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Publicações

2020

Student Research Abstract: Multimodal Deep Learning Based Approach for Cells State Classification

Autores
Silva, PR;

Publicação
PROCEEDINGS OF THE 35TH ANNUAL ACM SYMPOSIUM ON APPLIED COMPUTING (SAC'20)

Abstract
With the advances of the big data era in biology, deep learning have been incorporated in analysis pipelines trying to transform biological information into valuable knowledge. Deep learning demonstrated its power in promoting bioinformatics field including sequence analysis, bio-molecular property and function prediction, automatic medical diagnosis and to analyse cell imaging data. The ambition of this work is to create an approach that can fully explore the relationships across modalities and subjects through mining and fusing features from multi-modality data for cell state classification. The system should be able to classify cell state through multimodal deep learning techniques using heterogeneous data such as biological images, genomics and clinical annotations. Our pilot study addresses the data acquisition process and the framework capable to extract biological parameters from cell images.

2020

A strategy for electricity buyers in futures markets

Autores
Monteiro, C; Ramirez Rosado, IJ; Fernandez Jimenez, LA;

Publicação
E3S Web of Conferences

Abstract
This paper presents an original trading strategy for electricity buyers in futures markets. The strategy applies a medium-term electricity price forecasting model to predict the monthly average spot price which is used to evaluate the Risk Premium for a physical delivery under a monthly electricity futures contract. The proposed trading strategy aims to provide an advantage relatively to the traditional strategy of electricity buyers (used as benchmark), anticipating the good/wrong decision of buying electricity in the futures market instead in the day-ahead market. The mid-term monthly average spot price forecasting model, which supports the trading strategy, uses only information available from futures and spot markets at the decision moment. Both the new trading strategy and the monthly average spot price forecasting model, proposed in this paper, have been successfully tested with historical data of the Iberian Electricity Market (MIBEL), although they could be applied to other electricity markets. © 2020 The Authors, published by EDP Sciences.

2020

Motivating Students to Learn Computer Programming in Higher Education: The SimProgramming Approach

Autores
Nunes, RR; Cruz, G; Pedrosa, D; Maia, AM; Morgado, L; Paredes, H; Cravino, J; Martins, P;

Publicação
Technology and Innovation in Learning, Teaching and Education - Second International Conference, TECH-EDU 2020, Vila Real, Portugal, December 2-4, 2020, Proceedings, 3

Abstract
This paper presents an action research study aiming to motivate undergraduate students to develop their computer programming learning skills, particularly within the transition from beginner to proficient level. The SimProgramming motivational approach is presented as a didactic proposal for this context. From the results of this iterative research process, we concluded that SimProgramming is a promising tool for teaching computer programming skills in intermediate classes, with potential to be used and/or applied in other educational contexts. © 2021, Springer Nature Switzerland AG.

2020

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Autores
Shuai, S; Abascal, F; Amin, SB; Bader, GD; Bandopadhayay, P; Barenboim, J; Beroukhim, R; Bertl, J; Boroevich, KA; Brunak, S; Campbell, PJ; Carlevaro Fita, J; Chakravarty, D; Chan, CWY; Chen, K; Choi, JK; Deu Pons, J; Dhingra, P; Diamanti, K; Feuerbach, L; Fink, JL; Fonseca, NA; Frigola, J; Gambacorti Passerini, C; Garsed, DW; Gerstein, M; Getz, G; Guo, Q; Gut, IG; Haan, D; Hamilton, MP; Haradhvala, NJ; Harmanci, AO; Helmy, M; Herrmann, C; Hess, JM; Hobolth, A; Hodzic, E; Hong, C; Hornshøj, H; Isaev, K; Izarzugaza, JMG; Johnson, R; Johnson, TA; Juul, M; Juul, RI; Kahles, A; Kahraman, A; Kellis, M; Khurana, E; Kim, J; Kim, JK; Kim, Y; Komorowski, J; Korbel, JO; Kumar, S; Lanzós, A; Larsson, E; Lawrence, MS; Lee, D; Lehmann, KV; Li, S; Li, X; Lin, Z; Liu, EM; Lochovsky, L; Lou, S; Madsen, T; Marchal, K; Martincorena, I; Martinez Fundichely, A; Maruvka, YE; McGillivray, PD; Meyerson, W; Muiños, F; Mularoni, L; Nakagawa, H; Nielsen, MM; Paczkowska, M; Park, K; Park, K; Pedersen, JS; Pons, T; Pulido Tamayo, S; Raphael, BJ; Reimand, J; Reyes Salazar, I; Reyna, MA; Rheinbay, E; Rubin, MA; Rubio Perez, C; Sahinalp, SC; Saksena, G; Salichos, L; Sander, C; Schumacher, SE; Shackleton, M; Shapira, O; Shen, C; Shrestha, R; Shuai, S; Sidiropoulos, N; Sieverling, L; Sinnott Armstrong, N; Stein, LD; Stuart, JM; Tamborero, D; Tiao, G; Tsunoda, T; Umer, HM; Uusküla Reimand, L; Valencia, A; Vazquez, M; Verbeke, LPC; Wadelius, C; Wadi, L; Wang, J; Warrell, J; Waszak, SM; Weischenfeldt, J; Wheeler, DA; Wu, G; Yu, J; Zhang, J; Zhang, X; Zhang, Y; Zhao, Z; Zou, L; von Mering, C; Gallinger, S; Stein, L;

Publicação
Nature Communications

Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery. © 2020, The Author(s).

2020

Connecting school actors using mobile applications

Autores
Cunha C.R.; Gomes J.P.; Mendonça V.;

Publicação
IBIMA Business Review

Abstract
Communication between the different actors present in the school ecosystem is an essential issue. However, in a busy world where parents do not have much time to visit schools regularly, it is crucial to create mechanisms to better monitor student success and school demands. The current pandemic situation caused by the coronavirus has highlighted the role that technologies have in supporting the mission of schools and communication between the various school actors. The interaction between school, students and parents presents a growing and complex challenge. Technology has, in recent years, shaped the concepts of support and monitoring of learning - at school and outside it - as well as the way in which information flows between all actors in the school ecosystem. Emergently, the evolution of mobile applications, combined with the evolution of the capabilities of mobile devices, has enabled the creation of new and more effective intercommunication mechanisms, with ubiquitous approaches and in a predictable scenario of less willingness for physical interaction of the different actors. Based on these premises, this article reflects on the potential of mobile devices and their applications to support new models of intercommunication between parents or school sponsors, students and teachers. In this sense, a conceptual model is proposed that represents a work in progress that aims at creating and evaluating a prototype system capable of improving intercommunication and the overall success of the societal challenges of the school learning system.

2020

Bone scintigraphy and PET-CT: A necessary alliance for bone metastasis detection in breast cancer?

Autores
Santos, JC; Abreu, MH; Santos, MS; Duarte, H; Alpoim, T; Sousa, S; Abreu, PH;

Publicação
JOURNAL OF CLINICAL ONCOLOGY

Abstract
e13070 Background: Bone is one of the main sites of breast cancer metastasis. Staging of this kind of disease spread can be performed in locally advanced cases with PET-CT in conjunction with Bone Scintigraphy. The purpose of this work is to compare the efficiency of bone metastasis detection between PET-CT and bone scintigraphy. Methods: Prospective analysis of locally advanced breast cancer patients treated in a Comprehensive Cancer Center between 2014 and 2019 that performed PET-CT and Bone Scintigraphy in the staging. Interval between the two exams could not exceed 2 months. Clinical and pathological characteristics of the disease were collected from electronic files and independently clinical images reports were considered to evaluate the ability of each imaging modalities to identify bone disease. In discrepancy cases a re-analysis of the images by two independent nuclear physicians was performed to validate the findings. Results: We analyzed 204 cases. The majority of them had ductal carcinomas (72.5%), cT2/3 (70%), cN1/2(61.8%) and G2/3 (94.6%), luminal B- like, HER2 positive disease (49.2%). In this cohort, bone metastasis was documented in 52 (25.5%) patients. PET-CT presented 97.0% of accuracy, surpassing the 94.1% presented by Bone Scintigraphy. The latter failed to correctly detect bone metastasis in 11 (5.4%) patients and only outperformed PET-CT in 3 (1.5%) patients. The main difference between the two modalities was the non-detection of cranium lesions in PET-CT images. Conclusions: PET-CT showed higher efficiency in bone metastasis detection than Bone Scintigraphy, probably because it detects lytic lesions. The non-detection of cranium ones can be harmful and so modifications in the image acquisition are required to improve the quality of PET-CT, avoiding other exams in bone staging.

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