ゼミナール発表

日時: 7月6日(月)3限 (13:30-15:00)


会場: L1

司会: 伊原 彰紀
YANG XIN 1361209: D, 中間発表 飯田 元,松本 健一,市川 昊平
title: Peer Review Social Network (PeRSoN) in Open Source Projects
abstract: Software peer review (aka. code review), is regarded as one of the most important approaches to preserving software quality. Traditional peer review, which is based on formal face-to-face meeting, is devised for industrial development. Currently, due to the distributed collaborations and nature of broadcasting in the on-trend Open Source Software (OSS) development, techniques and processes conducted in peer review in this open source environment differ from the traditional method. Unlike other related works, this study investigated OSS peer review processes from the social perspective: development communication and interaction by using social network analysis (SNA). In this study, the relationship between peer review contributors and their activities has been studied. We proposed an approach to evaluating contributors¨ activeness and social relationship using SNA named Peer Review Social Network (PeRSoN). As a case study, the review history of three representative industrial OSS projects was extracted and analyzed. The results provide the review network structure of contributors, which can be used to evaluate the contributors¨ activeness. This approach could support project leader to assign review tasks, appoint reviewers and other activities to improve current software processes.
language of the presentation: English
 
JIN YONG 1351207: M, 2回目発表 飯田 元,松本 健一,市川 昊平
title: Study of Patching Status Confirmation Method in Linux Distributions
abstract: In Linux Operating System, there are various kinds of distributions, and users usually use package manage system to maintain softwares which released as packages by distributions. Distribution developers make modification as patches, and apply them to a release version of a software to make a package. For system administrators, when a new package released, it has necessary to confirm if the new fixes from software repository were included. However, it is difficult to confirm, because of the lack of information. In this research, we investigated the relationship between patch diff information and commits on software repository, and propose an approach to confirm how many fixes on repository have applied to packages.
language of the presentation: Japanese
 
坂口 英司 1351046: M, 2回目発表 松本 健一,安本 慶一,伊原 彰紀
title: Identifying Faulty-module not detected by testing in OSS
abstract: The most of industrial software companies often use Open Source Software (OSS) in their products. In order to use OSS, industrial developers look for a high quality software which is a few bugs. However, OSS is not always high quality because OSS developers does not enough work for testing before the release and often fix bugs after the release. In this study, I propose an approach to identify a faulty-module not found by testing in OSS development. In this presentation, I will show my approach with a case study.
language of the presentation: Japanese
 

会場: L2

司会: 川原 純
SONY HARTONO WIJAYA 1361207: D, 中間発表 金谷 重彦,安本 慶一,MD.ALTAF-UL-AMIN,杉浦 忠男,小野 直亮
Title: Systematization of Indonesian crude drug medicines

Abstract:
Indonesian mixing system of crude drugs is known as Jamu. Jamu is popular traditional medicines from Indonesia. As a country with the largest medicinal plant species in the world, Indonesians utilize these plants as Jamu ingredients. Jamu formulas are generally composed based on the experience of users for decades or even hundreds of years. However, it needs systemization of Jamu formulas and development of basic scientific principles of Jamu to meet the requirement of Indonesian Healthcare Systems. We proposed a new method to predict the relation between plant and disease using network analysis and supervised clustering. The correlation measures between Jamu pairs were determined based on their ingredients similarity. Networks were constructed and analyzed by selecting highly correlated Jamu pairs. Clusters were then generated by using the network-clustering algorithm DPClusO. By using matching score of a cluster, the dominant disease and high frequency plant associated to the cluster are determined. The plant to disease relations predicted by our method were evaluated in the context of previously published results and were found to produce around 90% successful predictions.

In addition, we assessed the capability of binary similarity and dissimilarity measures to classify the Jamu pairs into match and mismatch efficacies. It plays critical roles in the processing of data consisting of binary vectors in various fields because different binary measures may yield conflicting results and the high number of negative matches may influence the calculation of binary similarity or dissimilarity between Jamu pairs. The Receiver Operating Characteristic (ROC) curve analysis was used to compare the effectiveness of the equations to separate the Jamu pairs. The binary similarity and dissimilarity measures that include the negative match quantity d had a better capability to separate Jamu pairs compared to equations that excluded d. Out of all the equations, the Forbes-2 similarity measure had the biggest Area Under the ROC curve and is thus recommended for studying the relationship between Jamu formulas. The procedure followed in this work can also be used to find suitable binary similarity and dissimilarity measures for other applications.

Language of the presentation: English
 
BAI YU 1361202: D, 中間発表 金谷 重彦,笠原 正治,MD.ALTAF-UL-AMIN,杉浦 忠男,小野 直亮

title: A Novel Bioinformatics Method Batch-Learning SOM (BLSOM) for Efficient Knowledge Discovery from Big Sequence Data

abstract:

With remarkable increase of sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition and amino acid composition on a single map. By modifying the conventional SOM, we had previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, only depending on the number of oligonucleotide composition or amino acid composition.

In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We fist analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature”, and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences.

language of the presentation: English

 
DODI FITRA CHANDRA 1351205: M, 2回目発表 金谷 重彦,笠原 正治,MD.ALTAF-UL-AMIN,杉浦 忠男,小野 直亮

title: Relation of essentiality and functionality of Yeast proteins with their centrality values in a PPI network.

abstract:

It has long been investigated and understood that centrality of proteins in the context of PPI networks are related to their essentiality. In the present work we reconfirmed the relations between essentiality of yeast proteins and their centrality measures in a PPI network by following a different approach using the concept of the (receiver operating characteristic) ROC curve.


We evaluated the performance of various centrality measures by comparing the area under the ROC curves and the minimum distance of the ROC curves from the ideal optimum classification point where TPR (True Positive Rate) is 1 and FPR (False Positive Rate) is 0. We further investigated that the functions of yeast proteins also have some relations with their centrality measures. Different types of centrality values imply different types of importance of a node in a network. By deeply examining different centrality values of yeast proteins we found that they are not highly correlated, which leaded us to hypothesize that centralities might have some relations with gene/protein functionalities. Indeed, we found that many of the clusters generated based on the pattern of centrality values are rich with similar function proteins. The statistical significance of the protein clusters was assessed by hyper-geometric p-values. Using the statistically significant clusters, we established links between pattern of centrality measures and protein functions.

language of the presentation: English

 

会場: L3

司会: 南 裕樹
ABHINAV DADHICH 1351202: M, 2回目発表 池田 和司,小笠原 司,爲井 智也,柴田 智広
title: Map inference and learning for long term robot navigation
abstract: Map generation of mobile robots over long periods of working suffers from inconsistencies because of gradual changes in the environment. An example of such change is a table or chair that is displaced from its position after few weeks. However, traditional robot mapping and navigation assumes static environment. Further, these gradual changes causes hindrances in autonomous navigation of mobile robots as robot is not able to update the current state of map with dynamic and static objects. We present a novel method to infer such gradual changes and incorporate them in map generation by incorporating the duration for which the objects are observed at the same place. We model the environment using an occupancy grid structure and infer hidden state in each cell of the grid. We use a semi-markov model as Explicit-state-Duration Hidden Markov Model (EDHMM). We tested our method in simulation as well as on a real world dataset. On observing the environment for 5 weeks , our method is able to track efficiently dynamic changes in the grid map, even in the presence of occlusion.
language of the presentation: English
 
谷山 功紀 1451072: M, 1回目発表 ロボティクス
title: Analysis of hand roles based on long-term observation using multiple sensors
abstract: The human hand is a multi-functional tool and plays an important role in daily life. Analysis of hand roles is useful for designing robotic hands, development of services, planning rehabilitation, and understanding human behavior. However, the hand roles in daily life were not analyzed based on long-term observation from many directions. The purpose of our research is to examine the hand roles in daily life based on long-term observation data measured with omnidirectional cameras, EMG sensors, and accelerometers. In this presentation, we report a wearable system for measuring hand motions, annotation methods, and motion analysis approach.

language of the presentation: Japanese

発表題目: 複数センサを用いた長期的な観測に基づく日常生活における手の役割の分析
発表概要: 人間の手は多くの機能を持ち,日常生活において重要な役割を果たしている.日常生活で,手がどのように使われているかを分析することは,ロボットハンドの設計,サービスの開発,リハビリ計画の立案,人間行動の理解に有用である.しかしながら,日常生活における手の役割について長期にわたって網羅的に分析した研究はない.
 本研究では,全方位カメラ,筋電センサ,加速度センサなどの複数センサを用いて手の動作を長期にわたって観測し,さまざまな視点で分析することによって,手の役割を明らかにすることを目的とする.本発表では,手の動作を計測するウェアラブルシステム,計測データに対するアノテーション手法,動作分析の手法を提案する.
 
松田 裕貴 1551103: M, 1回目発表 ユビキタスコンピューティングシステム
title: A Safety Level Assessment System for Sidewalk at Night Utilizing Light Sensors of Mobile Devices.
In pedestrian navigation systems, there is a growing demand for managing public security information, such as the brightness of night sidewalks. In this study, we propose the safety inferring system for sidewalks at night based on the illuminance data of street lamps collected by the light sensors of smartphones. In this presentation, we propose the inferring method of the streetlamp illuminance utilizing sensor data of smartphones, and the method for improvement of user's motivation in participatory sensing.

language of the presentation: Japanese

発表題目: モバイル端末を用いた街灯照度センシングによる夜間道の安全性判定とその実用化
発表概要: 防犯意識の向上に伴い,歩行者向けナビゲーションにおいても夜道の明るさなど,「安心・安全面」 の情報整備が重要となる.本研究では、スマートフォン搭載照度センサを用いて街灯照度を収集,集合知を形成することによる,夜道の安全判定システムを検討している.本発表では,複数のスマートフォンのセンサデータをもとに街灯の照度を推定する手法,およびユーザ参加型センシングにおける参加ユーザのモチベーション向上のための手法について提案する.