Search results for: Medical datasets

Authors: Maninder Pal

Abstract:

Medical digital images usually have low resolution because of nature of their acquisition. Therefore, this paper focuses on zooming these images to obtain better level of information, required for the purpose of medical diagnosis. For this purpose, a strategy for selecting pixels in zooming operation is proposed. It is based on the principle of analog clock and utilizes a combination of point and neighborhood image processing. In this approach, the hour hand of clock covers the portion of image to be processed. For alignment, the center of clock points at middle pixel of the selected portion of image. The minute hand is longer in length, and is used to gain information about pixels of the surrounding area. This area is called neighborhood pixels region. This information is used to zoom the selected portion of the image. The proposed algorithm is implemented and its performance is evaluated for many medical images obtained from various sources such as X-ray, Computerized Tomography (CT) scan and Magnetic Resonance Imaging (MRI). However, for illustration and simplicity, the results obtained from a CT scanned image of head is presented. The performance of algorithm is evaluated in comparison to various traditional algorithms in terms of Peak signal-to-noise ratio (PSNR), maximum error, SSIM index, mutual information and processing time. From the results, the proposed algorithm is found to give better performance than traditional algorithms.

Keywords: Zooming, interpolation, medical images, resolution.

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Authors: Panos D. Kotsas, Tony Dodd

Abstract:

2D/3D registration is a special case of medical image registration which is of particular interest to surgeons. Applications of 2D/3D registration are [1] radiotherapy planning and treatment verification, spinal surgery, hip replacement, neurointerventions and aortic stenting. The purpose of this paper is to provide a literature review of the main methods for image registration for the 2D/3D case. At the end of the paper an algorithm is proposed for 2D/3D registration based on the Chebyssev polynomials iteration loop.

Keywords: Medical image registration, review, 2D/3D

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Authors: Naoki Yamamoto, Jun Murakami, Chiharu Okuma, Yutaro Shigeto, Satoko Saito, Takashi Izumi, Nozomi Hayashida

Abstract:

Multi-dimensional principal component analysis (PCA) is the extension of the PCA, which is used widely as the dimensionality reduction technique in multivariate data analysis, to handle multi-dimensional data. To calculate the PCA the singular value decomposition (SVD) is commonly employed by the reason of its numerical stability. The multi-dimensional PCA can be calculated by using the higher-order SVD (HOSVD), which is proposed by Lathauwer et al., similarly with the case of ordinary PCA. In this paper, we apply the multi-dimensional PCA to the multi-dimensional medical data including the functional independence measure (FIM) score, and describe the results of experimental analysis.

Keywords: multi-dimensional principal component analysis, higher-order SVD (HOSVD), functional independence measure (FIM), medical data, tensor decomposition

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Authors: J. Alamelu Mangai, Satej Wagle, V. Santhosh Kumar

Abstract:

The exponential increase in the volume of medical image database has imposed new challenges to clinical routine in maintaining patient history, diagnosis, treatment and monitoring. With the advent of data mining and machine learning techniques it is possible to automate and/or assist physicians in clinical diagnosis. In this research a medical image classification framework using data mining techniques is proposed. It involves feature extraction, feature selection, feature discretization and classification. In the classification phase, the performance of the traditional kNN k nearest neighbor classifier is improved using a feature weighting scheme and a distance weighted voting instead of simple majority voting. Feature weights are calculated using the interestingness measures used in association rule mining. Experiments on the retinal fundus images show that the proposed framework improves the classification accuracy of traditional kNN from 78.57 % to 92.85 %.

Keywords: Medical Image Mining, Data Mining, Feature Weighting, Association Rule Mining, k nearest neighbor classifier.

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Authors: R. Gomathi, D. Sharmila

Abstract:

The emergence of the Semantic Web technology increases day by day due to the rapid growth of multiple web pages. Many standard formats are available to store the semantic web data. The most popular format is the Resource Description Framework (RDF). Querying large RDF graphs becomes a tedious procedure with a vast increase in the amount of data. The problem of query optimization becomes an issue in querying large RDF graphs. Choosing the best query plan reduces the amount of query execution time. To address this problem, nature inspired algorithms can be used as an alternative to the traditional query optimization techniques. In this research, the optimal query plan is generated by the proposed SAPSO algorithm which is a hybrid of Simulated Annealing (SA) and Particle Swarm Optimization (PSO) algorithms. The proposed SAPSO algorithm has the ability to find the local optimistic result and it avoids the problem of local minimum. Experiments were performed on different datasets by changing the number of predicates and the amount of data. The proposed algorithm gives improved results compared to existing algorithms in terms of query execution time.

Keywords: Semantic web, RDF, Query optimization, Nature inspired algorithms, PSO, SA.

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Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

Abstract:

Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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Authors: Jorge Martinez-Garcia, Ingrid Stelzner, Joerg Stelzner, Damian Gwerder, Philipp Schuetz

Abstract:

Tree-ring analysis is an important part of the quality assessment and the dating of (archaeological) wood samples. It provides quantitative data about the whole anatomical ring structure, which can be used, for example, to measure the impact of the fluctuating environment on the tree growth, for the dendrochronological analysis of archaeological wooden artefacts and to estimate the wood mechanical properties. Despite advances in computer vision and edge recognition algorithms, detection and counting of annual rings are still limited to 2D datasets and performed in most cases manually, which is a time consuming, tedious task and depends strongly on the operator’s experience. This work presents an image processing approach to detect the whole 3D tree-ring structure directly from X-ray computed tomography imaging data. The approach relies on a modified Canny edge detection algorithm, which captures fully connected tree-ring edges throughout the measured image stack and is validated on X-ray computed tomography data taken from six wood species.

Keywords: Ring recognition, edge detection, X-ray computed tomography, dendrochronology.

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Authors: Amudha Kadirvelu, Sivalal Sadasivan

Abstract:

While the problem based learning (PBL) approach promotes unsupervised self-directed learning (SDL), many students experience difficulty juggling the role of being an information recipient and information seeker. Logbooks have been used to assess trainee doctors but not in other areas. This study aimed to determine the effectiveness of logbook for assessing SDL during PBL sessions in first year medical students. The log book included a learning checklist and knowledge and skills components. Comparisons with the baseline assessment of student performance in PBL and that at semester end after logbook intervention showed significant improvements in student performance (31.5 ± 8 vs. 17.7 ± 4.4; p<0.001) with a large effect size of 3.93. The learner-s log for PBL has played an important role in enhancing SDL in first year medical students. Learner-s log could be a good self-assessment tool for the undergraduate medical students.

Keywords: Problem based learning, self-directed learning, logbook, self-assessment.

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Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

Abstract:

The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: Aggregation prone regions, amyloids, thermophilic proteins, amino acid residues, machine learning.

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Authors: P. Gnanasekar, A. Nagappan, S. Sharavanan, O. Saravanan, D. Vinodkumar, T. Elayabharathi, G. Karthik

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In this paper we present the deep study about the Bio- Medical Images and tag it with some basic extracting features (e.g. color, pixel value etc). The classification is done by using a nearest neighbor classifier with various distance measures as well as the automatic combination of classifier results. This process selects a subset of relevant features from a group of features of the image. It also helps to acquire better understanding about the image by describing which the important features are. The accuracy can be improved by increasing the number of features selected. Various types of classifications were evolved for the medical images like Support Vector Machine (SVM) which is used for classifying the Bacterial types. Ant Colony Optimization method is used for optimal results. It has high approximation capability and much faster convergence, Texture feature extraction method based on Gabor wavelets etc..

Keywords: ACO Ant Colony Optimization, Correlogram, CCM Co-Occurrence Matrix, RTS Rough-Set theory

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Authors: Chimaobi V. Okolo, Kenneth A. Okpala, Johnbull S. Ogboi

Abstract:

A teeming set of doctors that graduated from various universities within and outside Nigeria with the hope of practicing in the country, has their hope shattered because of poor financing, lack of medical equipments and a very weak healthcare systems. Such hydra headed challenges, allows room for quackery which increasingly contributes to the cause of mortality in Nigeria. With a view of reversing the challenges of healthcare delivery and financing in Nigeria, African Health Market for Equity (AHME), a project funded by the Bill and Melinda Gates foundation [With contribution from Department For International Development (DFID)] and currently implemented in three African Countries (Nigeria, Kenya and Ghana) over a Five (5) year period supports the healthcare sector via Medical credit fund (MCF). The study examines the impact of credit policy and medical credit funding on Nigerian health market. Ordinary least square analysis, correlation and granger causality tests were employed to measure the extent to which the Nigerian healthcare market has been influenced. Medical credit fund significantly and positively influenced average monthly turnover of private healthcare providers and Commercial bank’s lending rate had a weak relationship with access to credit/approved loans (13.46%). The programme has so far made 13.91% progress, which is very poor, considering the minimum targeted private health care providers (437.6) and expected number of loan approvals (180.4) for the two years. Medical credit policy in Nigeria should be revised to include private healthcare providers in rural area for more positive impact and increased returns. Good brand advert and sensitization of the programme to stakeholders and health pressure group, and an extension of the programme beyond five years is necessary to better address the issues raised in the study.

Keywords: Credit, health market, medical credit facility, policy.

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Authors: Jiajun Wang, Xiaoge Li

Abstract:

The purpose of the aspect-level sentiment analysis task is to identify the sentiment polarity of aspects in a sentence. Currently, most methods mainly focus on using neural networks and attention mechanisms to model the relationship between aspects and context, but they ignore the dependence of words in different ranges in the sentence, resulting in deviation when assigning relationship weight to other words other than aspect words. To solve these problems, we propose an aspect-level sentiment analysis model that combines a multi-channel convolutional network and graph convolutional network (GCN). Firstly, the context and the degree of association between words are characterized by Long Short-Term Memory (LSTM) and self-attention mechanism. Besides, a multi-channel convolutional network is used to extract the features of words in different ranges. Finally, a convolutional graph network is used to associate the node information of the dependency tree structure. We conduct experiments on four benchmark datasets. The experimental results are compared with those of other models, which shows that our model is better and more effective.

Keywords: Aspect-level sentiment analysis, attention, multi-channel convolution network, graph convolution network, dependency tree.

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Authors: Mafarja Majdi, Salwani Abdullah, Najmeh S. Jaddi

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One of the global combinatorial optimization problems in machine learning is feature selection. It concerned with removing the irrelevant, noisy, and redundant data, along with keeping the original meaning of the original data. Attribute reduction in rough set theory is an important feature selection method. Since attribute reduction is an NP-hard problem, it is necessary to investigate fast and effective approximate algorithms. In this paper, we proposed two feature selection mechanisms based on memetic algorithms (MAs) which combine the genetic algorithm with a fuzzy record to record travel algorithm and a fuzzy controlled great deluge algorithm, to identify a good balance between local search and genetic search. In order to verify the proposed approaches, numerical experiments are carried out on thirteen datasets. The results show that the MAs approaches are efficient in solving attribute reduction problems when compared with other meta-heuristic approaches.

Keywords: Rough Set Theory, Attribute Reduction, Fuzzy Logic, Memetic Algorithms, Record to Record Algorithm, Great Deluge Algorithm.

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Authors: Osamah M. Al-Qershi, Khoo Bee Ee

Abstract:

In recent years image watermarking has become an important research area in data security, confidentiality and image integrity. Many watermarking techniques were proposed for medical images. However, medical images, unlike most of images, require extreme care when embedding additional data within them because the additional information must not affect the image quality and readability. Also the medical records, electronic or not, are linked to the medical secrecy, for that reason, the records must be confidential. To fulfill those requirements, this paper presents a lossless watermarking scheme for DICOM images. The proposed a fragile scheme combines two reversible techniques based on difference expansion for patient's data hiding and protecting the region of interest (ROI) with tamper detection and recovery capability. Patient's data are embedded into ROI, while recovery data are embedded into region of non-interest (RONI). The experimental results show that the original image can be exactly extracted from the watermarked one in case of no tampering. In case of tampered ROI, tampered area can be localized and recovered with a high quality version of the original area.

Keywords: DICOM, reversible, ROI-based, watermarking.

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Authors: Megha Gupta, Nupur Prakash

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Identification of plant diseases has been performed using machine learning and deep learning models on the datasets containing images of healthy and diseased plant leaves. The current study carries out an evaluation of some of the deep learning models based on convolutional neural network architectures for identification of plant diseases. For this purpose, the publicly available New Plant Diseases Dataset, an augmented version of PlantVillage dataset, available on Kaggle platform, containing 87,900 images has been used. The dataset contained images of 26 diseases of 14 different plants and images of 12 healthy plants. The CNN models selected for the study presented in this paper are AlexNet, ZFNet, VGGNet (four models), GoogLeNet, and ResNet (three models). The selected models are trained using PyTorch, an open-source machine learning library, on Google Colaboratory. A comparative study has been carried out to analyze the high degree of accuracy achieved using these models. The highest test accuracy and F1-score of 99.59% and 0.996, respectively, were achieved by using GoogLeNet with Mini-batch momentum based gradient descent learning algorithm.

Keywords: comparative analysis, convolutional neural networks, deep learning, plant disease identification

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Authors: L. Major, J. M. Lackner, M. Dyner, B. Major

Abstract:

Development of new generation bio-tribological, multilayer coatings opens an avenue for fabrication of future hightech functional surfaces. In the presented work, nano-composite, Cr/CrN+[Cr/ a-C:H implanted by metallic nanocrystals] multilayer coatings have been developed for surface protection of medical tools. Thin films were fabricated by a hybrid Pulsed Laser Deposition technique. Complex microstructure analysis of nanomultilayer coatings, subjected to mechanical and biological tests, were performed by means of transmission electron microscopy (TEM). Microstructure characterization revealed the layered arrangement of Cr23C6 nanoparticles in multilayer structure. Influence of deposition conditions on bio-tribological properties of the coatings was studied. The bio-tests were used as a screening tool for the analyzed nanomultilayer coatings before they could be deposited on medical tools. Bio-medical tests were done using fibroblasts. The mechanical properties of the coatings were investigated by means of a ball-ondisc mechanical test. The micro hardness was done using Berkovich indenter. The scratch adhesion test was done using Rockwell indenter. From the bio-tribological point of view, the optimal properties had the C106_1 material.

Keywords: Bio-tribological coatings, cell-material interaction, hybrid PLD, tribology.

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Authors: Shinoj T. K, Sunil Jacob John

Abstract:

In this paper a new concept named Intuitionistic Fuzzy Multiset is introduced. The basic operations on Intuitionistic Fuzzy Multisets such as union, intersection, addition, multiplication etc. are discussed. An application of Intuitionistic Fuzzy Multiset in Medical diagnosis problem using a distance function is discussed in detail.

Keywords: Intuitionistic Fuzzy set, Multiset, Intuitionistic Fuzzy Multiset

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Authors: M. Karbakhsh, M. Shamseddini Motlagh, M. Khansari

Abstract:

The purpose of this research was to demonstrate prevalence of post-exposure preventive measures (PEP) after needlestick injuries and its relationship with locus of control beliefs in a sample of medical students. In this cross-sectional study, 300 medical students with history of having experienced needle stick injuries (NSI) for at least once filled in a questionnaire to determine if they perceived themselves to be responsible and effective in preventing blood born infections after NSI. About 38% of students did not seek any professional consult or PEP after NSI due to lack of enough time or access, anxiety about tests results, belief in uselessness of followup and not being able to change destiny. These 114 students were not different from others regarding their scores on NSI specific scale of locus of health control. Thus, the potentiality of NSI locus of control beliefs in predicting PEP was not seen in this study.

Keywords: health care workers, locus of health control, needle stick injuries, post-exposure prevention.

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Authors: Ayman M. Mansour

Abstract:

In this paper, we propose a multi-agent intelligent system that is used for monitoring the health conditions of elderly people. Monitoring the health condition of elderly people is a complex problem that involves different medical units and requires continuous monitoring. Such expert system is highly needed in rural areas because of inadequate number of available specialized physicians or nurses. Such monitoring must have autonomous interactions between these medical units in order to be effective. A multi-agent system is formed by a community of agents that exchange information and proactively help one another to achieve the goal of elderly monitoring. The agents in the developed system are equipped with intelligent decision maker that arms them with the rule-based reasoning capability that can assist the physicians in making decisions regarding the medical condition of elderly people.

Keywords: Fuzzy Logic, Inference system, Monitoring system, Multi-agent system.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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Authors: R. Bremananth

Abstract:

Several computationally challenging issues are encountered while classifying complex natural scenes. In this paper, we address the problems that are encountered in rotation invariance with multi-intensity analysis for multi-scene overlapping. In the present literature, various algorithms proposed techniques for multi-intensity analysis, but there are several restrictions in these algorithms while deploying them in multi-scene overlapping classifications. In order to resolve the problem of multi-scenery overlapping classifications, we present a framework that is based on macro and micro basis functions. This algorithm conquers the minimum classification false alarm while pigeonholing multi-scene overlapping. Furthermore, a quadrangle multi-intensity decay is invoked. Several parameters are utilized to analyze invariance for multi-scenery classifications such as rotation, classification, correlation, contrast, homogeneity, and energy. Benchmark datasets were collected for complex natural scenes and experimented for the framework. The results depict that the framework achieves a significant improvement on gray-level matrix of co-occurrence features for overlapping in diverse degree of orientations while pigeonholing multi-scene overlapping.

Keywords: Automatic classification, contrast, homogeneity, invariant analysis, multi-scene analysis, overlapping.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

Abstract:

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: G. Aloisio, L. T. De Paolis, A. De Mauro, A. Mongelli

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One of the essential requirements of a realistic surgical simulator is to reproduce haptic sensations due to the interactions in the virtual environment. However, the interaction need to be performed in real-time, since a delay between the user action and the system reaction reduces the immersion sensation. In this paper, a prototype of a coronary stent implant simulator is present; this system allows real-time interactions with an artery by means of a specific haptic device. To improve the realism of the simulation, the building of the virtual environment is based on real patients- images and a Web Portal is used to search in the geographically remote medical centres a virtual environment with specific features in terms of pathology or anatomy. The functional architecture of the system defines several Medical Centres in which virtual environments built from the real patients- images and related metadata with specific features in terms of pathology or anatomy are stored. The searched data are downloaded from the Medical Centre to the Training Centre provided with a specific haptic device and with the software necessary both to manage the interaction in the virtual environment. After the integration of the virtual environment in the simulation system it is possible to perform training on the specific surgical procedure.

Keywords: Medical Simulation, Web Portal, Virtual Reality.

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Authors: Mariyam Arif, Ye Liu, Israr Ul Haq, Ahsan Ashfaq

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High cost of fossil fuels and intensifying installations of alternate energy generation sources are intimidating main challenges in power systems. Making accurate load forecasting an important and challenging task for optimal energy planning and management at both distribution and generation side. There are many techniques to forecast load but each technique comes with its own limitation and requires data to accurately predict the forecast load. Artificial Neural Network (ANN) is one such technique to efficiently forecast the load. Comparison between two different ranges of input datasets has been applied to dynamic ANN technique using MATLAB Neural Network Toolbox. It has been observed that selection of input data on training of a network has significant effects on forecasted results. Day-wise input data forecasted the load accurately as compared to year-wise input data. The forecasted load is then distributed among the six generators by using the linear programming to get the optimal point of generation. The algorithm is then verified by comparing the results of each generator with their respective generation limits.

Keywords: Artificial neural networks, demand-side management, economic dispatch, linear programming, power generation dispatch.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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Authors: Apoorva Vinod, Archana Mathur, Snehanshu Saha

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Though there exists a plethora of Activation Functions (AFs) used in single and multiple hidden layer Neural Networks (NN), their behavior always raised curiosity, whether used in combination or singly. The popular AFs – Sigmoid, ReLU, and Tanh – have performed prominently well for shallow and deep architectures. Most of the time, AFs are used singly in multi-layered NN, and, to the best of our knowledge, their performance is never studied and analyzed deeply when used in combination. In this manuscript, we experiment on multi-layered NN architecture (both on shallow and deep architectures; Convolutional NN and VGG16) and investigate how well the network responds to using two different AFs (Sigmoid-Tanh, Tanh-ReLU, ReLU-Sigmoid) used alternately against a traditional, single (Sigmoid-Sigmoid, Tanh-Tanh, ReLU-ReLU) combination. Our results show that on using two different AFs, the network achieves better accuracy, substantially lower loss, and faster convergence on 4 computer vision (CV) and 15 Non-CV (NCV) datasets. When using different AFs, not only was the accuracy greater by 6-7%, but we also accomplished convergence twice as fast. We present a case study to investigate the probability of networks suffering vanishing and exploding gradients when using two different AFs. Additionally, we theoretically showed that a composition of two or more AFs satisfies Universal Approximation Theorem (UAT).

Keywords: Activation Function, Universal Approximation function, Neural Networks, convergence.

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Authors: Nicoletta Adamo-Villani, Gerardo Beni, Jeremy White

Abstract:

We introduce, a new interactive 3D simulation system of ocular motion and expressions suitable for: (1) character animation applications to game design, film production, HCI (Human Computer Interface), conversational animated agents, and virtual reality; (2) medical applications (ophthalmic neurological and muscular pathologies: research and education); and (3) real time simulation of unconscious cognitive and emotional responses (for use, e.g., in psychological research). The system is comprised of: (1) a physiologically accurate parameterized 3D model of the eyes, eyelids, and eyebrow regions; and (2) a prototype device for realtime control of eye motions and expressions, including unconsciously produced expressions, for application as in (1), (2), and (3) above. The 3D eye simulation system, created using state-of-the-art computer animation technology and 'optimized' for use with an interactive and web deliverable platform, is, to our knowledge, the most advanced/realistic available so far for applications to character animation and medical pedagogy.

Keywords: 3D animation, HCI, medical simulation, ocularmotion and expression.

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Authors: Nicoletta Adamo-Villani, Gerardo Beni, Jeremy White

Abstract:

We introduce a new interactive 3D simulator of ocular motion and expressions suitable for: (1) character animation applications to game design, film production, HCI (Human Computer Interface), conversational animated agents, and virtual reality; (2) medical applications (ophthalmic neurological and muscular pathologies: research and education); and (3) real time simulation of unconscious cognitive and emotional responses (for use, e.g., in psychological research). Using state-of-the-art computer animation technology we have modeled and rigged a physiologically accurate 3D model of the eyes, eyelids, and eyebrow regions and we have 'optimized' it for use with an interactive and web deliverable platform. In addition, we have realized a prototype device for realtime control of eye motions and expressions, including unconsciously produced expressions, for application as in (1), (2), and (3) above. The 3D simulator of eye motion and ocular expression is, to our knowledge, the most advanced/realistic available so far for applications in character animation and medical pedagogy.

Keywords: 3D animation, HCI, medical simulation, ocularmotion and expression.

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Authors: Ghada Badr, Arwa Alturki

Abstract:

The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Alignment, RNA secondary structure, pairwise, component-based, data mining.

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Authors: A. F. Ali, D. M. Shawky

Abstract:

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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