BACKGROUND: The progress of the cell cycle of yeast involves the regulatory relationships between genes and the interactions proteins. However, it is still obscure which type of protein plays a decisive role in regulation and how to identify the vital nodes in the regulatory network. To elucidate the sensitive node or gene in the progression of yeast, here, we select 8 crucial regulatory factors from the yeast cell cycle to decipher a specific network and propose a simple mixed K2 algorithm to identify effectively the sensitive nodes and genes in the evolution of yeast. RESULTS: Considering the multivariate of cell cycle data, we first utilize the K2 algorithm limited to the stationary interval for the time series segmentation to measure the scores for refining the specific network. After that, we employ the network entropy to effectively screen the obtained specific network, and simulate the gene expression data by a normal distribution approximation and the screened specific network by the partial least squares method. We can conclude that the robustness of the specific network screened by network entropy is better than that of the specific network with the determined relationship by comparing the obtained specific network with the determined relationship. Finally, we can determine that the node CDH1 has the highest score in the specific network through a sensitivity score calculated by network entropy implying the gene CDH1 is the most sensitive regulatory factor. CONCLUSIONS: It is clearly of great potential value to reconstruct and visualize gene regulatory networks according to gene databases for life activities. Here, we present an available algorithm to achieve the network reconstruction by measuring the network entropy and identifying the vital nodes in the specific nodes. The results indicate that inhibiting or enhancing the expression of CDH1 can maximize the inhibition or enhancement of the yeast cell cycle. Although our algorithm is simple, it is also the first step in deciphering the profound mystery of gene regulation.

This article presents a technique of frequency-dependent implicit capacitance neutralization (FD-ICN) among capacitor bank and varactors in LC voltage-controlled oscillator (VCO) to facilitate ultralow VCO gain ($K_{\text {VCO}}$) across an octave frequency tuning range (TR). Series interconnect inductors are used between capacitor units to feature the inverse capacitance-frequency (C–f) relationship with varactors, thus yielding the proposed FD-ICN. A split 8-bit capacitor bank with centrosymmetric double-cross layout pattern is designed, enabling an enhanced FD-ICN through multiple capacitance equivalent iterations of the capacitor bank. The proposed FD-ICN technique is validated in a prototype of dual-mode electric-coupling VCO and fabricated in 130-nm CMOS process, exhibiting a measured frequency TR of 72.1% from 6.49 to 13.81 GHz with a$K_{\text {VCO}}$of 7–73 MHz/V. The VCO shows a competitive phase noise (PN) and figures-of-merit in TR (FoM$\rm {_{T}}$) from −121.3 to −111.4 dBc/Hz and 197.4 to 201.7 dBc/Hz at 1-MHz offset across the whole TR.

This paper investigates the sequential hypothesis testing problem with online sensor selection and sensor usage constraints. That is, in a sensor network, the fusion center sequentially acquires samples by selecting one “most informative” sensor at each time until a reliable decision can be made. In particular, the sensor selection is carried out in the online fashion since it depends on all the previous samples at each time. Our goal is to develop the sequential test (i.e., stopping rule and decision function) and sensor selection strategy that minimize the expected sample size subject to the constraints on the error probabilities and sensor usages. To this end, we first recast the usage-constrained formulation into a Bayesian optimal stopping problem with different sampling costs for the usage-contrained sensors. The Bayesian problem is then studied under both finite- and infinite-horizon setups, based on which, the optimal solution to the original usage-constrained problem can be readily established. Moreover, by capitalizing on the structures of the optimal solution, a lower bound is obtained for the optimal expected sample size. In addition, we also propose algorithms to approximately evaluate the parameters in the optimal sequential test so that the sensor usage and error probability constraints are satisfied. Finally, numerical experiments are provided to illustrate the theoretical findings, and compare with the existing methods.

This paper considers the sequential composite hypothesis test with multiple sensors. The sensors observe random samples in parallel and communicate with a fusion center, who makes the global decision based on the sensor inputs. On the one hand, in the centralized scenario, where local samples are precisely transmitted to the fusion center, the generalized sequential likelihood ratio test (GSPRT) is shown to be asymptotically optimal in terms of the expected sample size as error rates tend to zero. On the other hand, for systems with limited power and bandwidth resources, decentralized solutions that only send a summary of local samples (we particularly focus on a one-bit communication protocol) to the fusion center is of great importance. To this end, we first consider a decentralized scheme where sensors send their one-bit quantized statistics every fixed period of time to the fusion center. We show that such a uniform sampling and quantization scheme is strictly suboptimal and its suboptimality can be quantified by the KL divergence of the distributions of the quantized statistics under both the hypotheses. We then propose a decentralized GSPRT based on level-triggered sampling. That is, each sensor runs its own GSPRT repeatedly and reports its local decision to the fusion center asynchronously. We show that this scheme is asymptotically optimal as the local thresholds and global thresholds grow large at different rates. Finally, two particular models and their associated applications are studied to compare the centralized and decentralized approaches. Numerical results are provided to demonstrate that the proposed level-triggered sampling based decentralized scheme aligns closely with the centralized scheme with substantially lower communication overhead, and significantly outperforms the uniform sampling and quantization-based decentralized scheme.

This work considers the online sensor selection for the finite-horizon sequential hypothesis testing. In particular, at each step of the sequential test, the “most informative” sensor is selected based on all the previous samples so that the expected sample size is minimized. In addition, certain sensors cannot be used more than their prescribed budgets on average. Under this setup, we show that the optimal sensor selection strategy is a time-variant function of the running hypothesis posterior, and the optimal test takes the form of a truncated sequential probability ratio test. Both of these operations can be obtained through a simplified version of dynamic programming. Numerical results demonstrate that the proposed online approach outperforms the existing offline approach to the order of magnitude.

Dance is a dynamic art form that reflects a wide range of cultural diversity and individuality. With the advancement of motion-capture technology combined with crowd-sourcing and machine learning algorithms, we explore the complex relationship between perceived dance quality/dancer's gender and dance movements/music respectively. As a feasibility study, we construct a computational framework for an analysis-synthesis-feedback loop using a novel multimedia dance-music texture representation. Furthermore, we integrate crowd-sourcing, music and motion-capture data, and machine learning-based methods for dance segmentation, analysis and synthesis of new dancers. A quantitative validation of this framework on a motion-capture dataset of 172 dancers evaluated by more than 400 independent on-line raters demonstrates significant correlation between human perception and the algorithmically intended dance quality or gender of synthesized dancers. The technology illustrated in this work has a high potential to advance the multimedia entertainment industry via dancing with Turks.

We propose a novel regularity-driven framework for facade detection from aerial images of urban scenes. Gini-index is used in our work to form an edge-based regularity metric relating regularity and distribution sparsity. Facade regions are chosen so that these local regularities are maximized. We apply a greedy adaptive region expansion procedure for facade region detection and growing, followed by integer quadratic programming for removing overlapping facades to optimize facade coverage. Our algorithm can handle images that have wide viewing angles and contain more than 200 facades per image. The experimental results on images from three different cities (NYC, Rome, San-Francisco) demonstrate superior performance on facade detection in both accuracy and speed over state of the art methods. We also show an application of our facade detection for effective cross-view facade matching.

We employ hierarchical data association to track players in team sports. Player movements are often complex and highly correlated with both nearby and distant players. A single model would require many degrees of freedom to represent the full motion diversity and could be difficult to use in practice. Instead, we introduce a set of Game Context Features extracted from noisy detections to describe the current state of the match, such as how the players are spatially distributed. Our assumption is that players react to the current situation in only a finite number of ways. As a result, we are able to select an appropriate simplified affinity model for each player and time instant using a random decision forest based on current track and game context features. Our context-conditioned motion models implicitly incorporate complex inter-object correlations while remaining tractable. We demonstrate significant performance improvements over existing multi-target tracking algorithms on basketball and field hockey sequences several minutes in duration and containing 10 and 20 players respectively.

We propose a novel unsupervised method for discovering recurring patterns from a single view. A key contribution of our approach is the formulation and validation of a joint assignment optimization problem where multiple visual words and object instances of a potential recurring pattern are considered simultaneously. The optimization is achieved by a greedy randomized adaptive search procedure (GRASP) with moves specifically designed for fast convergence. We have quantified systematically the performance of our approach under stressed conditions of the input (missing features, geometric distortions). We demonstrate that our proposed algorithm outperforms state of the art methods for recurring pattern discovery on a diverse set of 400+ real world and synthesized test images.

We propose a novel approach for multi-camera autocalibration by observing multiview surveillance video of pedestrians walking through the scene. Unlike existing methods, we do NOT require tracking or explicit correspondences of the same person across time/views. Instead, we take noisy foreground blobs as the only input and rely on a joint optimization framework with robust statistics to achieve accurate calibration under challenging scenarios. First, each individual camera is roughly calibrated into its local World Coordinate System (lWCS) based on analysis of relative 3D pedestrian height distribution. Then, all lWCSs are iteratively registered with respect to a shared global World Coordinate System (gWCS) by incorporating robust matching with a partial Direct Linear Transform (pDLT). As demonstrated by extensive evaluation, our algorithm achieves satisfactory results in various camera settings with up to moderate crowd densities with a large proportion of foreground outliers.

MOTIVATION: Linking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value. RESULTS: We developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles. AVAILABILITY AND IMPLEMENTATION: The software is available at http://www.qanswers.net/GeneTUKit/.

BACKGROUND: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k). RESULTS: We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively. CONCLUSIONS: By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance.

Time-varying spatial patterns are common, but few computational tools exist for discovering and tracking multiple, sometimes overlapping, spatial structures of targets. We propose a multi-target tracking framework that takes advantage of spatial patterns inside the targets even though the number, the form and the regularity of such patterns vary with time. RANSAC-based model fitting algorithms are developed to automatically recognize (or dismiss) (il)legitimate patterns. Patterns are represented using a mixture of Markov Random Fields (MRF) with constraints (local and global) and preferences encoded into pairwise potential functions. To handle pattern variations continuously, we introduce a posterior probability for each spatial pattern modeled as a Bernoulli distribution. Tracking is achieved by inferring the optimal state configurations of the targets using belief propagation on a mixture of MRFs. We have evaluated our formulation on real video data with multiple targets containing time-varying lattice patterns and/or reflection symmetry patterns. Experimental results of our proposed algorithm show superior tracking performance over existing methods.