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General General

Semiology and Epileptic Networks.

In Neurosurgery clinics of North America

Seizure semiology represents the dynamic clinical expression of seizures and is an important behavioral data source providing clues to cerebral organization. It is produced through interactions between electrical seizure discharge and physiologic and pathologic brain networks. Semiology is described in spatial and temporal terms; its expression depends on spatial (localization) and temporal (eg, discharge frequency, synchrony) characteristics of cerebral electrical activity. Stereoelectroencephalography studies of electroclinical correlations, including with quantified signal analysis, have helped elucidate several semiological patterns. Future research could help improve pattern recognition of complex semiological patterns, possibly using deep learning methods in a multiscale, multimodal modelization framework.

McGonigal Aileen


Epileptic networks, SEEG, Seizure, Semiology, Stereoelectroencephalography, Stereotypies

Radiology Radiology

CT-based COVID-19 Triage: Deep Multitask Learning Improves Joint Identification and Severity Quantification

ArXiv Preprint

The current COVID-19 pandemic overloads healthcare systems, including radiology departments. Though several deep learning approaches were developed to assist in CT analysis, nobody considered study triage directly as a computer science problem. We describe two basic setups: Identification of COVID-19 to prioritize studies of potentially infected patients to isolate them as early as possible; Severity quantification to highlight studies of severe patients and direct them to a hospital or provide emergency medical care. We formalize these tasks as binary classification and estimation of affected lung percentage. Though similar problems were well-studied separately, we show that existing methods provide reasonable quality only for one of these setups. To consolidate both triage approaches, we employ a multitask learning and propose a convolutional neural network to combine all available labels within a single model. We train our model on approximately 2000 publicly available CT studies and test it with a carefully designed set consisting of 33 COVID patients, 32 healthy patients, and 36 patients with other lung pathologies to emulate a typical patient flow in an out-patient hospital. The developed model achieved 0.951 ROC AUC for Identification of COVID-19 and 0.98 Spearman Correlation for Severity quantification. We release all the code and create a public leaderboard, where other community members can test their models on our dataset.

Mikhail Goncharov, Maxim Pisov, Alexey Shevtsov, Boris Shirokikh, Anvar Kurmukov, Ivan Blokhin, Valeria Chernina, Alexander Solovev, Victor Gombolevskiy, Sergey Morozov, Mikhail Belyaev


General General

Powerful, transferable representations for molecules through intelligent task selection in deep multitask networks.

In Physical chemistry chemical physics : PCCP

Chemical representations derived from deep learning are emerging as a powerful tool in areas such as drug discovery and materials innovation. Currently, this methodology has three major limitations - the cost of representation generation, risk of inherited bias, and the requirement for large amounts of data. We propose the use of multi-task learning in tandem with transfer learning to address these limitations directly. In order to avoid introducing unknown bias into multi-task learning through the task selection itself, we calculate task similarity through pairwise task affinity, and use this measure to programmatically select tasks. We test this methodology on several real-world data sets to demonstrate its potential for execution in complex and low-data environments. Finally, we utilise the task similarity to further probe the expressiveness of the learned representation through a comparison to a commonly used cheminformatics fingerprint, and show that the deep representation is able to capture more expressive task-based information.

Fare Clyde, Turcani Lukas, Pyzer-Knapp Edward O


General General

Deep Theory of Functional Connections: A New Method for Estimating the Solutions of Partial Differential Equations.

In Machine learning and knowledge extraction

This article presents a new methodology called Deep Theory of Functional Connections (TFC) that estimates the solutions of partial differential equations (PDEs) by combining neural networks with the TFC. The TFC is used to transform PDEs into unconstrained optimization problems by analytically embedding the PDE's constraints into a "constrained expression" containing a free function. In this research, the free function is chosen to be a neural network, which is used to solve the now unconstrained optimization problem. This optimization problem consists of minimizing a loss function that is chosen to be the square of the residuals of the PDE. The neural network is trained in an unsupervised manner to minimize this loss function. This methodology has two major differences when compared with popular methods used to estimate the solutions of PDEs. First, this methodology does not need to discretize the domain into a grid, rather, this methodology can randomly sample points from the domain during the training phase. Second, after training, this methodology produces an accurate analytical approximation of the solution throughout the entire training domain. Because the methodology produces an analytical solution, it is straightforward to obtain the solution at any point within the domain and to perform further manipulation if needed, such as differentiation. In contrast, other popular methods require extra numerical techniques if the estimated solution is desired at points that do not lie on the discretized grid, or if further manipulation to the estimated solution must be performed.

Leake Carl, Mortari Daniele


deep learning, neural network, partial differential equation, theory of functional connections

General General

Automatic Pose Recognition for Monitoring Dangerous Situations in Ambient-Assisted Living.

In Frontiers in bioengineering and biotechnology

Continuous monitoring of frail individuals for detecting dangerous situations during their daily living at home can be a powerful tool toward their inclusion in the society by allowing living independently while safely. To this goal we developed a pose recognition system tailored to disabled students living in college dorms and based on skeleton tracking through four Kinect One devices independently recording the inhabitant with different viewpoints, while preserving the individual's privacy. The system is intended to classify each data frame and provide the classification result to a further decision-making algorithm, which may trigger an alarm based on the classified pose and the location of the subject with respect to the furniture in the room. An extensive dataset was recorded on 12 individuals moving in a mockup room and undertaking four poses to be recognized: standing, sitting, lying down, and "dangerous sitting." The latter consists of the subject slumped in a chair with his/her head lying forward or backward as if unconscious. Each skeleton frame was labeled and represented using 10 discriminative features: three skeletal joint vertical coordinates and seven relative and absolute angles describing articular joint positions and body segment orientation. In order to classify the pose of the subject in each skeleton frame we built a two hidden layers multi-layer perceptron neural network with a "SoftMax" output layer, which we trained on the data from 10 of the 12 subjects (495,728 frames), with the data from the two remaining subjects representing the test set (106,802 frames). The system achieved very promising results, with an average accuracy of 83.9% (ranging 82.7 and 94.3% in each of the four classes). Our work proves the usefulness of human pose recognition based on machine learning in the field of safety monitoring in assisted living conditions.

Guerra Bruna Maria Vittoria, Ramat Stefano, Beltrami Giorgio, Schmid Micaela


Ambient-Assisted Living, geometric features, machine learning, pose recognition, skeleton tracking, vision-based activity recognition

Radiology Radiology

Preoperative Prediction of Lymph Node Metastasis in Patients With Early-T-Stage Non-small Cell Lung Cancer by Machine Learning Algorithms.

In Frontiers in oncology

Background: Lymph node metastasis (LNM) is difficult to precisely predict before surgery in patients with early-T-stage non-small cell lung cancer (NSCLC). This study aimed to develop machine learning (ML)-based predictive models for LNM. Methods: Clinical characteristics and imaging features were retrospectively collected from 1,102 NSCLC ≤ 2 cm patients. A total of 23 variables were included to develop predictive models for LNM by multiple ML algorithms. The models were evaluated by the receiver operating characteristic (ROC) curve for predictive performance and decision curve analysis (DCA) for clinical values. A feature selection approach was used to identify optimal predictive factors. Results: The areas under the ROC curve (AUCs) of the 8 models ranged from 0.784 to 0.899. Some ML-based models performed better than models using conventional statistical methods in both ROC curves and decision curves. The random forest classifier (RFC) model with 9 variables introduced was identified as the best predictive model. The feature selection indicated the top five predictors were tumor size, imaging density, carcinoembryonic antigen (CEA), maximal standardized uptake value (SUVmax), and age. Conclusions: By incorporating clinical characteristics and radiographical features, it is feasible to develop ML-based models for the preoperative prediction of LNM in early-T-stage NSCLC, and the RFC model performed best.

Wu Yijun, Liu Jianghao, Han Chang, Liu Xinyu, Chong Yuming, Wang Zhile, Gong Liang, Zhang Jiaqi, Gao Xuehan, Guo Chao, Liang Naixin, Li Shanqing


cross-validation, lymph node metastasis, machine learning, non-small cell lung cancer, predictive model