MRI lung lobe segmentation in pediatric cystic fibrosis patients using a recurrent neural network trained with publicly accessible CT datasets.

PURPOSE To introduce a widely applicable workflow for pulmonary lobe segmentation of MR images using a recurrent neural network (RNN) trained with chest CT datasets. The feasibility is demonstrated for 2D coronal ultrafast balanced SSFP (ufSSFP) MRI. METHODS Lung lobes of 250 publicly accessible CT datasets of adults were segmented with an open-source CT-specific algorithm. To match 2D ufSSFP MRI data of pediatric patients, both CT data and segmentations were translated into pseudo-MR images that were masked to suppress anatomy outside the lung. Network-1 was trained with pseudo-MR images and lobe segmentations and then applied to 1000 masked ufSSFP images to predict lobe segmentations. These outputs were directly used as targets to train Network-2 and Network-3 with non-masked ufSSFP data as inputs, as well as an additional whole-lung mask as input for Network-2. Network predictions were compared to reference manual lobe segmentations of ufSSFP data in 20 pediatric cystic fibrosis patients. Manual lobe segmentations were performed by splitting available whole-lung segmentations into lobes. RESULTS Network-1 was able to segment the lobes of ufSSFP images, and Network-2 and Network-3 further increased segmentation accuracy and robustness. The average all-lobe Dice similarity coefficients were 95.0 ± 2.8 (mean ± pooled SD [%]) and 96.4 ± 2.5, 93.0 ± 2.0; and the average median Hausdorff distances were 6.1 ± 0.9 (mean ± SD [mm]), 5.3 ± 1.1, 7.1 ± 1.3 for Network-1, Network-2, and Network-3, respectively. CONCLUSION Recurrent neural network lung lobe segmentation of 2D ufSSFP imaging is feasible, in good agreement with manual segmentations. The proposed workflow might provide access to automated lobe segmentations for various lung MRI examinations and quantitative analyses

Using Lower Extremity Muscle Activations to Estimate Human Ankle Impedance in the External-Internal Direction

For millions of people, mobility has been afflicted by lower limb amputation. Lower extremity prostheses have been used to improve the mobility of an amputee; however, they often require additional compensation from other joints and do not allow for natural maneuverability. To improve upon the functionality of ankle-foot prostheses, it is necessary to understand the role of different muscle activations in the modulation of mechanical impedance of a healthy human ankle. This report presents the results of using artificial neural networks (ANN) to determine the functional relationship between lower extremity electromyography (EMG) signals and ankle impedance in the transverse plane. The Anklebot was used to apply pseudo-random perturbations to the human ankle in the transverse plane, while motion of the ankle in the sagittal and frontal planes was constrained. Using a stochastic system identification method, the mechanical impedance of the ankle in external-internal (EI) direction was determined as a function of the applied torque and corresponding ankle motion. The impedance of the ankle and muscle EMG signals were determined for three muscle activation levels, including with relaxed muscles, and with muscles activated and 10% and 20% of the subject’s maximum voluntary contraction (MVC). This information was used as the input and target matrices to train an ANN for each subject. The resulting ankle impedance from the proposed ANN was effectively predicted within 85% accuracy for nine out of ten subjects, and was within ±5 Nm/rad of the target impedance for all subjects. This work provides more understanding of the neuromuscular characteristics of the ankle and provides insight toward future design and control of ankle-foot prostheses

MRI lung lobe segmentation in pediatric cystic fibrosis patients using a recurrent neural network trained with publicly accessible CT datasets

PURPOSE To introduce a widely applicable workflow for pulmonary lobe segmentation of MR images using a recurrent neural network (RNN) trained with chest CT datasets. The feasibility is demonstrated for 2D coronal ultrafast balanced SSFP (ufSSFP) MRI. METHODS Lung lobes of 250 publicly accessible CT datasets of adults were segmented with an open-source CT-specific algorithm. To match 2D ufSSFP MRI data of pediatric patients, both CT data and segmentations were translated into pseudo-MR images that were masked to suppress anatomy outside the lung. Network-1 was trained with pseudo-MR images and lobe segmentations and then applied to 1000 masked ufSSFP images to predict lobe segmentations. These outputs were directly used as targets to train Network-2 and Network-3 with non-masked ufSSFP data as inputs, as well as an additional whole-lung mask as input for Network-2. Network predictions were compared to reference manual lobe segmentations of ufSSFP data in 20 pediatric cystic fibrosis patients. Manual lobe segmentations were performed by splitting available whole-lung segmentations into lobes. RESULTS Network-1 was able to segment the lobes of ufSSFP images, and Network-2 and Network-3 further increased segmentation accuracy and robustness. The average all-lobe Dice similarity coefficients were 95.0 ± 2.8 (mean ± pooled SD [%]) and 96.4 ± 2.5, 93.0 ± 2.0; and the average median Hausdorff distances were 6.1 ± 0.9 (mean ± SD [mm]), 5.3 ± 1.1, 7.1 ± 1.3 for Network-1, Network-2, and Network-3, respectively. CONCLUSION Recurrent neural network lung lobe segmentation of 2D ufSSFP imaging is feasible, in good agreement with manual segmentations. The proposed workflow might provide access to automated lobe segmentations for various lung MRI examinations and quantitative analyses

Cancer diagnosis using deep learning: A bibliographic review

In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann’s machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements

The LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation.

Publicly available Glioblastoma (GBM) datasets predominantly include pre-operative Magnetic Resonance Imaging (MRI) or contain few follow-up images for each patient. Access to fully longitudinal datasets is critical to advance the refinement of treatment response assessment. We release a single-center longitudinal GBM MRI dataset with expert ratings of selected follow-up studies according to the response assessment in neuro-oncology criteria (RANO). The expert rating includes details about the rationale of the ratings. For a subset of patients, we provide pathology information regarding methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter status and isocitrate dehydrogenase 1 (IDH1), as well as the overall survival time. The data includes T1-weighted pre- and post-contrast, T2-weighted, and fluid-attenuated inversion recovery (FLAIR) MRI. Segmentations from state-of-the-art automated segmentation tools, as well as radiomic features, complement the data. Possible applications of this dataset are radiomics research, the development and validation of automated segmentation methods, and studies on response assessment. This collection includes MRI data of 91 GBM patients with a total of 638 study dates and 2487 images

MIANN models in medicinal, physical and organic chemistry

[Abstract] Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.Ministerio de Ciencia e Innovación; CTQ2009-07733Universidad del Pais Vasco; UFI11/22Universidad del Pais Vasco; GIU 094

ESTIMATION OF MULTI-DIRECTIONAL ANKLE IMPEDANCE AS A FUNCTION OF LOWER EXTREMITY MUSCLE ACTIVATION

The purpose of this research is to investigate the relationship between the mechanical impedance of the human ankle and the corresponding lower extremity muscle activity. Three experimental studies were performed to measure the ankle impedance about multiple degrees of freedom (DOF), while the ankle was subjected to different loading conditions and different levels of muscle activity. The first study determined the non-loaded ankle impedance in the sagittal, frontal, and transverse anatomical planes while the ankle was suspended above the ground. The subjects actively co-contracted their agonist and antagonistic muscles to various levels, measured using electromyography (EMG). An Artificial Neural Network (ANN) was implemented to characterize the relationship between the EMG and non-loaded ankle impedance in 3-DOF. The next two studies determined the ankle impedance and muscle activity during standing, while the foot and ankle were subjected to ground perturbations in the sagittal and frontal planes. These studies investigate the performance of subject-dependent models, aggregated models, and the feasibility of a generic, subject-independent model to predict ankle impedance based on the muscle activity of any person. Several regression models, including Least Square, Support Vector Machine, Gaussian Process Regression, and ANN, and EMG feature extraction techniques were explored. The resulting subject-dependent and aggregated models were able to predict ankle impedance with reasonable accuracy. Furthermore, preliminary efforts toward a subject-independent model showed promising results for the design of an EMG-impedance model that can predict ankle impedance using new subjects. This work contributes to understanding the relationship between the lower extremity muscles and the mechanical impedance of the ankle in multiple DOF. Applications of this work could be used to improve user intent recognition for the control of active ankle-foot prostheses

A Concept for Deployment and Evaluation of Unsupervised Domain Adaptation in Cognitive Perception Systems

Jüngste Entwicklungen im Bereich des tiefen Lernens ermöglichen Perzeptionssystemen datengetrieben Wissen über einen vordefinierten Betriebsbereich, eine sogenannte Domäne, zu gewinnen. Diese Verfahren des überwachten Lernens werden durch das Aufkommen groß angelegter annotierter Datensätze und immer leistungsfähigerer Prozessoren vorangetrieben und zeigen unübertroffene Performanz bei Perzeptionsaufgaben in einer Vielzahl von Anwendungsbereichen.Jedoch sind überwacht-trainierte neuronale Netze durch die Menge an verfügbaren annotierten Daten limitiert und dies wiederum findet in einem begrenzten Betriebsbereich Ausdruck. Dabei beruht überwachtes Lernen stark auf manuell durchzuführender Datenannotation. Insbesondere durch die ständig steigende Verfügbarkeit von nicht annotierten großen Datenmengen ist der Gebrauch von unüberwachter Domänenanpassung entscheidend. Verfahren zur unüberwachten Domänenanpassung sind meist nicht geeignet, um eine notwendige Inbetriebnahme des neuronalen Netzes in einer zusätzlichen Domäne zu gewährleisten. Darüber hinaus sind vorhandene Metriken häufig unzureichend für eine auf die Anwendung der domänenangepassten neuronalen Netzen ausgerichtete Validierung. Der Hauptbeitrag der vorliegenden Dissertation besteht aus neuen Konzepten zur unüberwachten Domänenanpassung. Basierend auf einer Kategorisierung von Domänenübergängen und a priori verfügbaren Wissensrepräsentationen durch ein überwacht-trainiertes neuronales Netz wird eine unüberwachte Domänenanpassung auf nicht annotierten Daten ermöglicht. Um die kontinuierliche Bereitstellung von neuronalen Netzen für die Anwendung in der Perzeption zu adressieren, wurden neuartige Verfahren speziell für die unüberwachte Erweiterung des Betriebsbereichs eines neuronalen Netzes entwickelt. Beispielhafte Anwendungsfälle des Fahrzeugsehens zeigen, wie die neuartigen Verfahren kombiniert mit neu entwickelten Metriken zur kontinuierlichen Inbetriebnahme von neuronalen Netzen auf nicht annotierten Daten beitragen. Außerdem werden die Implementierungen aller entwickelten Verfahren und Algorithmen dargestellt und öffentlich zugänglich gemacht. Insbesondere wurden die neuartigen Verfahren erfolgreich auf die unüberwachte Domänenanpassung, ausgehend von der Tag- auf die Nachtobjekterkennung im Bereich des Fahrzeugsehens angewendet

MECHANICAL IMPEDANCE OF ANKLE AS A FUNCTION OF ELECTROMYOGRAPHY SIGNALS OF LOWER LEG MUSCLES USING ARTIFICIAL NEURAL NETWORK

This paper reports on the feasibility of developing a model to describe the nonlinear relationship between the mechanical impedance of the human ankle within a specified range of frequency and the root mean square (RMS) value of the Electromyography (EMG) signals of the muscles of human ankle using Artificial Neural Network (ANN). A lower extremity rehabilitation robot — Anklebot was used to apply pseudo-random mechanical perturbations to the ankle and measure the angular displacement of the ankle to estimate the data of ankle mechanical impedance. Meanwhile, the surface EMG signals from the selected muscles were monitored and recorded using a Delsys Trigno® system. The final ANN models in this paper were created in two degrees of freedom — dorsiflexion-plantarflexion (DP) and inversioneversion (IE) at 3 different muscle activation levels. The results of analysis of the ANN model showed the feasibility of developing models with adequate accuracy and to define the mechanical impedance of the human ankle in terms of lower extremity muscles’ EMG statistical properties