A genetic algorithms-based approach for optimizing similarity aggregation in ontology matching

[Abstract] Ontology matching consists of finding the semantic relations between different ontologies and is widely recognized as an essential process to achieve an adequate interoperability between people, systems or organizations that use different, overlapping ontologies to represent the same knowledge. There are several techniques to measure the semantic similarity of elements from separate ontologies, which must be adequately combined in order to obtain precise and complete results. Nevertheless, combining multiple similarity measures into a single metric is a complex problem, which has been traditionally solved using weights determined manually by an expert, or through general methods that do not provide optimal results. In this paper, a genetic algorithms based approach to aggregate different similarity metrics into a single function is presented. Starting from an initial population of individuals, each one representing a combination of similarity measures, our approach allows to find the combination that provides the optimal matching quality.Instituto de Salud Carlos III; FISPI10/02180Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; 209RT0366Xunta de Galicia; CN2012/217Xunta de Galicia; CN2011/034Xunta de Galicia; CN2012/21

Ontologies in medicinal chemistry: current status and future challenges

[Abstract] Recent years have seen a dramatic increase in the amount and availability of data in the diverse areas of medicinal chemistry, making it possible to achieve significant advances in fields such as the design, synthesis and biological evaluation of compounds. However, with this data explosion, the storage, management and analysis of available data to extract relevant information has become even a more complex task that offers challenging research issues to Artificial Intelligence (AI) scientists. Ontologies have emerged in AI as a key tool to formally represent and semantically organize aspects of the real world. Beyond glossaries or thesauri, ontologies facilitate communication between experts and allow the application of computational techniques to extract useful information from available data. In medicinal chemistry, multiple ontologies have been developed during the last years which contain knowledge about chemical compounds and processes of synthesis of pharmaceutical products. This article reviews the principal standards and ontologies in medicinal chemistry, analyzes their main applications and suggests future directions.Instituto de Salud Carlos III; FIS-PI10/02180Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; 209RT0366Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/217Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2011/034Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/21

BiOSS: A system for biomedical ontology selection

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service.Instituto de Salud Carlos III; FIS-PI10/02180Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/217Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2011/034Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/211Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; ref. 209RT036

Memory-efficient belief propagation for high-definition real-time stereo matching systems

Tele-presence systems will enable participants to feel like they are physically together. In order to improve this feeling, these systems are starting to include depth estimation capabilities. A typical requirement for these systems includes high definition, good quality results and low latency. Benchmarks demonstrate that stereo-matching algorithms using Belief Propagation (BP) produce the best results. The execution time of the BP algorithm in a CPU cannot satisfy real-time requirements with high-definition images. GPU-based implementations of BP algorithms are only able to work in real-time with small-medium size images because the traffic with memory limits their applicability. The inherent parallelism of the BP algorithm makes FPGA-based solutions a good choice. However, even though the memory traffic of a commercial FPGA-based ASIC-prototyping board is high, it is still not enough to comply with realtime, high definition and good immersive feeling requirements. The work presented estimates depth maps in less than 40 milliseconds for high-definition images at 30fps with 80 disparity levels. The proposed double BP topology and the new data-cost estimation improve the overall classical BP performance while they reduce the memory traffic by about 21%. Moreover, the adaptive message compression method and message distribution in memory reduce the number of memory accesses by more than 70% with an almost negligible loss of performance. The total memory traffic reduction is about 90%, demonstrating sufficient quality to be classified within the first 40 positions in the Middlebury ranking.This work has been partially supported by the CDTI under project CENIT-VISION 2007-1007 and the CICYT under TEC2008-04107

Robust asynchronous control of ERP-Based brain-Computer interfaces using deep learning

Producción CientíficaBackground and Objective. Brain-computer interfaces (BCI) based on event-related potentials (ERP) are a promising technology for alternative and augmented communication in an assistive context. However, most approaches to date are synchronous, requiring the intervention of a supervisor when the user wishes to turn his attention away from the BCI system. In order to bring these BCIs into real-life applications, a robust asynchronous control of the system is required through monitoring of user attention. Despite the great importance of this limitation, which prevents the deployment of these systems outside the laboratory, it is often overlooked in research articles. This study was aimed to propose a novel method to solve this problem, taking advantage of deep learning for the first time in this context to overcome the limitations of previous strategies based on hand-crafted features. Methods. The proposed method, based on EEG-Inception, a novel deep convolutional neural network, divides the problem in 2 stages to achieve the asynchronous control: (i) the model detects user’s control state, and (ii) decodes the command only if the user is attending to the stimuli. Additionally, we used transfer learning to reduce the calibration time, even exploring a calibration-less approach. Results. Our method was evaluated with 22 healthy subjects, analyzing the impact of the calibration time and number of stimulation sequences on the system’s performance. For the control state detection stage, we report average accuracies above 91% using only 1 sequence of stimulation and 30 calibration trials, reaching a maximum of 96.95% with 15 sequences. Moreover, our calibration-less approach also achieved suitable results, with a maximum accuracy of 89.36%, showing the benefits of transfer learning. As for the overall asynchronous system, which includes both stages, the maximum information transfer rate was 35.54 bpm, a suitable value for high-speed communication. Conclusions. The proposed strategy achieved higher performance with less calibration trials and stimulation sequences than former approaches, representing a promising step forward that paves the way for more practical applications of ERP-based spellers.Ministerio de Ciencia, Innovación y Universidades - Agencia Estatal de Investigación (grants PID2020-115468RB-I00 and RTC2019-007350-1)Comisión Europea - Fondo Europeo de Desarrollo Regional (cooperation programme Interreg V-A Spain-Portugal POCTEP 2014–2020

Early, time-approximate modeling of multi-OS Linux platforms in a systemC co-simulation environment

The increase of computational power in embedded systems has allowed integrating together hard real-time tasks and rich applications. Complex SW infrastructures containing both RTOS and GPOS are required to handle this complexity. To optimally map system functionality to the hard-RT SW domain, to the general purpose SW domain or to HW peripherals, early performance evaluations at the first steps of the design process are required. Approximate timed co-simulation has been proposed as a fast solution for system modeling at early design steps. This co-simulation technique allows simulating systems at speed close to functional execution, while considering timing effects. As a consequence, system performance estimations can be obtained early, allowing efficient design space exploration and system refinement. To achieve fast simulation speed, the SW code is pre-annotated with time information. The annotated code is then natively executed, performing what is called native-based co-simulation. Previous native-based simulation environments are not prepared to model multi-OS systems, so the performance evaluation of the different SW domains is not possible. This paper proposes a new embedded system modeling solution considering dual RTOS/GPOS systems. A real Linux-based infrastructure has been modeled an integrated into a state-of-the-art co-simulation environment. The resulting solution is capable of modeling and evaluating all HW and SW system components providing the designer with valuable information for early system optimization and design space exploration.This work has heen supported hy the Spanish MICyT and the EC through Complex FP7-247999 and the TEC2008-04107 projects

Non-binary m-sequences for more comfortable brain–computer interfaces based on c-VEPs

Producción CientíficaCode-modulated visual evoked potentials (c-VEPs) have marked a milestone in the scientific literature due to their ability to achieve reliable, high-speed brain–computer interfaces (BCIs) for communication and control. Generally, these expert systems rely on encoding each command with shifted versions of binary pseudorandom sequences, i.e., flashing black and white targets according to the shifted code. Despite the excellent results in terms of accuracy and selection time, these high-contrast stimuli cause eyestrain for some users. In this work, we propose the use of non-binary p-ary m-sequences, whose levels are encoded with different shades of gray, as a more pleasant alternative than traditional binary codes. The performance and visual fatigue of these p-ary m-sequences, as well as their ability to provide reliable c-VEP-based BCIs, are analyzed for the first time.Ministerio de Ciencia e Innovación/AEI- FEDER [TED2021-129915B-I00, RTC2019-007350-1 y PID2020-115468RB-I00

The iOSC3 system: using ontologies and SWRL rules for intelligent supervision and care of patients with acute cardiac disorders

[Abstract] Physicians in the Intensive Care Unit (ICU) are specially trained to deal constantly with very large and complex quantities of clinical data and make quick decisions as they face complications. However, the amount of information generated and the way the data are presented may overload the cognitive skills of even experienced professionals and lead to inaccurate or erroneous actions that put patients’ lives at risk. In this paper, we present the design, development, and validation of iOSC3, an ontology-based system for intelligent supervision and treatment of critical patients with acute cardiac disorders. The system analyzes the patient’s condition and provides a recommendation about the treatment that should be administered to achieve the fastest possible recovery. If the recommendation is accepted by the doctor, the system automatically modifies the quantity of drugs that are being delivered to the patient. The knowledge base is constituted by an OWL ontology and a set of SWRL rules that represent the expert’s knowledge. iOSC3 has been developed in collaboration with experts from the Cardiac Intensive Care Unit (CICU) of the Meixoeiro Hospital, one of the most significant hospitals in the northwest region of Spain.Instituto de Salud Carlos III; FIS-PI10/02180Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; 209RT0366Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/217Xunta. Consellería de Cultura, Educación e Ordenación Universitaria; CN2011/034Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/21

Developing a system for advanced monitoring and intelligent drug administration in critical care units using ontologies

Selected paper of the 16th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems, 2012 September 10-12, San Sebastian, Spain[Abstract] When a patient enters an intensive care unit (ICU), either after surgery or due to a serious clinical condition, his vital signs are continually changing, forcing the medical experts to make rapid and complex decisions, which frequently imply modifications on the dosage of drugs being administered. Life of patients at critical units depends largely on the wisdom of such decisions. However, the human factor is sometimes a source of mistakes that lead to incorrect or inaccurate actions. This work presents an expert system based on a domain ontology that acquires the vital parameters from the patient monitor, analyzes them and provides the expert with a recommendation regarding the treatment that should be administered. If the expert agrees, the system modifies the drug infusion rates being supplied at the infusion pumps in order to improve the patient's physiological status. The system is being developed at the IMEDIR Center (A Coruña, Spain) and it is being tested at the cardiac intensive care unit (CICU) of the Meixoeiro Hospital (Vigo, Spain), which is a specific type of ICU exclusively aimed to treat patients who have underwent heart surgery or that are affected by a serious coronary disorder.Instituto de Salud Carlos III; FIS-PI10/02180Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; ref. 209RT0366Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/217Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2011/034Galcia. Consellería de Cultura, Educación e Ordenación Universitaria; CN2012/21

MEDUSA©: A novel Python-based software ecosystem to accelerate brain-computer interface and cognitive neuroscience research

Producción CientíficaBackground and objective. Neurotechnologies have great potential to transform our society in ways that are yet to be uncovered. The rate of development in this field has increased significantly in recent years, but there are still barriers that need to be overcome before bringing neurotechnologies to the general public. One of these barriers is the difficulty of performing experiments that require complex software, such as brain-computer interfaces (BCI) or cognitive neuroscience experiments. Current platforms have limitations in terms of functionality and flexibility to meet the needs of researchers, who often need to implement new experimentation settings. This work was aimed to propose a novel software ecosystem, called MEDUSA©, to overcome these limitations. Methods. We followed strict development practices to optimize MEDUSA© for research in BCI and cognitive neuroscience, making special emphasis in the modularity, flexibility and scalability of our solution. Moreover, it was implemented in Python, an open-source programming language that reduces the development cost by taking advantage from its high-level syntax and large number of community packages. Results. MEDUSA© provides a complete suite of signal processing functions, including several deep learning architectures or connectivity analysis, and ready-to-use BCI and neuroscience experiments, making it one of the most complete solutions nowadays. We also put special effort in providing tools to facilitate the development of custom experiments, which can be easily shared with the community through an app market available in our website to promote reproducibility. Conclusions. MEDUSA© is a novel software ecosystem for modern BCI and neurotechnology experimentation that provides state-of-the-art tools and encourages the participation of the community to make a difference for the progress of these fields. Visit the official website at https://www.medusabci.com/ to know more about this project.Ministerio de Ciencia e Innovación/Agencia Estatal de Investigación/10.13039/501100011033/' y el Fondo Europeo de Desarrollo Regional (FEDER) grants (PID2020-115468RB-I00 and RTC2019-007350-1