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Register a new userIdentifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering
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Added by
Boleslaw Szymanski
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional clustering methods detect non-overlapping communities. These detected communities may also be unstable and difficult to replicate, because traditional methods are sensitive to noise and parameter settings. These aspects of traditional clustering methods limit our ability to detect biological communities, and therefore our ability to understand biological functions. To address these limitations and detect robust overlapping biological communities, we propose an unorthodox clustering method called SpeakEasy which identifies communities using top-down and bottom-up approaches simultaneously. Specifically, nodes join communities based on their local connections, as well as global information about the network structure. This method can quantify the stability of each community, automatically identify the number of communities, and quickly cluster networks with hundreds of thousands of nodes. SpeakEasy shows top performance on synthetic clustering benchmarks and accurately identifies meaningful biological communities in a range of datasets, including: gene microarrays, protein interactions, sorted cell populations, electrophysiology and fMRI brain imaging.
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In monocular video 3D multi-person pose estimation, inter-person occlusion and close interactions can cause human detection to be erroneous and human-joints grouping to be unreliable. Existing top-down methods rely on human detection and thus suffer from these problems. Existing bottom-up methods do not use human detection, but they process all persons at once at the same scale, causing them to be sensitive to multiple-persons scale variations. To address these challenges, we propose the integration of top-down and bottom-up approaches to exploit their strengths. Our top-down network estimates human joints from all persons instead of one in an image patch, making it robust to possible erroneous bounding boxes. Our bottom-up network incorporates human-detection based normalized heatmaps, allowing the network to be more robust in handling scale variations. Finally, the estimated 3D poses from the top-down and bottom-up networks are fed into our integration network for final 3D poses. Besides the integration of top-down and bottom-up networks, unlike existing pose discriminators that are designed solely for single person, and consequently cannot assess natural inter-person interactions, we propose a two-person pose discriminator that enforces natural two-person interactions. Lastly, we also apply a semi-supervised method to overcome the 3D ground-truth data scarcity. Our quantitative and qualitative evaluations show the effectiveness of our method compared to the state-of-the-art baselines.
Two-dimensional (2D) materials have been a hot research topic in the last decade, due to novel fundamental physics in the reduced dimension and appealing applications. Systematic discovery of functional 2D materials has been the focus of many studies. Here, we present a large dataset of 2D materials, with more than 6,000 monolayer structures, obtained from both top-down and bottom-up discovery procedures. First, we screened all bulk materials in the database of Materials Project for layered structures by a topology-based algorithm, and theoretically exfoliate them into monolayers. Then, we generated new 2D materials by chemical substitution of elements in known 2D materials by others from the same group in the periodic table. The structural, electronic and energetic properties of these 2D materials are consistently calculated, to provide a starting point for further material screening, data mining, data analysis and artificial intelligence applications. We present the details of computational methodology, data record and technical validation of our publicly available data (http://www.2dmatpedia.org/).
We consider the task of learning a classifier for semantic segmentation using weak supervision in the form of image labels which specify the object classes present in the image. Our method uses deep convolutional neural networks (CNNs) and adopts an Expectation-Maximization (EM) based approach. We focus on the following three aspects of EM: (i) initialization; (ii) latent posterior estimation (E-step) and (iii) the parameter update (M-step). We show that saliency and attention maps, our bottom-up and top-down cues respectively, of simple images provide very good cues to learn an initialization for the EM-based algorithm. Intuitively, we show that before trying to learn to segment complex images, it is much easier and highly effective to first learn to segment a set of simple images and then move towards the complex ones. Next, in order to update the parameters, we propose minimizing the combination of the standard softmax loss and the KL divergence between the true latent posterior and the likelihood given by the CNN. We argue that this combination is more robust to wrong predictions made by the expectation step of the EM method. We support this argument with empirical and visual results. Extensive experiments and discussions show that: (i) our method is very simple and intuitive; (ii) requires only image-level labels; and (iii) consistently outperforms other weakly-supervised state-of-the-art methods with a very high margin on the PASCAL VOC 2012 dataset.
We present a comprehensive review of recent developments in the field of chiral plasmonics. Significant advances have been made recently in understanding the working principles of chiral plasmonic structures. With advances in micro- and nanofabrication techniques, a variety of chiral plasmonic nanostructures have been experimentally realized; these tailored chiroptical properties vastly outperform those of their molecular counterparts. We focus on chiral plasmonic nanostructures created using bottom-up approaches, which not only allow for rational design and fabrication but most intriguingly in many cases also enable dynamic manipulation and tuning of chiroptical responses. We first discuss plasmon-induced chirality, resulting from the interaction of chiral molecules with plasmonic excitations. Subsequently, we discuss intrinsically chiral colloids, which give rise to optical chirality owing to their chiral shapes. Finally, we discuss plasmonic chirality, achieved by arranging achiral plasmonic particles into handed configurations on static or active templates. Chiral plasmonic nanostructures are very promising candidates for real-life applications owing to their significantly larger optical chirality than natural molecules. In addition, chiral plasmonic nanostructures offer engineerable and dynamic chiroptical responses, which are formidable to achieve in molecular systems. We thus anticipate that the field of chiral plasmonics will attract further widespread attention in applications ranging from enantioselective analysis to chiral sensing, structural determination, and in situ ultrasensitive detection of multiple disease biomarkers, as well as optical monitoring of transmembrane transport and intracellular metabolism.
Fully supervised object detection has achieved great success in recent years. However, abundant bounding boxes annotations are needed for training a detector for novel classes. To reduce the human labeling effort, we propose a novel webly supervised object detection (WebSOD) method for novel classes which only requires the web images without further annotations. Our proposed method combines bottom-up and top-down cues for novel class detection. Within our approach, we introduce a bottom-up mechanism based on the well-trained fully supervised object detector (i.e. Faster RCNN) as an object region estimator for web images by recognizing the common objectiveness shared by base and novel classes. With the estimated regions on the web images, we then utilize the top-down attention cues as the guidance for region classification. Furthermore, we propose a residual feature refinement (RFR) block to tackle the domain mismatch between web domain and the target domain. We demonstrate our proposed method on PASCAL VOC dataset with three different novel/base splits. Without any target-domain novel-class images and annotations, our proposed webly supervised object detection model is able to achieve promising performance for novel classes. Moreover, we also conduct transfer learning experiments on large scale ILSVRC 2013 detection dataset and achieve state-of-the-art performance.
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