Identification of periodic attractors in Boolean networks using a priori information

Boolean networks (BNs) have been developed to describe various biological processes, which requires analysis of attractors, the long-term stable states. While many methods have been proposed to detection and enumeration of attractors, there are no methods which have been demonstrated to be theoretically better than the naive method and be practically used for large biological BNs. Here, we present a novel method to calculate attractors based on a priori information, which works much and verifiably faster than the naive method. We apply the method to two BNs which differ in size, modeling formalism, and biological scope. Despite these differences, the method presented here provides a powerful tool for the analysis of both networks. First, our analysis of a BN studying the effect of the microenvironment during angiogenesis shows that the previously defined microenvironments inducing the specialized phalanx behavior in endothelial cells (ECs) additionally induce stalk behavior. We obtain this result from an extended network version which was previously not analyzed. Second, we were able to heuristically detect attractors in a cell cycle control network formalized as a bipartite Boolean model (bBM) with 3158 nodes. These attractors are directly interpretable in terms of genotype-to-phenotype relationships, allowing network validation equivalent to an in silico mutagenesis screen. Our approach contributes to the development of scalable analysis methods required for whole-cell modeling efforts.

The Method of Bifurcatory Division in Plato’s Sophist

The strange and challenging stretch of dialectic with which Plato’s Sophist begins and ends has confused and frustrated readers for generations, and despite receiving a fair amount of attention, there is no consensus regarding even basic issues concerning this method. Here I offer a new account of bifurcatory division as neither joke nor naïve method, but instead a valuable, propaedeutic method that Plato offers to us readers as a means of embarking upon the kind of mental gymnastics that will stretch us properly in preparation for further, more challenging dialectical work. Considering several interpretive issues, I argue that bifurcatory division is a process of collective inquiry into the common through which an account, both definitional and taxonomical, is discovered. Depending on the level of understanding exhibited by the inquirers, this account may or may not allow for noetic understanding of the object in the deepest sense.

Algorithmic Structures for Realizing Short-Length Circular Convolutions with Reduced Complexity

A set of efficient algorithmic solutions suitable to the fully parallel hardware implementation of the short-length circular convolution cores is proposed. The advantage of the presented algorithms is that they require significantly fewer multiplications as compared to the naive method of implementing this operation. During the synthesis of the presented algorithms, the matrix notation of the cyclic convolution operation was used, which made it possible to represent this operation using the matrix–vector product. The fact that the matrix multiplicand is a circulant matrix allows its successful factorization, which leads to a decrease in the number of multiplications when calculating such a product. The proposed algorithms are oriented towards a completely parallel hardware implementation, but in comparison with a naive approach to a completely parallel hardware implementation, they require a significantly smaller number of hardwired multipliers. Since the wired multiplier occupies a much larger area on the VLSI and consumes more power than the wired adder, the proposed solutions are resource efficient and energy efficient in terms of their hardware implementation. We considered circular convolutions for sequences of lengths N= 2, 3, 4, 5, 6, 7, 8, and 9.

A new method for obtaining a Born cross section using visible cross section data from e+e− colliders

In this paper, we propose a new method for obtaining a Born cross section using visible cross section data. It is assumed that the initial state radiation is taken into account in a visible cross section, while in a Born cross section this effect is ommited. Since the equation that connects Born and visible cross sections is an integral equation of the first kind, the problem of finding its numerical solution is ill-posed. Various regularization-based approaches are often used to solve ill-posed problems, since direct methods usually do not lead to an acceptable result. However, in this paper it is shown that a direct method can be successfully used to numerically solve the considered equation under the condition of a small beam energy spread and uncertainty. This naive method is based on finding a numerical solution to the integral equation by reducing it to a system of linear equations. The naive method works well because the kernel of the integral operator is a rapidly decreasing function of the variable x. This property of the kernel leads to the fact that the condition number of the matrix of the system of linear equations is of the order of unity, which makes it possible to neglect the ill-posedness of the problem when the above condition is satisfied. The advantages of the naive method are its model independence and the possibility of obtaining the covariance matrix of a Born cross section in a simple way.It should be noted that there are already a number of methods for obtaining a Born cross section using visible cross section data, which are commonly used in e+e− experiments. However, at least some of these methods have various disadvantages, such as model dependence and relative complexity of obtaining a Born cross section covariance matrix. It should be noted that this paper focuses on the naive method, while conventional methods are hardly covered. The paper also discusses solving the problem using the Tikhonov regularization, so that the reader can better understand the difference between regularized and non-regularized solutions. However, it should be noted that, in contrast to the naive method, regularization methods can hardly be used for precise obtaining of a Born cross section. The reason is that the regularized solution is biased and the covariance matrix of this solution do not represent the correct covariance matrix of a Born cross section.

A Parallel Algorithm for Dividing Octonions

The article presents a parallel hardware-oriented algorithm designed to speed up the division of two octonions. The advantage of the proposed algorithm is that the number of real multiplications is halved as compared to the naive method for implementing this operation. In the synthesis of the discussed algorithm, the matrix representation of this operation was used, which allows us to present the division of octonions by means of a vector–matrix product. Taking into account a specific structure of the matrix multiplicand allows for reducing the number of real multiplications necessary for the execution of the octonion division procedure.

Automatic identification of differences in behavioral co-occurrence between groups

Background Recent advances in sensing technologies have enabled us to attach small loggers to animals in their natural habitat. It allows measurement of the animals’ behavior, along with associated environmental and physiological data and to unravel the adaptive significance of the behavior. However, because animal-borne loggers can now record multi-dimensional (here defined as multimodal) time series information from a variety of sensors, it is becoming increasingly difficult to identify biologically important patterns hidden in the high-dimensional long-term data. In particular, it is important to identify co-occurrences of several behavioral modes recorded by different sensors in order to understand an internal hidden state of an animal because the observed behavioral modes are reflected by the hidden state. This study proposed a method for automatically detecting co-occurrence of behavioral modes that differs between two groups (e.g., males vs. females) from multimodal time-series sensor data. The proposed method first extracted behavioral modes from time-series data (e.g., resting and cruising modes in GPS trajectories or relaxed and stressed modes in heart rates) and then identified two different behavioral modes that were frequently co-occur (e.g., co-occurrence of the cruising mode and relaxed mode). Finally, behavioral modes that differ between the two groups in terms of the frequency of co-occurrence were identified. Results We demonstrated the effectiveness of our method using animal-locomotion data collected from male and female Streaked Shearwaters by showing co-occurrences of locomotion modes and diving behavior recorded by GPS and water-depth sensors. For example, we found that the behavioral mode of high-speed locomotion and that of multiple dives into the sea were highly correlated in male seabirds. In addition, compared to the naive method, the proposed method reduced the computation costs by about 99.9%. Conclusion Because our method can automatically mine meaningful behavioral modes from multimodal time-series data, it can be potentially applied to analyzing co-occurrences of locomotion modes and behavioral modes from various environmental and physiological data.

Acceleration of Inner-Pairing Product Operation for Secure Biometric Verification

With the recent advances in mobile technologies, biometric verification is being adopted in many smart devices as a means for authenticating their owners. As biometric data leakage may cause stringent privacy issues, many proposals have been offered to guarantee the security of stored biometric data, i.e., biometric template. One of the most promising solutions is the use of a remote server that stores the template in an encrypted form and performs a biometric comparison on the ciphertext domain, using recently proposed functional encryption (FE) techniques. However, the drawback of this approach is that considerable computation is required for the inner-pairing product operation used for the decryption procedure of the underlying FE, which is performed in the authentication phase. In this paper, we propose an enhanced method to accelerate the inner-pairing product computation and apply it to expedite the decryption operation of FE and for faster remote biometric verification. The following two important observations are the basis for our improvement—one of the two arguments for the decryption operation does not frequently change over authentication sessions, and we only need to evaluate the product of multiple pairings, rather than individual pairings. From the results of our experiments, the proposed method reduces the time required to compute an inner-pairing product by 30.7%, compared to the previous best method. With this improvement, the time required for biometric verification is expected to decrease by up to 10.0%, compared to a naive method.

Estimation of Traffic Flow Rate With Data From Connected-Automated Vehicles Using Bayesian Inference and Deep Learning

Connected automated vehicles (CAVs) hold promise to replace current traffic detection systems in the near future. However, traffic state estimation, particularly flow rate, poses a major challenge at low CAV penetration rates without other supporting infrastructure of sensors. This paper proposes flow rate estimation methods using headway data from CAVs. Specifically, Bayesian inference and deep learning based methods are developed and compared with a naïve method based on a simple arithmetic mean of observed headways. The proposed methods are investigated via numerical experiments to evaluate their performance with respect to the CAV penetration rate, traffic demand, and availability of historical data. The methods are further validated with real data. The results show that the Bayesian inference based method, which estimates the flow rate distribution by integrating current (real-time) data and previous knowledge, can perform well even at low penetration rates with good prior information. However, in high CAV penetration, its relative advantage to the other methods diminishes because the prior information always influences the flow rate estimation. The deep learning based method can be effective with a large amount of data to train the model; however, in low CAV penetration, it tends to converge to the mean of target output values regardless of the observed data. At last, in relatively high CAV penetration, the relative advantage of the advanced methods is negligible and in fact, the naïve method is preferred in terms of accuracy as well as efficiency.

GRAMMAR-Lambda: An Extreme Simplification for Genome-wide Mixed Model Association Analysis

A highly efficient genome-wide association method, GRAMMAR-Lambda is proposed to make simple genomic control for the test statistics deflated by GRAMMAR, producing statistical power as high as exact mixed model association method. Using the simulated and real phenotypes, we show that at a moderate or above genomic heritability, polygenic effects can be estimated using a small number of randomly selected markers, which extremely simplify genome-wide association analysis with an approximate computational complexity to naïve method in large-scale complex population. Upon a test at once, joint association analysis offers significant increase in statistical power over existing methods.

Metode Peramalan moving Average, 1000 ANALISIS PERBANDINGAN PERAMALAN PERMINTAAN PELUMAS PT XYZ DENGAN METODE MOVING AVERAGE, EXPONENTIAL SMOOTHING DAN NAIVE METHOD

Pelumas merupakan produk dari PT XYZ yang digunakan untuk kendaraan dan mesin-mesin industri. Peramalan umumnya dilakukan untuk meramalkan jumlah produksi di masa mendatang dengan menggunakan data historis atau data-data pada permintaan sebelumnya terhadap produk perusahaan. Penelitian ini dilakukan untuk menguji enam metode peramalan agar dapat mengetahui metode mana yang tepat untuk diterapkan pada PT XYZ. Peramalan pada PT XYZ ini menggunakan data historis permintaan tahun 2019 dari bulan januari hingga bulan desember yang telah merepresentasikan pola permintaan setiap tahun di PT XYZ. Data ini digunakan untuk meramalkan setahun kedepan.Penelitian kali ini akan membandingkan enam metode peramalan diantaranya metode moving average 3 bulanan, moving average 5 bulanan, exponential smoothing dengan α=0,1, exponential smoothing dengan α=0,5, exponential smoothing dengan α=0,9 dan naive method. Untuk bahan perbandingan dari keenam metode yang telah disebutkan maka diberikan peramalan yaitu dengan metode penyimpangan Mean Absolute Deviation (MAD), Mean Square Error (MSE), Root Mean Square Error (RMSE), dan Absolute Presentage Error (MAPE).Hasil penelitian ini menunjukkan metode peramalan exponential smoothing dengan α=0,9 dengan nilai penyimpangan MAD 2.364,50, MSE 12.448.875,06, RMSE 3.528,30 dan MAPE 0,60 dapat dikatakan metode yang lebih optimal untuk diterapkan di PT XYZ karena memiliki nilai penyimpangan paling rendah dari metode moving average 3 bulanan, moving average 5 bulanan, exponential smoothing dengan α=0,1, exponential smoothing dengan α=0,5 dan naive method.Sehingga PT XYZ untuk menentukan tingkat permintaan konsumen dapat menggunakan metode exponential smoothing dengan α=0,9, karena setelah dilakukan perbandingan dari hasil penyimpangan setiap metode dan telah terbukti bahwasannya metode exponential smoothing dengan α=0,9 memiliki nilai penyimpangan MAD 2.364,60, MSE 12.448.875,06, RMSE 3.528,30 dan MAPE 0,60 yang artinya merupakan nilai penyimpangan terkecil dari metode moving average 3 bulanan, moving average 5 bulanan, exponential smoothing dengan α=0,1, exponential smoothing dengan α=0,5, dan naive method.