Implementation of a computerized assessment system by using backpropagation neural networks with R and shiny

Las dificultades a las que los estudiantes se enfrentan y su lucha por dominar los temas, podría aumentar como consecuencia de la inadecuada utilización de materiales de evaluación. Generalmente se encuentran en el aula alumnos que hacen buen uso del material de los cursos y de una manera rápida, mientras que otros presentan dificultades con el aprendizaje del material. Esta situación es fácilmente visto en los resultados de los exámenes, un grupo de estudiantes podrían obtener buenas calificaciones animándoles, mientras que otros obtendrían la mala percepción de que los temas son difíciles, y en algunos casos, obligándolos a abandonar el curso o en otros casos a cambiar de carrera. Creemos que mediante el uso de técnicas de aprendizaje automático, y en nuestro caso la utilización de redes neuronales, sería factible crear un entorno de evaluación que podrían ajustarse a las necesidades de cada estudiante. Esto último disminuiría la sensación de insatisfacción de los alumnos y el abandono de los cursos.

A Recommender System based on Idiotypic Artificial Immune Networks

The immune system is a complex biological system with a highly distributed, adaptive and self-organising nature. This paper presents an Artificial Immune System (AIS) that exploits some of these characteristics and is applied to the task of film recommendation by Collaborative Filtering (CF). Natural evolution and in particular the immune system have not been designed for classical optimisation. However, for this problem, we are not interested in finding a single optimum. Rather we intend to identify a sub-set of good matches on which recommendations can be based. It is our hypothesis that an AIS built on two central aspects of the biological immune system will be an ideal candidate to achieve this: Antigen-antibody interaction for matching and idiotypic antibody-antibody interaction for diversity. Computational results are presented in support of this conjecture and compared to those found by other CF techniques.

Deep convolutional neural networks for semantic video object segmentation

In this thesis, we propose to infer pixel-level labelling in video by utilising only object category information, exploiting the intrinsic structure of video data. Our motivation is the observation that image-level labels are much more easily to be acquired than pixel-level labels, and it is natural to find a link between the image level recognition and pixel level classification in video data, which would transfer learned recognition models from one domain to the other one. To this end, this thesis proposes two domain adaptation approaches to adapt the deep convolutional neural network (CNN) image recognition model trained from labelled image data to the target domain exploiting both semantic evidence learned from CNN, and the intrinsic structures of unlabelled video data. Our proposed approaches explicitly model and compensate for the domain adaptation from the source domain to the target domain which in turn underpins a robust semantic object segmentation method for natural videos. We demonstrate the superior performance of our methods by presenting extensive evaluations on challenging datasets comparing with the state-of-the-art methods.

A Recommender System based on Idiotypic Artificial Immune Networks

The immune system is a complex biological system with a highly distributed, adaptive and self-organising nature. This paper presents an Artificial Immune System (AIS) that exploits some of these characteristics and is applied to the task of film recommendation by Collaborative Filtering (CF). Natural evolution and in particular the immune system have not been designed for classical optimisation. However, for this problem, we are not interested in finding a single optimum. Rather we intend to identify a sub-set of good matches on which recommendations can be based. It is our hypothesis that an AIS built on two central aspects of the biological immune system will be an ideal candidate to achieve this: Antigen-antibody interaction for matching and idiotypic antibody-antibody interaction for diversity. Computational results are presented in support of this conjecture and compared to those found by other CF techniques.

A Recommender System based on Idiotypic Artificial Immune Networks

The immune system is a complex biological system with a highly distributed, adaptive and self-organising nature. This paper presents an Artificial Immune System (AIS) that exploits some of these characteristics and is applied to the task of film recommendation by Collaborative Filtering (CF). Natural evolution and in particular the immune system have not been designed for classical optimisation. However, for this problem, we are not interested in finding a single optimum. Rather we intend to identify a sub-set of good matches on which recommendations can be based. It is our hypothesis that an AIS built on two central aspects of the biological immune system will be an ideal candidate to achieve this: Antigen-antibody interaction for matching and idiotypic antibody-antibody interaction for diversity. Computational results are presented in support of this conjecture and compared to those found by other CF techniques.

Investigation and prediction of sea level variations in the northern coasts of Persian Gulf using artificial neural network

Sea- level variations have a significant impact on coastal areas. Prediction of sea level variations expected from the pre most critical information needs associated with the sea environment. For this, various methods exist. In this study, on the northern coast of the Persian Gulf have been studied relation to the effectiveness of parameters such as pressure, temperature and wind speed on sea leve and associated with global parameters such as the North Atlantic Oscillation index and NAO index and present statistic models for prediction of sea level. In the next step by using artificial neural network predict sea level for first in this region. Then compared results of the models. Prediction using statistical models estimated in terms correlation coefficient R = 0.84 and root mean square error (RMS) 21.9 cm for the Bushehr station, and R = 0.85 and root mean square error (RMS) 48.4 cm for Rajai station, While neural network used to have 4 layers and each middle layer six neurons is best for prediction and produces the results reliably in terms of correlation coefficient with R = 0.90126 and the root mean square error (RMS) 13.7 cm for the Bushehr station, and R = 0.93916 and the root mean square error (RMS) 22.6 cm for Rajai station. Therefore, the proposed methodology could be successfully used in the study area.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.

Delays in activity based neural networks

In this paper we study the effect of two distinct discrete delays on the dynamics of a Wilson-Cowan neural network. This activity based model describes the dynamics of synaptically interacting excitatory and inhibitory neuronal populations. We discuss the interpretation of the delays in the language of neurobiology and show how they can contribute to the generation of network rhythms. First we focus on the use of linear stability theory to show how to destabilise a fixed point, leading to the onset of oscillatory behaviour. Next we show for the choice of a Heaviside nonlinearity for the firing rate that such emergent oscillations can be either synchronous or anti-synchronous depending on whether inhibition or excitation dominates the network architecture. To probe the behaviour of smooth (sigmoidal) nonlinear firing rates we use a mixture of numerical bifurcation analysis and direct simulations, and uncover parameter windows that support chaotic behaviour. Finally we comment on the role of delays in the generation of bursting oscillations, and discuss natural extensions of the work in this paper.

Depolarization induced suppression of excitation and the emergence of ultra-slow rhythms in neural networks

Ultra-slow fluctuations (0.01-0.1 Hz) are a feature of intrinsic brain activity of as yet unclear origin. We propose a candidate mechanism based on retrograde endocannabinoid signaling in a synaptically coupled network of excitatory neurons. This is known to cause depolarization-induced suppression of excitation (DISE), which we model phenomenologically. We construct emergent network oscillations in a globally coupled network and show that for strong synaptic coupling DISE can lead to a synchronized population burst at the frequencies of resting brain rhythms.

Mutual Information-based RBM Neural Networks

(Deep) neural networks are increasingly being used for various computer vision and pattern recognition tasks due to their strong ability to learn highly discriminative features. However, quantitative analysis of their classication ability and design philosophies are still nebulous. In this work, we use information theory to analyze the concatenated restricted Boltzmann machines (RBMs) and propose a mutual information-based RBM neural networks (MI-RBM). We develop a novel pretraining algorithm to maximize the mutual information between RBMs. Extensive experimental results on various classication tasks show the eectiveness of the proposed approach.

Adverse drug reaction classification with deep neural networks

We study the problem of detecting sentences describing adverse drug reactions (ADRs) and frame the problem as binary classification. We investigate different neural network (NN) architectures for ADR classification. In particular, we propose two new neural network models, Convolutional Recurrent Neural Network (CRNN) by concatenating convolutional neural networks with recurrent neural networks, and Convolutional Neural Network with Attention (CNNA) by adding attention weights into convolutional neural networks. We evaluate various NN architectures on a Twitter dataset containing informal language and an Adverse Drug Effects (ADE) dataset constructed by sampling from MEDLINE case reports. Experimental results show that all the NN architectures outperform the traditional maximum entropy classifiers trained from n-grams with different weighting strategies considerably on both datasets. On the Twitter dataset, all the NN architectures perform similarly. But on the ADE dataset, CNN performs better than other more complex CNN variants. Nevertheless, CNNA allows the visualisation of attention weights of words when making classification decisions and hence is more appropriate for the extraction of word subsequences describing ADRs.

Detection and Grading of Prostate Cancer in Temporal Enhanced Ultrasound using Convolutional Neural Networks

Prostate cancer is the most common non-dermatological cancer amongst men in the developed world. The current definitive diagnosis is core needle biopsy guided by transrectal ultrasound. However, this method suffers from low sensitivity and specificity in detecting cancer. Recently, a new ultrasound based tissue typing approach has been proposed, known as temporal enhanced ultrasound (TeUS). In this approach, a set of temporal ultrasound frames is collected from a stationary tissue location without any intentional mechanical excitation. The main aim of this thesis is to implement a deep learning-based solution for prostate cancer detection and grading using TeUS data. In the proposed solution, convolutional neural networks are trained to extract high-level features from time domain TeUS data in temporally and spatially adjacent frames in nine in vivo prostatectomy cases. This approach avoids information loss due to feature extraction and also improves cancer detection rate. The output likelihoods of two TeUS arrangements are then combined to form our novel decision support system. This deep learning-based approach results in the area under the receiver operating characteristic curve (AUC) of 0.80 and 0.73 for prostate cancer detection and grading, respectively, in leave-one-patient-out cross-validation. Recently, multi-parametric magnetic resonance imaging (mp-MRI) has been utilized to improve detection rate of aggressive prostate cancer. In this thesis, for the first time, we present the fusion of mp-MRI and TeUS for characterization of prostate cancer to compensates the deficiencies of each image modalities and improve cancer detection rate. The results obtained using TeUS are fused with those attained using consolidated mp-MRI maps from multiple MR modalities and cancer delineations on those by multiple clinicians. The proposed fusion approach yields the AUC of 0.86 in prostate cancer detection. The outcomes of this thesis emphasize the viable potential of TeUS as a tissue typing method. Employing this ultrasound-based intervention, which is non-invasive and inexpensive, can be a valuable and practical addition to enhance the current prostate cancer detection.

Interpretable Convolutional Neural Networks for Decoding and Analyzing Neural Time Series Data

Machine learning is widely adopted to decode multi-variate neural time series, including electroencephalographic (EEG) and single-cell recordings. Recent solutions based on deep learning (DL) outperformed traditional decoders by automatically extracting relevant discriminative features from raw or minimally pre-processed signals. Convolutional Neural Networks (CNNs) have been successfully applied to EEG and are the most common DL-based EEG decoders in the state-of-the-art (SOA). However, the current research is affected by some limitations. SOA CNNs for EEG decoding usually exploit deep and heavy structures with the risk of overfitting small datasets, and architectures are often defined empirically. Furthermore, CNNs are mainly validated by designing within-subject decoders. Crucially, the automatically learned features mainly remain unexplored; conversely, interpreting these features may be of great value to use decoders also as analysis tools, highlighting neural signatures underlying the different decoded brain or behavioral states in a data-driven way. Lastly, SOA DL-based algorithms used to decode single-cell recordings rely on more complex, slower to train and less interpretable networks than CNNs, and the use of CNNs with these signals has not been investigated. This PhD research addresses the previous limitations, with reference to P300 and motor decoding from EEG, and motor decoding from single-neuron activity. CNNs were designed light, compact, and interpretable. Moreover, multiple training strategies were adopted, including transfer learning, which could reduce training times promoting the application of CNNs in practice. Furthermore, CNN-based EEG analyses were proposed to study neural features in the spatial, temporal and frequency domains, and proved to better highlight and enhance relevant neural features related to P300 and motor states than canonical EEG analyses. Remarkably, these analyses could be used, in perspective, to design novel EEG biomarkers for neurological or neurodevelopmental disorders. Lastly, CNNs were developed to decode single-neuron activity, providing a better compromise between performance and model complexity.

Predicting corticospinal excitability from pre-TMS EEG using convolutional neural networks

The amplitude of motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) of the primary motor cortex (M1) shows a large variability from trial to trial, although MEPs are evoked by the same repeated stimulus. A multitude of factors is believed to influence MEP amplitudes, such as cortical, spinal and motor excitability state. The goal of this work is to explore to which degree the variation in MEP amplitudes can be explained by the cortical state right before the stimulation. Specifically, we analyzed a dataset acquired on eleven healthy subjects comprising, for each subject, 840 single TMS pulses applied to the left M1 during acquisition of electroencephalography (EEG) and electromyography (EMG). An interpretable convolutional neural network, named SincEEGNet, was utilized to discriminate between low- and high-corticospinal excitability trials, defined according to the MEP amplitude, using in input the pre-TMS EEG. This data-driven approach enabled considering multiple brain locations and frequency bands without any a priori selection. Post-hoc interpretation techniques were adopted to enhance interpretation by identifying the more relevant EEG features for the classification. Results show that individualized classifiers successfully discriminated between low and high M1 excitability states in all participants. Outcomes of the interpretation methods suggest the importance of the electrodes situated over the TMS stimulation site, as well as the relevance of the temporal samples of the input EEG closer to the stimulation time. This novel decoding method allows causal investigation of the cortical excitability state, which may be relevant for personalizing and increasing the efficacy of therapeutic brain-state dependent brain stimulation (for example in patients affected by Parkinson’s disease).