Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic biological processes involving composite genomic aberrations, key challenges are to effectively assimilate information from these domains to identify genomic signatures and biological entities that are druggable, develop accurate risk prediction profiles for future patients, and identify novel patient subgroups for tailored therapy and monitoring. We propose integrative probabilistic frameworks for high-dimensional multiple-domain cancer data that coherently incorporate dependence within and between domains to accurately detect tumor subtypes, thus providing a catalogue of genomic aberrations associated with cancer taxonomy. We propose an innovative, flexible and scalable Bayesian nonparametric framework for simultaneous clustering of both tumor samples and genomic probes. We describe an efficient variable selection procedure to identify relevant genomic aberrations that can potentially reveal underlying drivers of a disease. Although the work is motivated by several investigations related to lung cancer, the proposed methods are broadly applicable in a variety of contexts involving high-dimensional data. The success of the methodology is demonstrated using artificial data and lung cancer omics profiles publicly available from The Cancer Genome Atlas.
相關內容
Developing technology and changing lifestyles have made online grocery delivery applications an indispensable part of urban life. Since the beginning of the COVID-19 pandemic, the demand for such applications has dramatically increased, creating new competitors that disrupt the market. An increasing level of competition might prompt companies to frequently restructure their marketing and product pricing strategies. Therefore, identifying the change patterns in product prices and sales volumes would provide a competitive advantage for the companies in the marketplace. In this paper, we investigate alternative clustering methodologies to group the products based on the price patterns and sales volumes. We propose a novel distance metric that takes into account how product prices and sales move together rather than calculating the distance using numerical values. We compare our approach with traditional clustering algorithms, which typically rely on generic distance metrics such as Euclidean distance, and image clustering approaches that aim to group data by capturing its visual patterns. We evaluate the performances of different clustering algorithms using our custom evaluation metric as well as Calinski Harabasz and Davies Bouldin indices, which are commonly used internal validity metrics. We conduct our numerical study using a propriety price dataset from an online food and grocery delivery company, and the publicly available Favorita sales dataset. We find that our proposed clustering approach and image clustering both perform well for finding the products with similar price and sales patterns within large datasets.
Computing a maximum independent set (MaxIS) is a fundamental NP-hard problem in graph theory, which has important applications in a wide spectrum of fields. Since graphs in many applications are changing frequently over time, the problem of maintaining a MaxIS over dynamic graphs has attracted increasing attention over the past few years. Due to the intractability of maintaining an exact MaxIS, this paper aims to develop efficient algorithms that can maintain an approximate MaxIS with an accuracy guarantee theoretically. In particular, we propose a framework that maintains a $(\frac{\Delta}{2} + 1)$-approximate MaxIS over dynamic graphs and prove that it achieves a constant approximation ratio in many real-world networks. To the best of our knowledge, this is the first non-trivial approximability result for the dynamic MaxIS problem. Following the framework, we implement an efficient linear-time dynamic algorithm and a more effective dynamic algorithm with near-linear expected time complexity. Our thorough experiments over real and synthetic graphs demonstrate the effectiveness and efficiency of the proposed algorithms, especially when the graph is highly dynamic.
Steady-state visual evoked potential (SSVEP) recognition methods are equipped with learning from the subject's calibration data, and they can achieve extra high performance in the SSVEP-based brain-computer interfaces (BCIs), however their performance deteriorate drastically if the calibration trials are insufficient. This study develops a new method to learn from limited calibration data and it proposes and evaluates a novel adaptive data-driven spatial filtering approach for enhancing SSVEPs detection. The spatial filter learned from each stimulus utilizes temporal information from the corresponding EEG trials. To introduce the temporal information into the overall procedure, an multitask learning approach, based on the bayesian framework, is adopted. The performance of the proposed method was evaluated into two publicly available benchmark datasets, and the results demonstrated that our method outperform competing methods by a significant margin.
A High-dimensional and sparse (HiDS) matrix is frequently encountered in a big data-related application like an e-commerce system or a social network services system. To perform highly accurate representation learning on it is of great significance owing to the great desire of extracting latent knowledge and patterns from it. Latent factor analysis (LFA), which represents an HiDS matrix by learning the low-rank embeddings based on its observed entries only, is one of the most effective and efficient approaches to this issue. However, most existing LFA-based models perform such embeddings on a HiDS matrix directly without exploiting its hidden graph structures, thereby resulting in accuracy loss. To address this issue, this paper proposes a graph-incorporated latent factor analysis (GLFA) model. It adopts two-fold ideas: 1) a graph is constructed for identifying the hidden high-order interaction (HOI) among nodes described by an HiDS matrix, and 2) a recurrent LFA structure is carefully designed with the incorporation of HOI, thereby improving the representa-tion learning ability of a resultant model. Experimental results on three real-world datasets demonstrate that GLFA outperforms six state-of-the-art models in predicting the missing data of an HiDS matrix, which evidently supports its strong representation learning ability to HiDS data.
Recognizing the type of connected devices to a network helps to perform security policies. In smart grids, identifying massive number of grid metering terminals based on network traffic analysis is almost blank and existing research has not proposed a targeted end-to-end model to solve the flow classification problem. Therefore, we proposed a hierarchical terminal recognition approach that applies the details of grid data. We have formed a two-level model structure by segmenting the grid data, which uses the statistical characteristics of network traffic and the specific behavior characteristics of grid metering terminals. Moreover, through the selection and reconstruction of features, we combine three algorithms to achieve accurate identification of terminal types that transmit network traffic. We conduct extensive experiments on a real dataset containing three types of grid metering terminals, and the results show that our research has improved performance compared to common recognition models. The combination of an autoencoder, K-Means and GradientBoost algorithm achieved the best recognition rate with F1 value of 98.3%.
Bearing fault identification and analysis is an important research area in the field of machinery fault diagnosis. Aiming at the common faults of rolling bearings, we propose a data-driven diagnostic algorithm based on the characteristics of bearing vibrations called multi-size kernel based adaptive convolutional neural network (MSKACNN). Using raw bearing vibration signals as the inputs, MSKACNN provides vibration feature learning and signal classification capabilities to identify and analyze bearing faults. Ball mixing is a ball bearing production quality problem that is difficult to identify using traditional frequency domain analysis methods since it requires high frequency resolutions of the measurement signals and results in a long analyzing time. The proposed MSKACNN is shown to improve the efficiency and accuracy of ball mixing diagnosis. To further demonstrate the effectiveness of MSKACNN in bearing fault identification, a bearing vibration data acquisition system was developed, and vibration signal acquisition was performed on rolling bearings under five different fault conditions including ball mixing. The resulting datasets were used to analyze the performance of our proposed model. To validate the adaptive ability of MSKACNN, fault test data from the Case Western Reserve University Bearing Data Center were also used. Test results show that MSKACNN can identify the different bearing conditions with high accuracy with high generalization ability. We presented an implementation of the MSKACNN as a lightweight module for a real-time bearing fault diagnosis system that is suitable for production.
Designers reportedly struggle with design optimization tasks where they are asked to find a combination of design parameters that maximizes a given set of objectives. In HCI, design optimization problems are often exceedingly complex, involving multiple objectives and expensive empirical evaluations. Model-based computational design algorithms assist designers by generating design examples during design, however they assume a model of the interaction domain. Black box methods for assistance, on the other hand, can work with any design problem. However, virtually all empirical studies of this human-in-the-loop approach have been carried out by either researchers or end-users. The question stands out if such methods can help designers in realistic tasks. In this paper, we study Bayesian optimization as an algorithmic method to guide the design optimization process. It operates by proposing to a designer which design candidate to try next, given previous observations. We report observations from a comparative study with 40 novice designers who were tasked to optimize a complex 3D touch interaction technique. The optimizer helped designers explore larger proportions of the design space and arrive at a better solution, however they reported lower agency and expressiveness. Designers guided by an optimizer reported lower mental effort but also felt less creative and less in charge of the progress. We conclude that human-in-the-loop optimization can support novice designers in cases where agency is not critical.
Universal coding of integers~(UCI) is a class of variable-length code, such that the ratio of the expected codeword length to $\max\{1,H(P)\}$ is within a constant factor, where $H(P)$ is the Shannon entropy of the decreasing probability distribution $P$. However, if we consider the ratio of the expected codeword length to $H(P)$, the ratio tends to infinity by using UCI, when $H(P)$ tends to zero. To solve this issue, this paper introduces a class of codes, termed generalized universal coding of integers~(GUCI), such that the ratio of the expected codeword length to $H(P)$ is within a constant factor $K$. First, the definition of GUCI is proposed and the coding structure of GUCI is introduced. Next, we propose a class of GUCI $\mathcal{C}$ to achieve the expansion factor $K_{\mathcal{C}}=2$ and show that the optimal GUCI is in the range $1\leq K_{\mathcal{C}}^{*}\leq 2$. Then, by comparing UCI and GUCI, we show that when the entropy is very large or $P(0)$ is not large, there are also cases where the average codeword length of GUCI is shorter. Finally, the asymptotically optimal GUCI is presented.
In recent years, Graph Neural Networks (GNNs), which can naturally integrate node information and topological structure, have been demonstrated to be powerful in learning on graph data. These advantages of GNNs provide great potential to advance social recommendation since data in social recommender systems can be represented as user-user social graph and user-item graph; and learning latent factors of users and items is the key. However, building social recommender systems based on GNNs faces challenges. For example, the user-item graph encodes both interactions and their associated opinions; social relations have heterogeneous strengths; users involve in two graphs (e.g., the user-user social graph and the user-item graph). To address the three aforementioned challenges simultaneously, in this paper, we present a novel graph neural network framework (GraphRec) for social recommendations. In particular, we provide a principled approach to jointly capture interactions and opinions in the user-item graph and propose the framework GraphRec, which coherently models two graphs and heterogeneous strengths. Extensive experiments on two real-world datasets demonstrate the effectiveness of the proposed framework GraphRec. Our code is available at \url{//github.com/wenqifan03/GraphRec-WWW19}
To address the sparsity and cold start problem of collaborative filtering, researchers usually make use of side information, such as social networks or item attributes, to improve recommendation performance. This paper considers the knowledge graph as the source of side information. To address the limitations of existing embedding-based and path-based methods for knowledge-graph-aware recommendation, we propose Ripple Network, an end-to-end framework that naturally incorporates the knowledge graph into recommender systems. Similar to actual ripples propagating on the surface of water, Ripple Network stimulates the propagation of user preferences over the set of knowledge entities by automatically and iteratively extending a user's potential interests along links in the knowledge graph. The multiple "ripples" activated by a user's historically clicked items are thus superposed to form the preference distribution of the user with respect to a candidate item, which could be used for predicting the final clicking probability. Through extensive experiments on real-world datasets, we demonstrate that Ripple Network achieves substantial gains in a variety of scenarios, including movie, book and news recommendation, over several state-of-the-art baselines.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191