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Publications

Publications by BIO

2018

An Iterative MOLI-ZOFT Approach for the Identification of MISO LTI Systems

Authors
Saraiva, PG; dos Santos, PL; Pait, F; Romano, RA; Perdicoulis, TP;

Publication
2018 13TH APCA INTERNATIONAL CONFERENCE ON CONTROL AND SOFT COMPUTING (CONTROLO)

Abstract
In this paper, a new system identification algorithm is proposed for linear and time invariant systems with multiple input and single output. The system is described by a state-space model in the canonical observable form and represented by a Luenberger observer with a known state matrix. Thence, the identification problem is reduced to the estimation of the system input matrix and the observer gain which can be performed by a simple Least Square Estimator. The quality of the estimator depends on the observer state matrix. In the proposed algorithm, this matrix is found by an iterative process where, in each iteration, a state matrix called curiosity is generated. A weight depending on the value of the Least Square Cost is associated to each curiosity. The optimal state matrix is the barycenter of the curiosities. This iterative process is a free derivative optimization algorithm with its roots in non-iterative barycenter methods previously introduced to solve adaptive control and system identification problems. Although the Barycenter iterative version was recently proposed as an optimization method, here it will be implemented in an identification algorithm for the first time.

2018

Bi-level and Bi-objective p-Median Type Problems for Integrative Clustering: Application to Analysis of Cancer Gene-Expression and Drug-Response Data

Authors
Ushakov, AV; Klimentova, X; Vasilyev, I;

Publication
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Abstract
Recent advances in high-throughput technologies have given rise to collecting large amounts of multidimensional heterogeneous data that provide diverse information on the same biological samples. Integrative analysis of such multisource datasets may reveal new biological insights into complex biological mechanisms and therefore remains an important research field in systems biology. Most of the modern integrative clustering approaches rely on independent analysis of each dataset and consensus clustering, probabilistic or statistical modeling, while flexible distance-based integrative clustering techniques are sparsely covered. We propose two distance-based integrative clustering frameworks based on bi-level and bi-objective extensions of the p-median problem. A hybrid branch-and-cut method is developed to find global optimal solutions to the bi-level p-median model. As to the bi-objective problem, an epsilon-constraint algorithm is proposed to generate an approximation to the Pareto optimal set. Every solution found by any of the frameworks corresponds to an integrative clustering. We present an application of our approaches to integrative analysis of NCI-60 human tumor cell lines characterized by gene expression and drug activity profiles. We demonstrate that the proposed mathematical optimization-based approaches outperform some state-of-the-art and traditional distance-based integrative and non-integrative clustering techniques.

2018

A Pixel-Wise Distance Regression Approach for Joint Retinal Optical Disc and Fovea Detection

Authors
Meyer, MI; Galdran, A; Mendonca, AM; Campilho, A;

Publication
MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION - MICCAI 2018, PT II

Abstract
This paper introduces a novel strategy for the task of simultaneously locating two key anatomical landmarks in retinal images of the eye fundus, namely the optic disc and the fovea. For that, instead of attempting to classify each pixel as belonging to the background, the optic disc, or the fovea center, which would lead to a highly class-imbalanced setting, the problem is reformulated as a pixelwise regression task. The regressed quantity consists of the distance from the closest landmark of interest. A Fully-Convolutional Deep Neural Network is optimized to predict this distance for each image location, implicitly casting the problem into a per-pixel Multi-Task Learning approach by which a globally consistent distribution of distances across the entire image can be learned. Once trained, the two minimal distances predicted by the model are selected as the locations of the optic disc and the fovea. The joint learning of every pixel position relative to the optic disc and the fovea favors an automatic understanding of the overall anatomical distribution. This results in an effective technique that can detect both locations simultaneously, as opposed to previous methods that handle both tasks separately. Comprehensive experimental results on a large public dataset validate the proposed approach.

2018

Wearable Health Devices-Vital Sign Monitoring, Systems and Technologies

Authors
Dias, D; Cunha, JPS;

Publication
SENSORS

Abstract
Wearable Health Devices (WHDs) are increasingly helping people to better monitor their health status both at an activity/fitness level for self-health tracking and at a medical level providing more data to clinicians with a potential for earlier diagnostic and guidance of treatment. The technology revolution in the miniaturization of electronic devices is enabling to design more reliable and adaptable wearables, contributing for a world-wide change in the health monitoring approach. In this paper we review important aspects in the WHDs area, listing the state-of-the-art of wearable vital signs sensing technologies plus their system architectures and specifications. A focus on vital signs acquired by WHDs is made: first a discussion about the most important vital signs for health assessment using WHDs is presented and then for each vital sign a description is made concerning its origin and effect on heath, monitoring needs, acquisition methods and WHDs and recent scientific developments on the area (electrocardiogram, heart rate, blood pressure, respiration rate, blood oxygen saturation, blood glucose, skin perspiration, capnography, body temperature, motion evaluation, cardiac implantable devices and ambient parameters). A general WHDs system architecture is presented based on the state-of-the-art. After a global review of WHDs, we zoom in into cardiovascular WHDs, analysing commercial devices and their applicability versus quality, extending this subject to smart t-shirts for medical purposes. Furthermore we present a resumed evolution of these devices based on the prototypes developed along the years. Finally we discuss likely market trends and future challenges for the emerging WHDs area.

2018

Automatic Characterization of the Serous Retinal Detachment Associated with the Subretinal Fluid Presence in Optical Coherence Tomography Images

Authors
Moura, Jd; Novo, J; Penas, S; Ortega, M; Silva, JA; Mendonça, AM;

Publication
Knowledge-Based and Intelligent Information & Engineering Systems: Proceedings of the 22nd International Conference KES-2018, Belgrade, Serbia, 3-5 September 2018.

Abstract
An accurate detection of the macular edema (ME) presence constitutes a crucial ophthalmological issue as it provides useful information for the identification, diagnosis and treatment of different relevant ocular and Systemic diseaseS. serous Retinal Detachment (sRD) is a particular type of ME, which is characterized by the leakage of fluid that has a propensity of being accumulated in the macular region. This paper proposes a new methodology for the automatic identification and characterization of the sRD edema using Optical Coherence Tomography (OCT) imageS. The subretinal fluids and the External Limiting Membrane (ELM) retinal layers are identified and characterized to measure the disease severity. Four different visualization modules were designed including representative derived parameters to facilitate the doctor's work in the diagnostic evaluation of ME. The different steps of this method were validated using the manual labelling provided by an expert clinician. The validation of the proposed method offered satisfactory results, constituting a suitable scenario with intuitive visual representations that also include different relevant biomarkerS. © 2018 The Author(s).

2018

Evaluation of Coherence-Based Beamforming for B-Mode and Speckle Tracking Echocardiography

Authors
Santos, P; Koriakina, N; Chakraborty, B; Pedrosa, J; Petrescu, AM; Voigt, JU; D'hooge, J;

Publication
IEEE International Ultrasonics Symposium, IUS

Abstract
Phase coherence methods have been proposed to improve the delay-and-sum (DAS) beamforming in terms of contrast and spatial resolution. However, they could be equally beneficial for speckle tracking echocadiography, given the higher variance they introduce in the speckle texture. The aim of this study was to compare, in a close-to-clinical scenario, the B-mode and speckle tracking performance of the DAS beamformer and 4 phase coherence methods: generalized coherence factor, phase coherence factor, sign coherence factor and short lag spatial coherence. Both simulation and experimental imaging of a tissue mimicking phantom were used to assess classical imaging metrics, whereas in-vivo imaging was performed to evaluate myocardial visibility and tissue tracking. Results showed improved resolution and contrast from the coherence beamformers, as well as a reduction of clutter noise, especially in the near field. Similarly, apical strain curves were more reliably estimated following coherence processing. Overall, these methods seem to better derive both morphological and functional imaging, although no method outperformed in all scenarios. © 2018 IEEE.

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