9,293 research outputs found

    Scaling up integrated photonic reservoirs towards low-power high-bandwidth computing

    No full text

    Decoding spatial location of attended audio-visual stimulus with EEG and fNIRS

    Get PDF
    When analyzing complex scenes, humans often focus their attention on an object at a particular spatial location in the presence of background noises and irrelevant visual objects. The ability to decode the attended spatial location would facilitate brain computer interfaces (BCI) for complex scene analysis. Here, we tested two different neuroimaging technologies and investigated their capability to decode audio-visual spatial attention in the presence of competing stimuli from multiple locations. For functional near-infrared spectroscopy (fNIRS), we targeted dorsal frontoparietal network including frontal eye field (FEF) and intra-parietal sulcus (IPS) as well as superior temporal gyrus/planum temporal (STG/PT). They all were shown in previous functional magnetic resonance imaging (fMRI) studies to be activated by auditory, visual, or audio-visual spatial tasks. We found that fNIRS provides robust decoding of attended spatial locations for most participants and correlates with behavioral performance. Moreover, we found that FEF makes a large contribution to decoding performance. Surprisingly, the performance was significantly above chance level 1s after cue onset, which is well before the peak of the fNIRS response. For electroencephalography (EEG), while there are several successful EEG-based algorithms, to date, all of them focused exclusively on auditory modality where eye-related artifacts are minimized or controlled. Successful integration into a more ecological typical usage requires careful consideration for eye-related artifacts which are inevitable. We showed that fast and reliable decoding can be done with or without ocular-removal algorithm. Our results show that EEG and fNIRS are promising platforms for compact, wearable technologies that could be applied to decode attended spatial location and reveal contributions of specific brain regions during complex scene analysis

    MUFFLE: Multi-Modal Fake News Influence Estimator on Twitter

    Get PDF
    To alleviate the impact of fake news on our society, predicting the popularity of fake news posts on social media is a crucial problem worthy of study. However, most related studies on fake news emphasize detection only. In this paper, we focus on the issue of fake news influence prediction, i.e., inferring how popular a fake news post might become on social platforms. To achieve our goal, we propose a comprehensive framework, MUFFLE, which captures multi-modal dynamics by encoding the representation of news-related social networks, user characteristics, and content in text. The attention mechanism developed in the model can provide explainability for social or psychological analysis. To examine the effectiveness of MUFFLE, we conducted extensive experiments on real-world datasets. The experimental results show that our proposed method outperforms both state-of-the-art methods of popularity prediction and machine-based baselines in top-k NDCG and hit rate. Through the experiments, we also analyze the feature importance for predicting fake news influence via the explainability provided by MUFFLE

    Classification of Anomalies in Gastrointestinal Tract Using Deep Learning

    Get PDF
    Automatic detection of diseases and anatomical landmarks in medical images by the use of computers is important and considered a challenging process that could help medical diagnosis and reduce the cost and time of investigational procedures and refine health care systems all over the world. Recently, gastrointestinal (GI) tract disease diagnosis through endoscopic image classification is an active research area in the biomedical field. Several GI tract disease classification methods based on image processing and machine learning techniques have been proposed by diverse research groups in the recent past. However, yet effective and comprehensive deep ensemble neural network-based classification model with high accuracy classification results is not available in the literature. In this thesis, we review ways and mechanisms to use deep learning techniques to research on multi-disease computer-aided detection about gastrointestinal and identify these images. We re-trained five state-of-the-art neural network architectures, VGG16, ResNet, MobileNet, Inception-v3, and Xception on the Kvasir dataset to classify eight categories that include an anatomical landmark (pylorus, z-line, cecum), a diseased state (esophagitis, ulcerative colitis, polyps), or a medical procedure (dyed lifted polyps, dyed resection margins) in the Gastrointestinal Tract. Our models have showed results with a promising accuracy which is a remarkable performance with respect to the state-of-the-art approaches. The resulting accuracies achieved using VGG, ResNet, MobileNet, Inception-v3, and Xception were 98.3%, 92.3%, 97.6%, 90% and 98.2%, respectively. As it appears, the most accurate result has been achieved when retraining VGG16 and Xception neural networks with accuracy reache to 98% due to its high performance on training on ImageNet dataset and internal structure that support classification problems

    The Role of Transient Vibration of the Skull on Concussion

    Get PDF
    Concussion is a traumatic brain injury usually caused by a direct or indirect blow to the head that affects brain function. The maximum mechanical impedance of the brain tissue occurs at 450±50 Hz and may be affected by the skull resonant frequencies. After an impact to the head, vibration resonance of the skull damages the underlying cortex. The skull deforms and vibrates, like a bell for 3 to 5 milliseconds, bruising the cortex. Furthermore, the deceleration forces the frontal and temporal cortex against the skull, eliminating a layer of cerebrospinal fluid. When the skull vibrates, the force spreads directly to the cortex, with no layer of cerebrospinal fluid to reflect the wave or cushion its force. To date, there is few researches investigating the effect of transient vibration of the skull. Therefore, the overall goal of the proposed research is to gain better understanding of the role of transient vibration of the skull on concussion. This goal will be achieved by addressing three research objectives. First, a MRI skull and brain segmentation automatic technique is developed. Due to bones’ weak magnetic resonance signal, MRI scans struggle with differentiating bone tissue from other structures. One of the most important components for a successful segmentation is high-quality ground truth labels. Therefore, we introduce a deep learning framework for skull segmentation purpose where the ground truth labels are created from CT imaging using the standard tessellation language (STL). Furthermore, the brain region will be important for a future work, thus, we explore a new initialization concept of the convolutional neural network (CNN) by orthogonal moments to improve brain segmentation in MRI. Second, the creation of a novel 2D and 3D Automatic Method to Align the Facial Skeleton is introduced. An important aspect for further impact analysis is the ability to precisely simulate the same point of impact on multiple bone models. To perform this task, the skull must be precisely aligned in all anatomical planes. Therefore, we introduce a 2D/3D technique to align the facial skeleton that was initially developed for automatically calculating the craniofacial symmetry midline. In the 2D version, the entire concept of using cephalometric landmarks and manual image grid alignment to construct the training dataset was introduced. Then, this concept was extended to a 3D version where coronal and transverse planes are aligned using CNN approach. As the alignment in the sagittal plane is still undefined, a new alignment based on these techniques will be created to align the sagittal plane using Frankfort plane as a framework. Finally, the resonant frequencies of multiple skulls are assessed to determine how the skull resonant frequency vibrations propagate into the brain tissue. After applying material properties and mesh to the skull, modal analysis is performed to assess the skull natural frequencies. Finally, theories will be raised regarding the relation between the skull geometry, such as shape and thickness, and vibration with brain tissue injury, which may result in concussive injury

    Robustness against adversarial attacks on deep neural networks

    Get PDF
    While deep neural networks have been successfully applied in several different domains, they exhibit vulnerabilities to artificially-crafted perturbations in data. Moreover, these perturbations have been shown to be transferable across different networks where the same perturbations can be transferred between different models. In response to this problem, many robust learning approaches have emerged. Adversarial training is regarded as a mainstream approach to enhance the robustness of deep neural networks with respect to norm-constrained perturbations. However, adversarial training requires a large number of perturbed examples (e.g., over 100,000 examples are required for MNIST dataset) trained on the deep neural networks before robustness can be considerably enhanced. This is problematic due to the large computational cost of obtaining attacks. Developing computationally effective approaches while retaining robustness against norm-constrained perturbations remains a challenge in the literature. In this research we present two novel robust training algorithms based on Monte-Carlo Tree Search (MCTS) [1] to enhance robustness under norm-constrained perturbations [2, 3]. The first algorithm searches potential candidates with Scale Invariant Feature Transform method and makes decisions with Monte-Carlo Tree Search method [2]. The second algorithm adopts Decision Tree Search method (DTS) to accelerate the search process while maintaining efficiency [3]. Our overarching objective is to provide computationally effective approaches that can be deployed to train deep neural networks robust against perturbations in data. We illustrate the robustness with these algorithms by studying the resistances to adversarial examples obtained in the context of the MNIST and CIFAR10 datasets. For MNIST, the results showed an average training efforts saving of 21.1\% when compared to Projected Gradient Descent (PGD) and 28.3\% when compared to Fast Gradient Sign Methods (FGSM). For CIFAR10, we obtained an average improvement of efficiency of 9.8\% compared to PGD and 13.8\% compared to FGSM. The results suggest that these two methods here introduced are not only robust to norm-constrained perturbations but also efficient during training. In regards to transferability of defences, our experiments [4] reveal that across different network architectures, across a variety of attack methods from white-box to black-box and across various datasets including MNIST and CIFAR10, our algorithms outperform other state-of-the-art methods, e.g., PGD and FGSM. Furthermore, the derived attacks and robust models obtained on our framework are reusable in the sense that the same norm-constrained perturbations can facilitate robust training across different networks. Lastly, we investigate the robustness of intra-technique and cross-technique transferability and the relations with different impact factors from adversarial strength to network capacity. The results suggest that known attacks on the resulting models are less transferable than those models trained by other state-of-the-art attack algorithms. Our results suggest that exploiting these tree search frameworks can result in significant improvements in the robustness of deep neural networks while saving computational cost on robust training. This paves the way for several future directions, both algorithmic and theoretical, as well as numerous applications to establish the robustness of deep neural networks with increasing trust and safety.Open Acces

    Machine learning for managing structured and semi-structured data

    Get PDF
    As the digitalization of private, commercial, and public sectors advances rapidly, an increasing amount of data is becoming available. In order to gain insights or knowledge from these enormous amounts of raw data, a deep analysis is essential. The immense volume requires highly automated processes with minimal manual interaction. In recent years, machine learning methods have taken on a central role in this task. In addition to the individual data points, their interrelationships often play a decisive role, e.g. whether two patients are related to each other or whether they are treated by the same physician. Hence, relational learning is an important branch of research, which studies how to harness this explicitly available structural information between different data points. Recently, graph neural networks have gained importance. These can be considered an extension of convolutional neural networks from regular grids to general (irregular) graphs. Knowledge graphs play an essential role in representing facts about entities in a machine-readable way. While great efforts are made to store as many facts as possible in these graphs, they often remain incomplete, i.e., true facts are missing. Manual verification and expansion of the graphs is becoming increasingly difficult due to the large volume of data and must therefore be assisted or substituted by automated procedures which predict missing facts. The field of knowledge graph completion can be roughly divided into two categories: Link Prediction and Entity Alignment. In Link Prediction, machine learning models are trained to predict unknown facts between entities based on the known facts. Entity Alignment aims at identifying shared entities between graphs in order to link several such knowledge graphs based on some provided seed alignment pairs. In this thesis, we present important advances in the field of knowledge graph completion. For Entity Alignment, we show how to reduce the number of required seed alignments while maintaining performance by novel active learning techniques. We also discuss the power of textual features and show that graph-neural-network-based methods have difficulties with noisy alignment data. For Link Prediction, we demonstrate how to improve the prediction for unknown entities at training time by exploiting additional metadata on individual statements, often available in modern graphs. Supported with results from a large-scale experimental study, we present an analysis of the effect of individual components of machine learning models, e.g., the interaction function or loss criterion, on the task of link prediction. We also introduce a software library that simplifies the implementation and study of such components and makes them accessible to a wide research community, ranging from relational learning researchers to applied fields, such as life sciences. Finally, we propose a novel metric for evaluating ranking results, as used for both completion tasks. It allows for easier interpretation and comparison, especially in cases with different numbers of ranking candidates, as encountered in the de-facto standard evaluation protocols for both tasks.Mit der rasant fortschreitenden Digitalisierung des privaten, kommerziellen und öffentlichen Sektors werden immer größere Datenmengen verfügbar. Um aus diesen enormen Mengen an Rohdaten Erkenntnisse oder Wissen zu gewinnen, ist eine tiefgehende Analyse unerlässlich. Das immense Volumen erfordert hochautomatisierte Prozesse mit minimaler manueller Interaktion. In den letzten Jahren haben Methoden des maschinellen Lernens eine zentrale Rolle bei dieser Aufgabe eingenommen. Neben den einzelnen Datenpunkten spielen oft auch deren Zusammenhänge eine entscheidende Rolle, z.B. ob zwei Patienten miteinander verwandt sind oder ob sie vom selben Arzt behandelt werden. Daher ist das relationale Lernen ein wichtiger Forschungszweig, der untersucht, wie diese explizit verfügbaren strukturellen Informationen zwischen verschiedenen Datenpunkten nutzbar gemacht werden können. In letzter Zeit haben Graph Neural Networks an Bedeutung gewonnen. Diese können als eine Erweiterung von CNNs von regelmäßigen Gittern auf allgemeine (unregelmäßige) Graphen betrachtet werden. Wissensgraphen spielen eine wesentliche Rolle bei der Darstellung von Fakten über Entitäten in maschinenlesbaren Form. Obwohl große Anstrengungen unternommen werden, so viele Fakten wie möglich in diesen Graphen zu speichern, bleiben sie oft unvollständig, d. h. es fehlen Fakten. Die manuelle Überprüfung und Erweiterung der Graphen wird aufgrund der großen Datenmengen immer schwieriger und muss daher durch automatisierte Verfahren unterstützt oder ersetzt werden, die fehlende Fakten vorhersagen. Das Gebiet der Wissensgraphenvervollständigung lässt sich grob in zwei Kategorien einteilen: Link Prediction und Entity Alignment. Bei der Link Prediction werden maschinelle Lernmodelle trainiert, um unbekannte Fakten zwischen Entitäten auf der Grundlage der bekannten Fakten vorherzusagen. Entity Alignment zielt darauf ab, gemeinsame Entitäten zwischen Graphen zu identifizieren, um mehrere solcher Wissensgraphen auf der Grundlage einiger vorgegebener Paare zu verknüpfen. In dieser Arbeit stellen wir wichtige Fortschritte auf dem Gebiet der Vervollständigung von Wissensgraphen vor. Für das Entity Alignment zeigen wir, wie die Anzahl der benötigten Paare reduziert werden kann, während die Leistung durch neuartige aktive Lerntechniken erhalten bleibt. Wir erörtern auch die Leistungsfähigkeit von Textmerkmalen und zeigen, dass auf Graph-Neural-Networks basierende Methoden Schwierigkeiten mit verrauschten Paar-Daten haben. Für die Link Prediction demonstrieren wir, wie die Vorhersage für unbekannte Entitäten zur Trainingszeit verbessert werden kann, indem zusätzliche Metadaten zu einzelnen Aussagen genutzt werden, die oft in modernen Graphen verfügbar sind. Gestützt auf Ergebnisse einer groß angelegten experimentellen Studie präsentieren wir eine Analyse der Auswirkungen einzelner Komponenten von Modellen des maschinellen Lernens, z. B. der Interaktionsfunktion oder des Verlustkriteriums, auf die Aufgabe der Link Prediction. Außerdem stellen wir eine Softwarebibliothek vor, die die Implementierung und Untersuchung solcher Komponenten vereinfacht und sie einer breiten Forschungsgemeinschaft zugänglich macht, die von Forschern im Bereich des relationalen Lernens bis hin zu angewandten Bereichen wie den Biowissenschaften reicht. Schließlich schlagen wir eine neuartige Metrik für die Bewertung von Ranking-Ergebnissen vor, wie sie für beide Aufgaben verwendet wird. Sie ermöglicht eine einfachere Interpretation und einen leichteren Vergleich, insbesondere in Fällen mit einer unterschiedlichen Anzahl von Kandidaten, wie sie in den de-facto Standardbewertungsprotokollen für beide Aufgaben vorkommen

    Deep Learning Language Models for music analysis and generation

    Get PDF
    [Abstract] In this project, we tackle the problem of predicting the next note in a monophonic musical piece. We choose a symbolic representation and extract it from digital sheet music. The problem is approached as four separate tasks, each of them corresponding to a specific property of the musical note. For each task, we compare the performance of both single and multi-output deep learning algorithms. Despite the severe class imbalance in our dataset, our models manage to generate balanced predictions for the four features.[Resumo] Neste proxecto tratamos o problema de predicir a seguinte nota nunha peza musical monofónica. Escollemos unha representación simbólica e extraémola dun conxunto de partituras dixitais. Afrontamos o problema como catro tarefas de predicción de propiedades inherentes á nota musical. Para cada tarefa, comparamos o rendemento de algoritmos de aprendizaxe profundo dunha e varias saídas. Aínda que o conxunto de datos está moi descompensado, os nosos modelos son capaces de xerar predicións equilibradas nos catro problemas.Traballo fin de grao. Enxeñaría Informática. Curso 2021/202

    Cis-Regulation of Gremlin1 Expression during Mouse Limb Bud Development and its Diversification during Vertebrate Evolution

    Get PDF
    Embryonic development and organogenesis rely on tightly controlled gene expression, which is achieved by cis-regulatory modules (CRMs) interacting with distinct transcription factors (TFs) that control spatio-temporal and tissue-specific gene expression. During organogenesis, gene regulatory networks (GRNs) with selfregulatory feedback properties coordinately control growth and patterning and provide systemic robustness against genetic and/or environmental perturbations. During limb bud development, various interlinked GRNs control outgrowth and patterning along all three limb axes. A paradigm network is the epithelial-mesenchymal (e-m) SHH/GREM1/AER-FGF feedback signaling system which controls limb bud outgrowth and digit patterning. The BMP antagonist GREMLIN1 (GREM1) is central to this e-m interactions as its antagonism of BMP activity is essential to maintain both AER-Fgf and Shh expression. In turn, SHH signaling upregulates Grem1 expression, which results in establishment of a self-regulatory signaling network. One previous study provided evidence that several CRMs could regulate Grem1 expression during limb bud development. However, the cis-regulatory logics underlying the spatio-temporal regulation of the Grem1 expression dynamics remained obscure. From an evolutionary point of view, diversification of CRMs can result in diversification of gene regulation which can drive the establishment of morphological novelties and adaptions. This was evidenced by the observed differences in Grem1 expression in different species that correlates with the evolutionary plasticity of tetrapod digit patterning. Hence, a better understanding of spatio-temporal regulation of the Grem1 expression dynamics and underlying cis-regulatory logic is of interest from both adevelopmental and an evolutionary perspective. Recently, multiple candidate CRMs have been identified that might be functionally relevant for Grem1 expression during mouse limb bud development. For my PhD project, I genetically analyzed which of these CRMs are involved in the regulation of the spatial-temporal Grem1 expression dynamics in limb buds. Therefore, we generated various single and compound CRM mutant alleles using CRISPR/Cas9. Our CRMs allelic series revealed a complex Grem1 cis-regulation among a minimum of six CRMs, where a subset of CRMs regulates Grem1 transcript levels in an additive manner. Surprisingly, phenotypic robustness depends not on threshold transcript levels but the spatial integrity of the Grem1 expression domain. In particular, interactions among five CRMs control the characteristic asymmetrical and posteriorly biased Grem1 expression in mouse limb buds. Our results provide an example of how multiple seemingly redundant limb-specific CRMs provide phenotypical robustness by cooperative/synergistic regulation of the spatial Grem1 expression dynamics. Three CRMs are conserved along the phylogeny of extant vertebrates with paired appendages. Of those, the activities of two CRMs recapitulate the major spatiotemporal aspects of Grem1 expression in mouse limb buds. In order to study their functions in species-specific regulation of Grem1 expression and their functional diversification in tetrapods, I tested the orthologous of both CRMs from representative species using LacZ reporter assays in transgenic mice, in comparison to the endogenous Grem1 expression in limb buds of the species of origin. Surprisingly, the activities of CRM orthologues display high evolutionary plasticity, which correlates better with the Grem1 expression pattern in limb buds of the species of origin than its mouse orthologue. This differential responsiveness to the GRNs in mouse suggests that TF binding site alterations in CRMs could underlie the spatial diversification of Grem1 in limb buds during tetrapod evolution. While the fish fin and tetrapod limb share some homologies of proximal bones, the autopod is a neomorphic feature of tetrapods. The Grem1 requirement for digit patterning and conserved expression in fin buds prompted us to assess the enhancer activity of fish CRM orthologues in transgenic mice. Surprisingly, all tested fish CRMs are active in the mouse autopod primordia providing strong evidence that Grem1 CRMs are active in fin buds and that they predate the fin-to-limb transition. Our results corroborate increasing evidence that CRMs governing autopodial gene expression have been co-opted during the emergence of tetrapod autopod. Furthermore, as part of a collaboration with Dr. S. Jhanwar, I contributed to the study of shared and species-specific epigenomic and genomic variations during mouse and chicken limb bud development. In this analysis, Dr. S. Jhanwar identified putative enhancers that show higher chicken-specific sequence turnover rates in comparison to their mouse orthologues, which defines them as so-called chicken accelerated regions (CARs). Here, I analyzed the CAR activities in comparison to their mouse orthologues by transgenic LacZ reporter assays, which was complemented by analysis of the endogenous gene expression in limb buds of both species. This analysis indicates that diversified activity of CARs and their mouse orthologues could be linked to the differential gene expression patterns in limb buds of both species

    Developing automated meta-research approaches in the preclinical Alzheimer's disease literature

    Get PDF
    Alzheimer’s disease is a devastating neurodegenerative disorder for which there is no cure. A crucial part of the drug development pipeline involves testing therapeutic interventions in animal disease models. However, promising findings in preclinical experiments have not translated into clinical trial success. Reproducibility has often been cited as a major issue affecting biomedical research, where experimental results in one laboratory cannot be replicated in another. By using meta-research (research on research) approaches such as systematic reviews, researchers aim to identify and summarise all available evidence relating to a specific research question. By conducting a meta-analysis, researchers can also combine the results from different experiments statistically to understand the overall effect of an intervention and to explore reasons for variations seen across different publications. Systematic reviews of the preclinical Alzheimer’s disease literature could inform decision making, encourage research improvement, and identify gaps in the literature to guide future research. However, due to the vast amount of potentially useful evidence from animal models of Alzheimer’s disease, it remains difficult to make sense of and utilise this data effectively. Systematic reviews are common practice within evidence based medicine, yet their application to preclinical research is often limited by the time and resources required. In this thesis, I develop, build-upon, and implement automated meta-research approaches to collect, curate, and evaluate the preclinical Alzheimer’s literature. I searched several biomedical databases to obtain all research relevant to Alzheimer’s disease. I developed a novel deduplication tool to automatically identify and remove duplicate publications identified across different databases with minimal human effort. I trained a crowd of reviewers to annotate a subset of the publications identified and used this data to train a machine learning algorithm to screen through the remaining publications for relevance. I developed text-mining tools to extract model, intervention, and treatment information from publications and I improved existing automated tools to extract reported measures to reduce the risk of bias. Using these tools, I created a categorised database of research in transgenic Alzheimer’s disease animal models and created a visual summary of this dataset on an interactive, openly accessible online platform. Using the techniques described, I also identified relevant publications within the categorised dataset to perform systematic reviews of two key outcomes of interest in transgenic Alzheimer’s disease models: (1) synaptic plasticity and transmission in hippocampal slices and (2) motor activity in the open field test. Over 400,000 publications were identified across biomedical research databases, with 230,203 unique publications. In a performance evaluation across different preclinical datasets, the automated deduplication tool I developed could identify over 97% of duplicate citations and a had an error rate similar to that of human performance. When evaluated on a test set of publications, the machine learning classifier trained to identify relevant research in transgenic models performed was highly sensitive (captured 96.5% of relevant publications) and excluded 87.8% of irrelevant publications. Tools to identify the model(s) and outcome measure(s) within the full-text of publications may reduce the burden on reviewers and were found to be more sensitive than searching only the title and abstract of citations. Automated tools to assess risk of bias reporting were highly sensitive and could have the potential to monitor research improvement over time. The final dataset of categorised Alzheimer’s disease research contained 22,375 publications which were then visualised in the interactive web application. Within the application, users can see how many publications report measures to reduce the risk of bias and how many have been classified as using each transgenic model, testing each intervention, and measuring each outcome. Users can also filter to obtain curated lists of relevant research, allowing them to perform systematic reviews at an accelerated pace with reduced effort required to search across databases, and a reduced number of publications to screen for relevance. Both systematic reviews and meta-analyses highlighted failures to report key methodological information within publications. Poor transparency of reporting limited the statistical power I had to understand the sources of between-study variation. However, some variables were found to explain a significant proportion of the heterogeneity. Transgenic animal model had a significant impact on results in both reviews. For certain open field test outcomes, wall colour of the open field arena and the reporting of measures to reduce the risk of bias were found to impact results. For in vitro electrophysiology experiments measuring synaptic plasticity, several electrophysiology parameters, including magnesium concentration of the recording solution, were found to explain a significant proportion of the heterogeneity. Automated meta-research approaches and curated web platforms summarising preclinical research could have the potential to accelerate the conduct of systematic reviews and maximise the potential of existing evidence to inform translation
    corecore