IMCAD: Computer Aided System for Breast Masses Detection based on Immune Recognition

Computer Aided Detection (CAD) systems are very important tools which help radiologists as a second reader in detecting early breast cancer in an efficient way, specially on screening mammograms. One of the challenging problems is the detection of masses, which are powerful signs of cancer, because of their poor apperance on mammograms. This paper investigates an automatic CAD for detection of breast masses in screening mammograms based on fuzzy segmentation and a bio-inspired method for pattern recognition: Artificial Immune Recognition System. The proposed approach is applied to real clinical images from the full field digital mammographic database: Inbreast. In order to validate our proposition, we propose the Receiver Operating Characteristic Curve as an analyzer of our IMCAD classifier system, which achieves a good area under curve, with a sensitivity of 100% and a specificity of 95%. The recognition system based on artificial immunity has shown its efficiency on recognizing masses from a very restricted set of training regions

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments

Automatic Wi-Fi Fingerprint System based on Unsupervised Learning

Recently, smartphones and Wi-Fi appliances have been generalized in daily life, and location-based service(LBS) has gradually been extended to indoor environments. Unlike outdoor positioning, which is typically handled by the global positioning system(GPS), indoor positioning technologies for providing LBSs have been studied with algorithms using various short-range wireless communications such as Wi-Fi, Ultra-wideband, Bluetooth, etc. Fingerprint-based positioning technology, a representative indoor LBS, estimates user locations using the received signal strength indicator(RSSI), indicating the relative transmission power of the access point(AP). Therefore, a fingerprint-based algorithm has the advantage of being robust to distorted wireless environments, such as radio wave reflections and refractions, compared to the time-of-arrival(TOA) method for non-line-of-sight(NLOS), where many obstacles exist. Fingerprint is divided into a training phase in which a radio map is generated by measuring the RSSIs of all indoor APs and positioning phase in which the positions of users are estimated by comparing the RSSIs of the generated radio map in real-time. In the training phase, the user collects the RSSIs of all APs measured at reference points set at regular intervals of 2 to 3m, creating a radio map. In the positioning phase, the reference point, which is most similar to the RSSI, compares the generated radio map from the training phase to the RSSI measured from user movements. This estimates the real-time indoor position. Fingerprint algorithms based on supervised and semi-supervised learning such as support vector machines and principal component analysis are essential for measuring the RSSIs in all indoor areas to produce a radio map. As the building size and the complexity of structures increases, the amount of work and time required also increase. The radio map generation algorithm that uses channel modeling does not require direct measurement, but it requires considerable effort because of building material, three-dimensional reflection coefficient, and numerical modeling of all obstacles. To overcome these problems, this thesis proposes an automatic Wi-Fi fingerprint system that combines an unsupervised dual radio mapping(UDRM) algorithm that reduces the time taken to acquire Wi-Fi signals and leverages an indoor environment with a minimum description length principle(MDLP)-based radio map feedback(RMF) algorithm to simultaneously optimize and update the radio map. The proposed UDRM algorithm in the training phase generates a radio map of the entire building based on the measured radio map of one reference floor by selectively applying the autoencoder and the generative adversarial network(GAN) according to the spatial structures. The proposed learning-based UDRM algorithm does not require labeled data, which is essential for supervised and semi-supervised learning algorithms. It has a relatively low dependency on RSSI datasets. Additionally, it has a high accuracy of radio map prediction than existing models because it learns the indoor environment simultaneously via a indoor two-dimensional map(2-D map). The produced radio map is used to estimate the real-time positioning of users in the positioning phase. Simultaneously, the proposed MDLP-based RMF algorithm analyzes the distribution characteristics of the RSSIs of newly measured APs and feeds the analyzed results back to the radio map. The MDLP, which is applied to the proposed algorithm, improves the performance of the positioning and optimizes the size of the radio map by preventing the indefinite update of the RSSI and by updating the newly added APs to the radio map. The proposed algorithm is compared with a real measurement-based radio map, confirming the high stability and accuracy of the proposed fingerprint system. Additionally, by generating a radio map of indoor areas with different structures, the proposed system is shown to be robust against the change in indoor environment, thus reducing the time cost. Finally, via a euclidean distance-based experiment, it is confirmed that the accuracy of the proposed fingerprint system is almost the same as that of the RSSI-based fingerprint system.|최근 스마트폰과 Wi-Fi가 실생활에 보편화되면서 위치기반 서비스에 대한 개발 분야가 실내 환경으로 점차 확대되고 있다. GPS로 대표되는 실외 위치 인식과 달리 위치기반 서비스를 제공하기 위한 실내 위치 인식 기술은 Wi-Fi, UWB, 블루투스 등과 같은 다양한 근거리 무선 통신 기반의 알고리즘들이 연구되고 있다. 대표적인 실내 위치인식 알고리즘 중 하나인 Fingerprint는 사용자가 수신한 AP 신호의 상대적인 크기를 나타내는 RSSI를 사용하여 위치를 추정한다. 따라서 Fingerprint기반의 알고리즘은 장애물이 많이 존재하는 비가시 거리에서 TOA 방식에 비해 전파의 반사 및 굴절과 같이 왜곡된 무선 환경에 강인하다는 장점이 있다. Fingerprint는 실내의 모든 AP의 RSSI들을 측정하여 Radio map을 제작하는 과정인 학습 단계와 생성된 Radio map의 RSSI들을 실시간으로 측정된 RSSI와 비교하여 사용자의 위치를 추정하는 위치인식 단계로 나누어진다. 학습 단계에서는 위치를 구분하기 위하여 사용자가 2~3m의 일정한 간격으로 설정된 참조 위치들마다 측정되는 모든 AP들의 RSSI를 수집하고 Radio map으로 제작한다. 위치인식 단계에서는 학습 단계에서 제작된 Radio map과 사용자의 이동에 의해 측정되는 RSSI의 비교를 통해 가장 유사한 RSSI 패턴을 가지는 참조 위치가 실시간 실내 위치로 추정된다. 서포트 벡터 머신(SVM), 주성분 분석(PCA) 등과 같이 지도 및 준지도 학습기반의 Fingerprint 알고리즘은 Radio map을 제작하기 위해 모든 실내 공간에서 RSSI의 측정이 필수적이다. 이러한 알고리즘들은 건물이 대형화되고 구조가 복잡해질수록 측정 공간이 늘어나면서 작업과 시간 소모가 또한 급격히 증가한다. 채널모델링을 통한 Radio map 생성 알고리즘은 직접적인 측정 과정이 불필요한 반면에 건물의 재질, 3차원적인 구조에 따른 반사 계수 및 모든 장애물에 대한 수치적인 모델링이 필수적이기 때문에 상당히 많은 작업량이 요구된다. 따라서 본 논문에서는 이러한 문제점들을 해결하고자 학습 단계에서 Wi-Fi 신호의 수집시간을 최소화하면서 실내 환경이 고려된 Unsupervised Dual Radio Mapping(UDRM) 알고리즘과 위치인식 단계에서 Radio map의 최적화가 동시에 가능한 Minimum description length principle(MDLP)기반의 Radio map Feedback(RMF) 알고리즘이 결합된 비지도학습기반의 자동 Wi-Fi Fingerprint를 제안한다. 학습 단계에서 제안하는 UDRM 알고리즘은 뉴럴 네트워크 기반의 비지도 학습 알고리즘인 Autoencoder와 Generative Adversarial Network (GAN)를 공간구조에 따라 선택적으로 적용하여 하나의 참조 층에서 측정된 Radio map을 기반으로 건물전체의 Radio map을 생성한다. 제안하는 비지도 학습 기반 UDRM 알고리즘은 지도 및 준지도 학습에서 필수적인 Labeled data가 필요하지 않으며 RSSI 데이터 세트의 의존성이 상대적으로 낮다. 또한 2차원 실내 지도를 통해 실내 환경을 동시에 학습하기 때문에 기존의 예측 모델에 비해 Radio map의 예측 정확도가 높다. 제안한 알고리즘에 의해 제작된 Radio map은 위치인식 단계에서 사용자의 실시간 위치인식에 적용된다. 동시에 제안하는 MDLP 기반의 자동 Wi-Fi 업데이트 알고리즘은 새롭게 측정되는 AP들의 RSSI의 분포특성을 분석하고 그 결과를 Radio map에 피드백한다. 제안한 알고리즘에 적용된 MDLP는 무분별한 RSSI의 업데이팅을 방지하고 추가되는 AP를 Radio map에 업데이트함으로서 위치인식의 성능을 향상시키고 Radio map의 크기의 최적화가 가능하다. 제안한 알고리즘은 실제 측정기반의 Radio map과 서로 비교를 통해 제안한 Fingerprint 시스템의 높은 안정성과 정확도를 확인하였다. 또한 구조가 다른 실내공간의 Radio map 생성 결과를 통해 실내 환경 변화에 강인함과 학습 시간 측정을 통한 시간 비용이 감소함을 확인하였다. 마지막으로 Euclidean distance 기반 실험을 통하여 실제 측정한 RSSI기반의 Fingerprint 시스템과 제안한 시스템의 위치인식 정확도가 거의 일치함을 확인하였다.Contents Contents ⅰ Lists of Figures and Tables ⅲ Abstract ⅵ Chapter 1 Introduction 01 1.1 Background and Necessity for Research 01 1.2 Objectives and Contents for Research 04 Chapter 2 Wi-Fi Positioning and Unsupervised Learning 07 2.1 Wi-Fi Positioning 07 2.1.1 Wi-Fi Signal and Fingerprint 07 2.1.2 Fingerprint Techniques 15 2.2 Unsupervised Learning 23 2.2.1 Neural Network 23 2.2.2 Autoencoder 28 2.2.3 Generative Adversarial Network 31 Chapter 3 Proposed Fingerprint System 36 3.1 Unsupervised Dual Radio Mapping Algorithm 36 3.2 MDLP-based Radio Map Feedback Algorithm 47 Chapter 4 Experiment and Result 51 4.1 Experimental Environment and Configuration 51 4.2 Results of Unsupervised Dual Radio Mapping Algorithm 56 4.2 Results of MDLP-based Radio Map Feedback Algorithm 69 Chapter 5 Conclusion 79 Reference 81Docto

A Comprehensive Review of Bio-Inspired Optimization Algorithms Including Applications in Microelectronics and Nanophotonics

The application of artificial intelligence in everyday life is becoming all-pervasive and unavoidable. Within that vast field, a special place belongs to biomimetic/bio-inspired algorithms for multiparameter optimization, which find their use in a large number of areas. Novel methods and advances are being published at an accelerated pace. Because of that, in spite of the fact that there are a lot of surveys and reviews in the field, they quickly become dated. Thus, it is of importance to keep pace with the current developments. In this review, we first consider a possible classification of bio-inspired multiparameter optimization methods because papers dedicated to that area are relatively scarce and often contradictory. We proceed by describing in some detail some more prominent approaches, as well as those most recently published. Finally, we consider the use of biomimetic algorithms in two related wide fields, namely microelectronics (including circuit design optimization) and nanophotonics (including inverse design of structures such as photonic crystals, nanoplasmonic configurations and metamaterials). We attempted to keep this broad survey self-contained so it can be of use not only to scholars in the related fields, but also to all those interested in the latest developments in this attractive area

Complexity in Developmental Systems: Toward an Integrated Understanding of Organ Formation

During animal development, embryonic cells assemble into intricately structured organs by working together in organized groups capable of implementing tightly coordinated collective behaviors, including patterning, morphogenesis and migration. Although many of the molecular components and basic mechanisms underlying such collective phenomena are known, the complexity emerging from their interplay still represents a major challenge for developmental biology. Here, we first clarify the nature of this challenge and outline three key strategies for addressing it: precision perturbation, synthetic developmental biology, and data-driven inference. We then present the results of our effort to develop a set of tools rooted in two of these strategies and to apply them to uncover new mechanisms and principles underlying the coordination of collective cell behaviors during organogenesis, using the zebrafish posterior lateral line primordium as a model system. To enable precision perturbation of migration and morphogenesis, we sought to adapt optogenetic tools to control chemokine and actin signaling. This endeavor proved far from trivial and we were ultimately unable to derive functional optogenetic constructs. However, our work toward this goal led to a useful new way of perturbing cortical contractility, which in turn revealed a potential role for cell surface tension in lateral line organogenesis. Independently, we hypothesized that the lateral line primordium might employ plithotaxis to coordinate organ formation with collective migration. We tested this hypothesis using a novel optical tool that allows targeted arrest of cell migration, finding that contrary to previous assumptions plithotaxis does not substantially contribute to primordium guidance. Finally, we developed a computational framework for automated single-cell segmentation, latent feature extraction and quantitative analysis of cellular architecture. We identified the key factors defining shape heterogeneity across primordium cells and went on to use this shape space as a reference for mapping the results of multiple experiments into a quantitative atlas of primordium cell architecture. We also propose a number of data-driven approaches to help bridge the gap from big data to mechanistic models. Overall, this study presents several conceptual and methodological advances toward an integrated understanding of complex multi-cellular systems

IST Austria Thesis

Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity

Microarray image processing: A novel neural network framework

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.Aleppo University, Syri

miRNA Dysregulation Drives Neuronal Intracellular Chloride Accumulation in Down Syndrome

Down syndrome (DS) is caused by the presence of an extra-copy of chromosome 21 and is the most frequent genetic cause of mental retardation. DS cognitive disabilities primary arise from the triplication of dosage-sensitive genes on chromosome 21. However, a global dysregulation in the expression of extra-chromosome 21 genes greatly complicates the understanding of the underling pathological mechanisms. We have recently found that cognitive impairment in the Ts65Dn mouse model of DS depends on the upregulation of a non-triplicated gene encoding for the chloride importer NKCC1, which we found increased also in brain tissue from individuals with DS. Consequently, the intracellular chloride concentration is increased and GABAergic signaling, through chloride-permeable GABAA receptors, is depolarizing rather than hyperpolarizing. Here, we aimed at addressing the molecular mechanisms responsible for NKCC1 overexpression in DS. Real-time qPRC and Western Blot analysis showed that NKCC1 overexpression in trisomic neurons does not derive from greater mRNA transcription or decreased protein turnover but rather from a diminished translational repression exerted on the 3\u2019 untranslated region (3'UTR) of the gene. As 3\u2019 UTRs are the preferred sites of action of microRNAs (miRs), we applied a combination of bioinformatics prediction tools and gene expression screening to identify candidate miRs downregulated in trisomic samples that could mediate NKCC1 overexpression. Our results show that different candidates miRs interact with NKCC1 3\u2019UTR and repress its expression. Additionally, overexpression of the same miRs can normalize NKCC1 levels and intracellular chloride concentration in trisomic neurons, restoring GABAergic inhibitory signaling at the network level as shown by Multi-Electrode Array recordings. Our findings will help to elucidate molecular pathways dysregulated in DS and suggest possible targets for future therapeutic intervention

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here