2020
Authors
Santos, PM; Lopes, CT;
Publication
Advances in Information Retrieval - 42nd European Conference on IR Research, ECIR 2020, Lisbon, Portugal, April 14-17, 2020, Proceedings, Part II
Abstract
Medico-scientific concepts are not easily understood by laypeople that frequently use lay synonyms. For this reason, strategies that help users formulate health queries are essential. Health Suggestions is an existing extension for Google Chrome that provides suggestions in lay and medico-scientific terminologies, both in English and Portuguese. This work proposes, evaluates, and compares further strategies for generating suggestions based on the initial consumer query, using multi-concept recognition and the Unified Medical Language System (UMLS). The evaluation was done with an English and a Portuguese test collection, considering as baseline the suggestions initially provided by Health Suggestions. Given the importance of understandability, we used measures that combine relevance and understandability, namely, uRBP and uRBPgr. Our best method merges the Consumer Health Vocabulary (CHV)-preferred expression for each concept identified in the initial query for lay suggestions and the UMLS-preferred expressions for medico-scientific suggestions. Multi-concept recognition was critical for this improvement. © Springer Nature Switzerland AG 2020.
2020
Authors
Mendes, R; Cunha, M; Vilela, JP;
Publication
Proceedings on Privacy Enhancing Technologies
Abstract
2020
Authors
Reyna, MA; Haan, D; Paczkowska, M; Verbeke, LPC; Vazquez, M; Kahraman, A; Pulido Tamayo, S; Barenboim, J; Wadi, L; Dhingra, P; Shrestha, R; Getz, G; Lawrence, MS; Pedersen, JS; Rubin, MA; Wheeler, DA; Brunak, S; Izarzugaza, JMG; Khurana, E; Marchal, K; von Mering, C; Sahinalp, SC; Valencia, A; Abascal, F; Amin, SB; Bader, GD; Bandopadhayay, P; Beroukhim, R; Bertl, J; Boroevich, KA; Busanovich, J; Campbell, PJ; Carlevaro Fita, J; Chakravarty, D; Chan, CWY; Chen, K; Choi, JK; Deu Pons, J; Diamanti, K; Feuerbach, L; Fink, JL; Fonseca, NA; Frigola, J; Gambacorti Passerini, C; Garsed, DW; Gerstein, M; Guo, Q; Gut, IG; Hamilton, MP; Haradhvala, NJ; Harmanci, AO; Helmy, M; Herrmann, C; Hess, JM; Hobolth, A; Hodzic, E; Hong, C; Hornshøj, H; Isaev, K; Johnson, R; Johnson, TA; Juul, M; Juul, RI; Kahles, A; Kellis, M; Kim, J; Kim, JK; Kim, Y; Komorowski, J; Korbel, JO; Kumar, S; Lanzós, A; Larsson, E; Lee, D; Lehmann, KV; Li, S; Li, X; Lin, Z; Liu, EM; Lochovsky, L; Lou, S; Madsen, T; Martincorena, I; Martinez Fundichely, A; Maruvka, YE; McGillivray, PD; Meyerson, W; Muiños, F; Mularoni, L; Nakagawa, H; Nielsen, MM; Park, K; Park, K; Pons, T; Reyes Salazar, I; Rheinbay, E; Rubio Perez, C; Saksena, G; Salichos, L; Sander, C; Schumacher, SE; Shackleton, M; Shapira, O; Shen, C; Shuai, S; Sidiropoulos, N; Sieverling, L; Sinnott Armstrong, N; Stein, LD; Tamborero, D; Tiao, G; Tsunoda, T; Umer, HM; Uusküla Reimand, L; Wadelius, C; Wang, J; Warrell, J; Waszak, SM; Weischenfeldt, J; Wu, G; Yu, J; Zhang, J; Zhang, X; Zhang, Y; Zhao, Z; Zou, L; Reimand, J; Stuart, JM; Raphael, BJ;
Publication
Nature Communications
Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments. © 2020, The Author(s).
2020
Authors
Tome, ES; Pimentel, M; Figueiras, J;
Publication
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
Abstract
One of the main challenges that Structural Health Monitoring (SHM) faces when transitioning from academia to real-world applications is the discernment between structural changes due to damage and normal environmental, operational and long-term effects. In this context, a strategy for early damage detection based on multivariate cointegration analysis and statistical process control is proposed. The effects of environmental and operational variations are suppressed using cointegration analysis, being the cointegrating vector estimated following the multivariate Johansen procedure. The cointegrated residuals are then used for novelty detection by means of the Hotelling T-2 control chart. The proposed strategy is systematised and is applied to a large prestressed concrete cable-stayed bridge of which 3.5 years of data are available, being the stay-cable forces used as damage sensitive-features. Several damage scenarios are studied involving increasing section loss of the stay cables. The damage intensities that can be detected using the proposed methodology and the available sensory system are quantified.
2020
Authors
Freitas, V; Costa, AS; Miranda, V;
Publication
IET GENERATION TRANSMISSION & DISTRIBUTION
Abstract
This study introduces a robust orthogonal implementation for a new class of information theory-based state estimation algorithms that rely on the maximum correntropy criterion (MCC). They are attractive due to their capability to suppress bad data. In practice, applying the MCC concept amounts to solving a matrix equation similar to the weighted least-squares normal equation, with difference that measurement weights change as a function of iteratively adjusted observation window widths. Since widely distinct measurement weights are a source of numerical ill-conditioning, the proposed orthogonal implementation is beneficial to impart numerical robustness to the MCC solution. Furthermore, the row-processing nature of the proposed solver greatly facilitates bad data removal as soon as outliers are identified by the MCC algorithm. Another desirable feature of the orthogonal MCC estimator is that it avoids the need of post-processing stages for bad data treatment. The performance of the proposed scheme is assessed through tests conducted on the IEEE 14-bus, 30-bus, 57-bus and 118-bus test systems. Simulation results indicate that the MCC orthogonal implementation exhibits superior bad data suppression capability as compared with conventional methods. It is also advantageous in terms of computational effort, particularly as the number of simultaneous bad data grows.
2020
Authors
Coutinho, JC; Moreira, JM; de Sa, CR;
Publication
MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2019, PT III
Abstract
Labelled football (soccer) data is hard to acquire and it usually needs humans to annotate the match events. This process makes it more expensive to be obtained by smaller clubs. UnFOOT (Unsupervised Football Analytics Tool) combines data mining techniques and basic statistics to measure the performance of players and teams from positional data. The capabilities of the tool involve preprocessing the match data, extraction of features, visualization of player and team performance. It also has built-in data mining techniques, such as association rule mining, subgroup discovery and a proposed approach to look for frequent distributions.
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