <p>The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively). The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real-time qRT-PCR supported the meta-analysis results.</p> <p>Conclusion</p> <p>The proposed meta-analysis approach has the ability to detect a set of differentially expressed genes with the least amount of within-group variability, thus providing highly stable gene lists for class prediction. Increased statistical power and stringent filtering criteria used in the present study also make identification of novel candidate genes possible and may provide further insight to improve our understanding of breast cancer development.</p

Flow shop rescheduling under different types of disruption

This is an Accepted Manuscript of an article published by Taylor & Francis in International Journal of Production Research on 2013, available online:http://www.tandfonline.com/10.1080/00207543.2012.666856Almost all manufacturing facilities need to use production planning and scheduling systems to increase productivity and to reduce production costs. Real-life production operations are subject to a large number of unexpected disruptions that may invalidate the original schedules. In these cases, rescheduling is essential to minimise the impact on the performance of the system. In this work we consider flow shop layouts that have seldom been studied in the rescheduling literature. We generate and employ three types of disruption that interrupt the original schedules simultaneously. We develop rescheduling algorithms to finally accomplish the twofold objective of establishing a standard framework on the one hand, and proposing rescheduling methods that seek a good trade-off between schedule quality and stability on the other.The authors would like to thank the anonymous referees for their careful and detailed comments that helped to improve the paper considerably. This work is partially financed by the Small and Medium Industry of the Generalitat Valenciana (IMPIVA) and by the European Union through the European Regional Development Fund (FEDER) inside the R + D program "Ayudas dirigidas a Institutos tecnologicos de la Red IMPIVA" during the year 2011, with project number IMDEEA/2011/142.Katragjini Prifti, K.; Vallada Regalado, E.; Ruiz García, R. (2013). Flow shop rescheduling under different types of disruption. International Journal of Production Research. 51(3):780-797. https://doi.org/10.1080/00207543.2012.666856S780797513Abumaizar, R. J., & Svestka, J. A. 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Remembrance of things past: an inquiry into the fate of the Istanbul medical students who fought in the Gallipoli campaign

During the Great War, university students, like all young men at the age of military service, were called up as part of the general conscription in the Ottoman Empire. According to a popular story, which is the subject of this study, all Darulfunun (today Istanbul University) students who took part in the Gallipoli campaign as volunteers in May, 1915, were annihilated in the May 19th attack. As all students of 1915 were lost, the medical school was said to have had no graduates in 1921. This investigation was carried out, using material from the university and military archives, to identify the medical students who died on the Gallipoli battlefield, and to clarify their situation at that time. It was found that, as academic staff and students were distributed to the troops, education never commenced in 1915 and that the faculty building was closed for more than a year to serve as an inland war hospital. As all students were drafted into the army, there were no graduates in 1915. While it has been possible to identify eight physicians who died on the Gallipoli battlefield, no records were found concerning the medical students who were killed at Gallipoli. (c) 2004 Published by Elsevier Ltd

A medical class lost at Gallipoli

In 1915, the second year of the First World War, one of the big battles was the Gallipoli Campaign. Many students of the Istanbul Darulfunun (today Istanbul University) and of the Istanbul Men's High School joined the second battalion to participate in the defence of the Dardanelles as volunteers. All of the soldiers of that battalion died in 19 May 1915. The Medical School of Darulfunun, which lost all of the students of the class of 1915, had no student to graduate in 1921. (C) 2002 Elsevier Science Ltd. All rights reserved