Dependency parsing of biomedical text with BERT

Autor: Jenna Kanerva, Filip Ginter, Sampo Pyysalo

Publikováno v: BMC Bioinformatics, Vol 21, Iss S23, Pp 1-12 (2020)

Abstract Background: Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading formalism for dependen

Externí odkaz: https://doaj.org/article/980e92cad093490ab14fb2d2b804c910

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Autor: Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)

Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third C

Externí odkaz: https://doaj.org/article/4c2b017b155b41ceab8d6d078186cafa

Paimen, piika ja emäntä

Autor: Hannu Salmi, Jenna Kanerva, Harri Kiiskinen, Filip Ginter

Publikováno v: Lähikuva – audiovisuaalisen kulttuurin tieteellinen julkaisu. 35:8-18

Artikkeli käsittelee digitaalisten ihmistieteiden menetelmien mahdollisuuksia suomalaisen näytelmäelokuvan tutkimuksessa. Tarkastelu perustuu Movie Making Finland: Finnish fiction films as audiovisual big data, 1907–2017 (MoMaF) -hankkeessa teht

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::dfebea2128c52ba7e3ce5e716a74866f
https://doi.org/10.23994/lk.125666

Tekstien pitkä elämä

Autor: Heli Rantala, Hannu Salmi, Aleksi Vesanto, Filip Ginter

Publikováno v: Ennen ja Nyt: Historian Tietosanomat, Iss 2 (2019)

Externí odkaz: https://doaj.org/article/5b13f6fa8de34d4ba64e532b744add1a

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

Autor: Sanna M. Kreula, Suwisa Kaewphan, Filip Ginter, Patrik R. Jones

Publikováno v: PeerJ, Vol 6, p e4806 (2018)

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’.

Externí odkaz: https://doaj.org/article/45e4fe1aeebc4bdbbec73870c1f0b720