2023
Authors
Baptista, D; Ferreira, PG; Rocha, M;
Publication
PLOS COMPUTATIONAL BIOLOGY
Abstract
Author summaryCancer therapies often fail because tumor cells become resistant to treatment. One way to overcome resistance is by treating patients with a combination of two or more drugs. Some combinations may be more effective than when considering individual drug effects, a phenomenon called drug synergy. Computational drug synergy prediction methods can help to identify new, clinically relevant drug combinations. In this study, we developed several deep learning models for drug synergy prediction. We examined the effect of using different types of deep learning architectures, and different ways of representing drugs and cancer cell lines. We explored the use of biological prior knowledge to select relevant cell line features, and also tested data-driven feature reduction methods. We tested both precomputed drug features and deep learning methods that can directly learn features from raw representations of molecules. We also evaluated whether including genomic features, in addition to gene expression data, improves the predictive performance of the models. Through these experiments, we were able to identify strategies that will help guide the development of new deep learning models for drug synergy prediction in the future. One of the main obstacles to the successful treatment of cancer is the phenomenon of drug resistance. A common strategy to overcome resistance is the use of combination therapies. However, the space of possibilities is huge and efficient search strategies are required. Machine Learning (ML) can be a useful tool for the discovery of novel, clinically relevant anti-cancer drug combinations. In particular, deep learning (DL) has become a popular choice for modeling drug combination effects. Here, we set out to examine the impact of different methodological choices on the performance of multimodal DL-based drug synergy prediction methods, including the use of different input data types, preprocessing steps and model architectures. Focusing on the NCI ALMANAC dataset, we found that feature selection based on prior biological knowledge has a positive impact-limiting gene expression data to cancer or drug response-specific genes improved performance. Drug features appeared to be more predictive of drug response, with a 41% increase in coefficient of determination (R-2) and 26% increase in Spearman correlation relative to a baseline model that used only cell line and drug identifiers. Molecular fingerprint-based drug representations performed slightly better than learned representations-ECFP4 fingerprints increased R-2 by 5.3% and Spearman correlation by 2.8% w.r.t the best learned representations. In general, fully connected feature-encoding subnetworks outperformed other architectures. DL outperformed other ML methods by more than 35% (R-2) and 14% (Spearman). Additionally, an ensemble combining the top DL and ML models improved performance by about 6.5% (R-2) and 4% (Spearman). Using a state-of-the-art interpretability method, we showed that DL models can learn to associate drug and cell line features with drug response in a biologically meaningful way. The strategies explored in this study will help to improve the development of computational methods for the rational design of effective drug combinations for cancer therapy.
2023
Authors
Lacerda, M; Silva, CD; Louro, M; Glória, G; Egorov, A; Toro Cardenas, M; Pestana, R; Lucas, A;
Publication
IET Conference Proceedings
Abstract
The short-circuit current is one of the most important security operational parameters. With the increased penetration of DERs, it is crucial to frequently and periodically monitor it, ideally every 24 hours and with high granularity (e.g., 30 minutes). This paper develops a short-circuit computation methodology to calculate the complete short-circuit current in the TSO/DSO interface nodes (extra high voltage/high voltage (EHV/HV) substations), which could be used for operational planning purposes, considering the active contributions to the short-circuit current originating from both transmission and distribution networks. A TSO-DSO coordination procedure is presented to obtain the day-ahead short-circuit currents forecast. Moreover, two real cases are provided as examples for validation of the demonstrated procedures. © The Institution of Engineering and Technology 2023.
2023
Authors
Backhouse, R; Oliveira, JN;
Publication
JOURNAL OF LOGICAL AND ALGEBRAIC METHODS IN PROGRAMMING
Abstract
The notion of a difunction was introduced by Jacques Riguet in 1948. Since then it has played a prominent role in database theory, type theory, program specification and process theory. The theory of difunctions is, however, less known in computing than it perhaps should be. The main purpose of the current paper is to give an account of difunction theory in relation algebra, with the aim of making the topic more mainstream.As is common with many important concepts, there are several different but equivalent characterisations of difunctionality, each with its own strength and practical significance. This paper compares different proofs of the equivalence of the characterisations. A well-known property is that a difunction is a set of completely disjoint rectangles. This property suggests the introduction of the (general) notion of the core of a relation; we use this notion to give a novel and, we believe, illuminating characterisation of difunctionality as a bijection between the classes of certain partial equivalence relations.& COPY; 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons .org /licenses /by /4 .0/).
2023
Authors
Castro, H; Costa, F; Ferreira, T; Avila, P; Cruz Cunha, M; Ferreira, L; Putnik, GD; Bastos, J;
Publication
MACHINES
Abstract
In the last few years, the industrial, scientific, and technological fields have been subject to a revolutionary process of digitalization and automation called Industry 4.0. Its implementation has been successful mainly in the economic field of sustainability, while the environmental field has been gaining more attention from researchers recently. However, the social scope of Industry 4.0 is still somewhat neglected by researchers and organizations. This research aimed to study Industry 4.0 and sustainability themes using data science, by incorporating open data and open-source tools to achieve sustainable Industry 4.0. To that end, a quantitative analysis based on open data was developed using open-source software in order to study Industry 4.0 and sustainability trends. The main results show that manufacturing is a relevant value-added activity in the worldwide economy; that, foreseeing the importance of Industry 4.0, countries in America, Asia, Europe, and Oceania are incorporating technological principles of Industry 4.0 in their cities, creating so-called smart cities; and that the industries that invest most in technology are computers and electronics, pharmaceuticals, transport equipment, and IT (information technology) services. Furthermore, the G7 countries have a prevalent positive trend for the migration of technological and social skills toward sustainability, as it relates to the social pillar, and to Industry 4.0. Finally, on the global scale, a positive correlation between data openness and happiness was found.
2023
Authors
Franco-Goncalo, P; Alves-Pimenta, S; Goncalves, L; Colaco, B; Leite, P; Ribeiro, A; Ferreira, M; McEvoy, F; Ginja, M;
Publication
FRONTIERS IN VETERINARY SCIENCE
Abstract
Adequate radiographic positioning on the X-ray table is paramount for canine hip dysplasia (HD) screening. The aims of this study were to evaluate femoral parallelism on normal ventrodorsal hip extended (VDHE) view and the effect of femoral angulation (FA) on Norberg Angle (NA) and Hip Congruency Index (HCI). The femoral parallelism was evaluated comparing the alignment of the long femoral axis with the long body axis in normal VDHE views and the effect of FA on NA and HCI on repeated VDHE views with different levels of FA. The femoral long axis in normal VDHE views showed a ranged of FA from -4.85 degrees to 5.85 degrees, mean +/- standard deviation (SD) of -0.06 +/- 2.41 degrees, 95% CI [-4.88, 4.76 degrees]. In the paired views, the mean +/- SD femur adduction of 3.69 +/- 1.96 degrees led to a statistically significant decrease NA, and HCI, and femur abduction of 2.89 +/- 2.12 led to a statistically significant increase in NA and HCI (p < 0.05). The FA differences were also significantly correlated with both NA differences (r = 0.83) and HCI differences (r = 0.44) (p < 0.001). This work describes a methodology that allows evaluation of femoral parallelism in VDHE views and the results suggest that femur abduction yielded more desirable NA and HCI values and adduction impaired NA and HCI values. The positive linear association of FA with NA and HCI allows the use of regression equations to create corrections, to reduce the influence of poor femoral parallelism in the HD scoring.
2023
Authors
Spilere Nandi, G; Pereira, D; Proença, J; Tovar, E; Rodriguez, A; Garrido, P;
Publication
Open Research Europe
Abstract
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