11,522 research outputs found
Networking for Historical Justice: The Application of Graph Database Management Systems to Network Analysis Projects and the Case Study of the Reparation Movement for Japanese Colonial and Wartime Atrocities
No full textThis is an ongoing project to digitize reparation lawsuits against Japanese colonial and wartime atrocities (most famously the "comfort women" system and Nanjing Massacre) into a graph database. Information about the lawsuits is taken from publicly available sources such as the 日本戦後補償裁判総覧 (http://justice.skr.jp/souran/souran-jp-web.htm), digitized, processed, and exported as cypher codes executable by graph database management or processing systems such as Neo4j. The database seeks to not only preserve historical materials produced in this transnational movement but also aid academic research and teaching of it.
The project explores the applicability of graph database management systems to network analysis research and teaching in the field of digital humanities. By inputting the data about lawsuits and lawyers in the movement into a graph database, the project demonstrates the advantages of managing network data in graph database structure over relational database structure, which is the mainstream in network analysis research, in terms of scalability, modifiability, intuitive visibility, and query efficiency.
The all-plain.cypher file can be loaded into graph database systems like Neo4j (https://sandbox.neo4j.com) to generate the database. The all data Kineviz-graphxr DATE.graphxr file can be loaded into the web-based graph visualization and processing tool GraphXR(https://graphxr.kineviz.com/register) with an account
Structure-based model for light-harvesting properties of nucleic acid nanostructures
No full textProgrammed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.United States. Office of Naval Research (ONR N000141210621)United States. Army Research Office (ARO MURI W911NF1210420
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
No full textDNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science.United States. Office of Naval Research (ONR N000141210621)National Science Foundation (U.S.) (NSF-DMREF Program CMMI1334109
Structure and conformational dynamics of scaffolded DNA origami nanoparticles
No full textSynthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fu lly determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5- 100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarsegrained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DXbased DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural andmechanical properties of DXbased assemblies that are inaccessible to all-atom based models alone.United States. Office of Naval Research (Grant N00014-12-1-0621)United States. Army Research Office (Grant W911NF1210420)National Science Foundation (U.S.) (Grant 1560425)United States. Office of Naval Research (Grant N00014-13-1-0664)United States. Office of Naval Research (Grant N00014-15-1-2830
Overview of the Author Profiling Task at PAN 2013
No full text[EN] This overview presents the framework and results for the Author Profiling
task at PAN 2013. We describe in detail the corpus and its characteristics,
and the evaluation framework we used to measure the participants performance to
solve the problem of identifying age and gender from anonymous texts. Finally,
the approaches of the 21 participants and their results are described.The author profiling task @PAN-2013 was an activity of the WIQ-EI IRSES project (Grant No. 269180) within the FP 7 Marie Curie People Framework of the European Commission. We want to thank the Forensic Lab of the Universitat Pompeu Fabra Barcelona for sponsoring the award for the winner team. The work of the first author was partially funded by Autoritas Consulting SA and by Ministerio de Economía y Competitividad de España under grant ECOPORTUNITY IPT-2012-1220-430000. The work of the second author was in the framework the DIANA-APPLICATIONS-Finding Hidden Knowledge in Texts: Applications (TIN2012-38603-C02-01) project, and the VLC/CAMPUS Microcluster on Multimodal Interaction in Intelligent Systems. The work of fifth author was funded in part by the Swiss National Science Foundation (SNF) project "Mining Conversational Content for Topic Modelling and Author Identification (ChatMiner)" under grant number 200021_130208.Rangel, F.; Rosso, P.; Koppel, M.; Stamatatos, E.; Inches, G. (2013). Overview of the Author Profiling Task at PAN 2013. CLEF Conference on Multilingual and Multimodal Information Access Evaluation. 352-365. https://riunet.upv.es/handle/10251/46636S35236
Uncovering Plagiarism - Author Profiling at PAN
No full text[ES] PAN is a yearly workshop and evaluation lab on uncovering plagiarism, authorship, and social software misuse. Since 2009, PAN has been organizing benchmark activities on uncovering plagiarism, authorship, and social software misuse . An additional task - author profiling - has also recently been proposed. Author profiling, instead of focusing on individual authors, studies how language is shared by a class of people. Author profiling is a problem of growing importance in applications in forensics, security and marketing. For instance, a person working in the area of forensic linguistics may need to know the linguistic profile of a suspected text message (language used by a certain type of person) and identify characteristics (with language as evidence). Similarly, from a marketing viewpoint, companies may be interested in determining, through the analysis of blogs and online product reviews, what types of people like or dislike their products.Rosso, P.; Rangel Pardo, FM. (2014). Uncovering Plagiarism - Author Profiling at PAN. Ercim News. (96):49-49. https://riunet.upv.es/handle/10251/49303S49499
Overview of PAN 2018 : author identification, author profiling, and author obfuscation
No full textAbstract: PAN 2018 explores several authorship analysis tasks enabling a systematic comparison of competitive approaches and advancing research in digital text forensics. More specifically, this edition of PAN introduces a shared task in cross-domain authorship attribution, where texts of known and unknown authorship belong to distinct domains, and another task in style change detection that distinguishes between single-author and multi-author texts. In addition, a shared task in multimodal author profiling examines, for the first time, a combination of information from both texts and images posted by social media users to estimate their gender. Finally, the author obfuscation task studies how a text by a certain author can be paraphrased so that existing author identification tools are confused and cannot recognize the similarity with other texts of the same author. New corpora have been built to support these shared tasks. A relatively large number of software submissions (41 in total) was received and evaluated. Best paradigms are highlighted while baselines indicate the pros and cons of submitted approaches
E.: Overview of the Author Identification Task at PAN-2013
No full textAbstract. The author identification task at PAN-2014 focuses on author verification. Similar to PAN-2013 we are given a set of documents by the same author along with exactly one document of questioned authorship, and the task is to determine whether the known and the questioned documents are by the same author or not. In comparison to PAN-2013, a significantly larger corpus was built comprising hundreds of documents in four natural languages (Dutch, English, Greek, and Spanish) and four genres (essays, reviews, novels, opinion articles). In addition, more suitable performance measures are used focusing on the accuracy and the confidence of the predictions as well as the ability of the submitted methods to leave some problems unanswered in case there is great uncertainty. To this end, we adopt the c@1 measure, originally proposed for the question answering task. We received 13 software submissions that were evaluated in the TIRA framework. Analytical evaluation results are presented where one language-independent approach serves as a challenging baseline. Moreover, we continue the successful practice of the PAN labs to examine meta-models based on the combination of all submitted systems. Last but not least, we provide statistical significance tests to demonstrate the important differences between the submitted approaches.
Overview of the author identification task at PAN 2014
No full textThe author identification task at PAN-2014 focuses on author verification. Similar to PAN-2013 we are given a set of documents by the same author along with exactly one document of questioned authorship, and the task is to determine whether the known and the questioned documents are by the same author or not. In comparison to PAN-2013, a significantly larger corpus was built comprising hundreds of documents in four natural languages (Dutch, English, Greek, and Spanish) and four genres (essays, reviews, novels, opinion articles). In addition, more suitable performance measures are used focusing on the accuracy and the confidence of the predictions as well as the ability of the submitted methods to leave some problems unanswered in case there is great uncertainty. To this end, we adopt the c@1 measure, originally proposed for the question answering task. We received 13 software submissions that were evaluated in the TIRA framework. Analytical evaluation results are presented where one language-independent approach serves as a challenging baseline. Moreover, we continue the successful practice of the PAN labs to examine meta-models based on the combination of all submitted systems. Last but not least, we provide statistical significance tests to demonstrate the important differences between the submitted approaches
Tweet Author Gender Identification. PAN 2016 Task
No full textThe paper presents an experiment of tweet’s author gender detection. We used PAN 2016 data and task description and have build an application that decides whether an analysed tweet has been written by man or woman. Multiple texts’ characteristics are used as features in the application, such as: references to pictures, to web pages, to other people, emojis, hashtags and a number of words that are associated with tweets written by women and men respectively. For 100 random tweets we obtained average accuracy 0.61. This is good result although it is not as good as the best one in PAN 2016 task
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