Software defect prediction: do different classifiers find the same defects?

Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.During the last 10 years, hundreds of different defect prediction models have been published. The performance of the classifiers used in these models is reported to be similar with models rarely performing above the predictive performance ceiling of about 80% recall. We investigate the individual defects that four classifiers predict and analyse the level of prediction uncertainty produced by these classifiers. We perform a sensitivity analysis to compare the performance of Random Forest, Naïve Bayes, RPart and SVM classifiers when predicting defects in NASA, open source and commercial datasets. The defect predictions that each classifier makes is captured in a confusion matrix and the prediction uncertainty of each classifier is compared. Despite similar predictive performance values for these four classifiers, each detects different sets of defects. Some classifiers are more consistent in predicting defects than others. Our results confirm that a unique subset of defects can be detected by specific classifiers. However, while some classifiers are consistent in the predictions they make, other classifiers vary in their predictions. Given our results, we conclude that classifier ensembles with decision-making strategies not based on majority voting are likely to perform best in defect prediction.Peer reviewedFinal Published versio

İzmir‐Ankara suture as a Triassic to Cretaceous plate boundary – data from central Anatolia

The İzmir‐Ankara suture represents part of the boundary between Laurasia and Gondwana along which a wide Tethyan ocean was subducted. In northwest Turkey, it is associated with distinct oceanic subduction‐accretion complexes of Late Triassic, Jurassic and Late Cretaceous ages. The Late Triassic and Jurassic accretion complexes consist predominantly of basalt with lesser amounts of shale, limestone, chert, Permian (274 Ma zircon U‐Pb age) metagabbro and serpentinite, which have undergone greenschist facies metamorphism. Ar‐Ar muscovite ages from the phyllites range from 210 Ma down to 145 Ma with a broad southward younging. The Late Cretaceous subduction‐accretion complex, the ophiolitic mélange, consists of basalt, radiolarian chert, shale and minor amounts of recrystallized limestone, serpentinite and greywacke, showing various degrees of blueschist facies metamorphism and penetrative deformation. Ar‐Ar phengite ages from two blueschist metabasites are ca. 80 Ma (Campanian). The ophiolitic mélange includes large Jurassic peridotite‐gabbro bodies with plagiogranites with ca. 180 Ma U‐Pb zircon ages. Geochronological and geological data show that Permian to Cretaceous oceanic lithosphere was subducted north under the Pontides from the Late Triassic to the Late Cretaceous. This period was characterized generally by subduction‐accretion, except in the Early Cretaceous, when subduction‐erosion took place. In the Sakarya segment all the subduction accretion complexes, as well as the adjacent continental sequences, are unconformably overlain by Lower Eocene red beds. This, along with the stratigraphy of the Sakarya Zone indicate that the hard collision between the Sakarya Zone and the Anatolide‐Tauride Block took place in Paleocene

The Effects of Cocaine on Different Redox Forms of Cysteine and Homocysteine, and on Labile, Reduced Sulfur in the Rat Plasma Following Active versus Passive Drug Injections

Received: 28 November 2012 / Revised: 19 April 2013 / Accepted: 6 May 2013 / Published online: 16 May 2013 The Author(s) 2013. This article is published with open access at Springerlink.comThe aim of the present studies was to evaluate cocaine-induced changes in the concentrations of different redox forms of cysteine (Cys) and homocysteine (Hcy), and products of anaerobic Cys metabolism, i.e., labile, reduced sulfur (LS) in the rat plasma. The above-mentioned parameters were determined after i.p. acute and subchronic cocaine treatment as well as following i.v. cocaine self-administration using the yoked procedure. Additionally, Cys, Hcy, and LS levels were measured during the 10-day extinction training in rats that underwent i.v. cocaine administration. Acute i.p. cocaine treatment increased the total and protein-bound Hcy contents, decreased LS, and did not change the concentrations of Cys fractions in the rat plasma. In turn, subchronic i.p. cocaine administration significantly increased free Hcy and lowered the total and protein-bound Cys concentrations while LS level was unchanged. Cocaine self-administration enhanced the total and protein-bound Hcy levels, decreased LS content, and did not affect the Cys fractions. On the other hand, yoked cocaine infusions did not alter the concentration of Hcy fractions while decreased the total and protein-bound Cys and LS content. This extinction training resulted in the lack of changes in the examined parameters in rats with a history of cocaine self-administration while in the yoked cocaine group an increase in the plasma free Cys fraction and LS was seen. Our results demonstrate for the first time that cocaine does evoke significant changes in homeostasis of thiol amino acids Cys and Hcy, and in some products of anaerobic Cys metabolism, which are dependent on the way of cocaine administration

EVALUATION OF A HAEMOSTATIC AGENT IN RABBITS

Topical hemostatic agents are applied locally to areas of injured vascular endothelium to control local bleeding. Ankaferd Blood Stopper (ABS) has gained approval in Turkey and Bosnia-Herzegovina as a topical haemostatic agent for external post-surgical and post-dental surgery bleeding. The safety of topical use of ABS has been demonstrated in numerous in vitro and in vivo animal models, as well as in a clinical Phase I trial in humans. ABS, besides its haemostatic activity, also has in vitro anti-infectious and anti-neoplastic effects. To assess potential detrimental effects of intravenous administration of ABS into intact systemic circulation in a rabbit experimental model, one milliliter of ABS was administered intravenously into the systemic circulation of twelve rabbits which were included in the study via the marginal ear vein. Animals were observed for 1 hr before euthanasia was performed by administering 40 mg of intracardiac suxamethonium chloride. In the event of death (cardiopulmonary arrest) before the end of the planned observation period of 60 minutes, time of death was recorded and histopathological examination of the liver and spleen was commenced. Ten rabbits were alive by the end of the planned observation period, without showing any clear signs of discomfort, whereas two animals died within five minutes after systemic administration of intravenous ABS. Postmortem histopathological examination of the livers and spleens of all animals’ revealed findings consistent with hepatic venous outflow obstruction. Systemic intravascular administration of ABS into intact vascular endothelium should never be performed in any setting. Further experimental and clinical studies on this liquid hemostatic agent should proceed by accepting ABS as purely a topical haemostatic agent, to be applied solely to areas of injured vascular endothelium

A combined ULBP2 and SEMA5A expression signature as a prognostic and predictive biomarker for colon cancer

Background: Prognostic biomarkers for cancer have the power to change the course of disease if they add value beyond known prognostic factors, if they can help shape treatment protocols, and if they are reliable. The aim of this study was to identify such biomarkers for colon cancer and to understand the molecular mechanisms leading to prognostic stratifications based on these biomarkers. Methods and Findings: We used an in house R based script (SSAT) for the in silico discovery of stage-independent prognostic biomarkers using two cohorts, GSE17536 and GSE17537, that include 177 and 55 colon cancer patients, respectively. This identified 2 genes, ULBP2 and SEMA5A, which when used jointly, could distinguish patients with distinct prognosis. We validated our findings using a third cohort of 48 patients ex vivo. We find that in all cohorts, a combined ULBP2/SEMA5A classification (SU-GIB) can stratify distinct prognostic sub-groups with hazard ratios that range from 2.4 to 4.5 (p=0.01) when overall- or cancer-specific survival is used as an end-measure, independent of confounding prognostic parameters. In addition, our preliminary analyses suggest SU-GIB is comparable to Oncotype DX colon(®) in predicting recurrence in two different cohorts (HR: 1.5-2; p=0.02). SU-GIB has potential as a companion diagnostic for several drugs including the PI3K/mTOR inhibitor BEZ235, which are suitable for the treatment of patients within the bad prognosis group. We show that tumors from patients with worse prognosis have low EGFR autophosphorylation rates, but high caspase 7 activity, and show upregulation of pro-inflammatory cytokines that relate to a relatively mesenchymal phenotype. Conclusions: We describe two novel genes that can be used to prognosticate colon cancer and suggest approaches by which such tumors can be treated. We also describe molecular characteristics of tumors stratified by the SU-GIB signature. © Ivyspring International Publisher

Impact of antimicrobial drug restrictions on doctors' behaviors

Background/aim: Broad-spectrum antibiotics have become available for use only with the approval of infectious disease specialists (IDSs) since 2003 in Turkey. This study aimed to analyze the tendencies of doctors who are not disease specialists (non-IDSs) towards the restriction of antibiotics.Materials and methods: A questionnaire form was prepared, which included a total of 22 questions about the impact of antibiotic restriction (AR) policy, the role of IDSs in the restriction, and the perception of this change in antibiotic consumption. The questionnaire was completed by each participating physician.Results: A total of 1906 specialists from 20 cities in Turkey participated in the study. Of those who participated, 1271 (67.5%) had 5 years of occupational experience in their branch expressed that they followed the antibiotic guidelines more strictly than the JSs (P < 0.05) and 755 of physicians (88%) and 720 of surgeons (84.6%) thought that the AR policy was necessary and useful (P < 0.05).Conclusion: This study indicated that the AR policy was supported by most of the specialists. Physicians supported this restriction policy more so than surgeons did

Treatment of head lice with dimeticone 4% lotion: comparison of two formulations in a randomised controlled trial in rural Turkey

<p>Abstract</p> <p>Background</p> <p>Dimeticone 4% lotion was shown to be an effective treatment for head louse infestation in two randomised controlled trials in England. It is not affected by insecticide resistance but efficacy obtained (70-75%) was lower than expected. This study was designed to evaluate efficacy of dimeticone 4% lotion in a geographically, socially, and culturally different setting, in rural Turkey and, in order to achieve blinding, it was compared with a potential alternative formulation.</p> <p>Methods</p> <p>Children from two village schools were screened for head lice by detection combing. All infested students and family members could participate, giving access to treatment for the whole community. Two investigator applied treatments were given 7 days apart. Outcome was assessed by detection combing three times between treatments and twice the week following second treatment.</p> <p>Results</p> <p>In the intention to treat group 35/36 treated using dimeticone 4% had no lice after the second treatment but there were two protocol violators giving 91.7% treatment success. The alternative product gave 30/36 (83.3%) treatment success, a difference of 8.4% (95% CI -9.8% to 26.2%). The cure rates per-protocol were 33/34 (97.1%) and 30/35 (85.7%) respectively. We were unable to find any newly emerged louse nymphs on 77.8% of dimeticone 4% treated participants or on 66.7% of those treated with the alternative formulation. No adverse events were identified.</p> <p>Conclusion</p> <p>Our results confirm the efficacy of dimeticone 4% lotion against lice and eggs and we found no detectable difference between this product and dimeticone 4% lotion with nerolidol 2% added. We believe that the high cure rate was related to the lower intensity of infestation in Turkey, together with the level of community engagement, compared with previous studies in the UK.</p> <p>Trial Registration</p> <p>Current Controlled Trials ISRCTN10431107</p

Inferencing into the void: problems with implicit populations Comments on `Empirical software engineering experts on the use of students and professionals in experiments'

I welcome the contribution from Falessi et al. [1] hereafter referred to as F++ , and the ensuing debate. Experimentation is an important tool within empirical software engineering, so how we select participants is clearly a relevant question. Moreover as F++ point out, the question is considerably more nuanced than the simple dichotomy it might appear to be at first sight. This commentary is structured as follows. In Section 2 I briefly summarise the arguments of F++ and comment on their approach. Next, in Section 3, I take a step back to consider the nature of representativeness in inferential arguments and the need for careful definition. Then I give three examples of using different types of participant to consider impact. I conclude by arguing, largely in agreement with F++, that the question of whether student participants are representative or not depends on the target population. However, we need to give careful consideration to defining that population and, in particular, not to overlook the representativeness of tasks and environment. This is facilitated by explicit description of the target populations.Comment: This is a commentary on the article in Empirical Software Engineering entitled `Empirical software engineering experts on the use of students and professionals in experiments' by Falessi et al. It will form part of an accepted an article for EMSE (Dec 2018) comprising commentary and a response from the original author