Dockground scoring benchmarks for protein docking

Protein docking protocols typically involve global docking scan, followed by re-ranking of the scan predictions by more accurate scoring functions that are either computationally too expensive or algorithmically impossible to include in the global scan. Development and validation of scoring methodologies are often performed on scoring benchmark sets (docking decoys) which offer concise and nonredundant representation of the global docking scan output for a large and diverse set of protein-protein complexes. Two such protein-protein scoring benchmarks were built for the Dockground resource, which contains various datasets for the development and testing of protein docking methodologies. One set was generated based on the Dockground unbound docking benchmark 4, and the other based on protein models from the Dockground model-model benchmark 2. The docking decoys were designed to reflect the reality of the real-case docking applications (e.g., correct docking predictions defined as near-native rather than native structures), and to minimize applicability of approaches not directly related to the development of scoring functions (reducing clustering of predictions in the binding funnel and disparity in structural quality of the near-native and non-native matches). The sets were further characterized by the source organism and the function of the protein-protein complexes. The sets, freely available to the research community on the Dockground webpage, present a unique, user-friendly resource for the developing and testing of protein-protein scoring approaches.

Peramalan Produksi Pertanian Menggunakan Model Long Short-Term Memory

Abstrak: Masalah yang timbul dalam peramalan hasil produksi pertanian antara lain adalah sulit untuk mendapatkan data yang lengkap dari variabel-variabel yang mempengaruhi hasil pertanian dalam jangka panjang. Kondisi ini akan semakin sulit ketika peramalan mencakup wilayah yang cukup luas. Akibatnya, variabel-variabel tersebut harus diinterpolasi sehingga akan menyebabkan bias terhadap hasil peramalan. (1) Mengetahui gambaran meta analisis penelitian peramalan produk pertanian menggunakan Long Short Term Memory (LSTM), (2) Mengetahui penelitian meta analisis cakupan wilayah, komoditi dan periode data terkait produk pertanian terutama gandum, kedelai jagung dan pisang, (3) Mengetahui praproses data antara lain menghilangkan data yang tidak sesuai, menangani data yang kosong, serta memilih variabel tertentu. Sebagai solusi dari masalah tersebut, peramalan hasil produksi pertanian dilakukan berdasarkan data historis hasil produksi pertanian. Salah model peramalan yang saat ini banyak dikembangkan adalah model jaringan syaraf LSTM yang merupakan pengembangan dari model jaringan syaraf recurrent (RNN). Tulisan ini merupakan hasil kajian literatur pengembangan model-model LSTM untuk peramalan hasil produksi pertanian meliputi gandum, kedelai, jagung dan pisang. Perbaikan kinerja model LSTM dilakukan mulai dari praproses, tuning hyperparameter, sampai dengan penggabungan dengan metode lain. Berdasarkan kajian tersebut, model-model LSTM memiliki kinerja yang lebih baik dibandingkan dengan model benchmark. Kata kunci: jaringan syaraf, LSTM, peramalan, produksi pertanian, RNN. Abstract: Problems that arise in forecasting agricultural products include the difficulty of obtaining complete data on the variables that affect agricultural yields in the long term. This condition will be more difficult when the forecast covers a large area. As a result, these variables must be interpolated so that it will cause a bias towards the forecasting results. (1) Knowing the description of research maps for forecasting agricultural products using Long short term memory (LSTM), (2) Knowing Research Coverage areas, commodities, and data periods related to agricultural products, especially Wheat, Soybeans, corn, and bananas, (3) Knowing Preprocessing data between others remove inappropriate data, handle blank data, and select certain variables. This paper is the result of a literature review on the development of LSTM models for crop yields forecasting including wheat, soybeans, corn, and bananas. The Performance Improvements of the LSTM models were carried out by preprocessing data, hyperparameter tuning, and combining LSTM with other methods. Based on this study, LSTM models have better performance compared to the benchmark model. Keywords: neural network, LSTM, forecasting, crop yield, RNN.

CP violating hW+W− coupling in the Standard Model and beyond

Inspired by the recent development in determining the property of the observed Higgs boson, we explore the CP-violating (CPV) $$ -{c}_{\mathrm{CPV}}{hW}^{+\mu \nu}{\tilde{W}}_{\mu \nu}^{-}/\upsilon $$ − c CPV hW + μν W ˜ μν − / υ coupling in the Standard Model (SM) and beyond, where W±μν and $$ {\tilde{W}}^{\pm \mu \nu} $$ W ˜ ± μν denote the W-boson field strength and its dual. To begin with, we show that the leading-order SM contribution to this CPV vertex appears at two-loop level. By summing over the quark flavor indices in the two loop integrals analytically, we can estimate the order of the corresponding Wilson coefficient to be $$ {c}_{\mathrm{CPV}}^{\mathrm{SM}}\sim \mathcal{O}\left({10}^{-23}\right) $$ c CPV SM ∼ O 10 − 23 , which is obviously too small to be probed at the LHC and planned future colliders. Then we investigate this CPV hW+W− interaction in two Beyond the Standard Model benchmark models: the left-right model and the complex 2-Higgs doublet model (C2HDM). Unlike what happens for the SM, the dominant contributions in both models arise at the one-loop level, and the corresponding Wilson coefficient can be as large as of $$ \mathcal{O} $$ O (10−9) in the former model and of $$ \mathcal{O} $$ O (10−3) for the latter. In light of such a large CPV effect in the hW+W− coupling, we also give the formulae for the leading one-loop contribution to the related CPV hZZ effective operator in the complex 2-Higgs doublet model. The order of magnitude of the Wilson coefficients in the C2HDM may be within reach of the high-luminosity LHC or planned future colliders.

Testing for the Effectiveness of Inflation Targeting in India: A Factor Augmented Vector Autoregression (FAVAR) Approach

Employing Factor Augmented Vector Autoregression (FAVAR) model where factors are obtained using the principal component analysis (PCA) and the parameters of the model are estimated using Vector Autoregression framework, we analyse how changes in monetary policy variables impact inflation, output, money supply, and the financial sector in India. Our results for the period 2001:04 to 2016:03 show that the benchmark FAVAR model showed more reliable results than baseline VAR model. Benchmark FAVAR model shows the existence of weak ‘liquidity puzzle’ in India. The impulse responses from the FAVAR approach reveal that monetary policy is more efficient in explaining the variations in inflation rather than stimulating output indicating its effectiveness in attaining the objective of price stability.

Locally tuned hybridized particle swarm optimization for the calibration of the nonlinear Muskingum flood routing model

In the literature about the parameter estimation of the nonlinear Muskingum (NL-MUSK) model, benchmark hydrographs have been subjected to various metaheuristics, and in these studies the minor improvements of the algorithms on objective functions are imposed as ‘state-of-the-art’. With the metaheuristics involving more control variables, the attempt to search global results in a restricted solution space is not actually practical. Although metaheuristics provide reasonable results compared with many derivative methods, they cannot guarantee the same global solution when they run under different initial conditions. In this study, one of the most practical of metaheuristics, the particle swarm optimization (PSO) algorithm, was chosen, and the aim was to develop its local search capability. In this context, the hybrid use of the PSO with the Levenberg–Marquardt (LM) algorithm was considered. It was detected that the hybrid PSO–LM gave stable global solutions as a result of each random experiment in the application for four different flood data. The PSO–LM, which stands out with its stable aspect, also achieved rapid convergence compared with the PSO and another hybrid variant called mutated PSO.

Large-scale biospheric drought response intensifies linearly with drought duration in arid regions

Soil moisture droughts have comprehensive implications for terrestrial ecosystems. Here we study time-accumulated impacts of the strongest observed droughts on vegetation. The results show that drought duration, the time during which surface soil moisture is below seasonal average, is a key diagnostic variable for predicting drought-integrated changes in (i) gross primary productivity, (ii) evapotranspiration, (iii) vegetation greenness, and (iv) crop yields. Drought-integrated anomalies in these vegetation-related variables scale linearly with drought duration with a slope depending on climate. In arid regions, the slope is steep such that vegetation drought response intensifies with drought duration, whereas in humid regions, it is small such that drought impacts on vegetation are weak even for long droughts. These emergent large-scale linearities are not well captured by state-of-the-art hydrological, land surface, and vegetation models. Overall, the linear relationship of drought duration versus vegetation response and crop yield reductions can serve as a model benchmark and support drought impact interpretation and prediction.

Holistic evaluation in multi-model databases benchmarking

A multi-model database (MMDB) is designed to support multiple data models against a single, integrated back-end. Examples of data models include document, graph, relational, and key-value. As more and more platforms are developed to deal with multi-model data, it has become crucial to establish a benchmark for evaluating the performance and usability of MMDBs. In this paper, we propose UniBench, a generic multi-model benchmark for a holistic evaluation of state-of-the-art MMDBs. UniBench consists of a set of mixed data models that mimics a social commerce application, which covers data models including JSON, XML, key-value, tabular, and graph. We propose a three-phase framework to simulate the real-life distributions and develop a multi-model data generator to produce the benchmarking data. Furthermore, in order to generate a comprehensive and unbiased query set, we develop an efficient algorithm to solve a new problem called multi-model parameter curation to judiciously control the query selectivity on diverse models. Finally, the extensive experiments based on the proposed benchmark were performed on four representatives of MMDBs: ArangoDB, OrientDB, AgensGraph and Spark SQL. We provide a comprehensive analysis with respect to internal data representations, multi-model query and transaction processing, and performance results for distributed execution.

Large-scale biospheric drought response intensifies linearly with drought duration

Soil moisture droughts have comprehensive implications for terrestrial ecosystems. Here we study accumulated impacts of the strongest observed droughts on vegetation. The results show that drought duration, the time during which surface soil moisture is below seasonal average, is a key diagnostic variable for predicting drought-integrated changes in (i) gross primary productivity, (ii) evapotranspiration, (iii) vegetation greenness, and (iv) crop yields. Drought-integrated anomalies in these vegetation-related variables scale linearly with drought duration with a slope depending on climate. In arid regions, the slope is steep such that vegetation drought response intensifies with drought duration, whereas in humid regions, it is small such that drought impacts on vegetation are weak even for long droughts. These emergent large-scale linearities are not well captured by state- of-the-art hydrological, land surface and vegetation models. Overall, the linear relationship of drought duration versus vegetation response and crop yield reductions can serve as model benchmark, and support drought impact interpretation and prediction.

Sentiment Analysis Using Cuckoo Search for Optimized Feature Selection on Kaggle Tweets

Selecting the optimal set of features to determine sentiment in online textual content is imperative for superior classification results. Optimal feature selection is computationally hard task and fosters the need for devising novel techniques to improve the classifier performance. In this work, the binary adaptation of cuckoo search (nature inspired, meta-heuristic algorithm) known as the Binary Cuckoo Search is proposed for the optimum feature selection for a sentiment analysis of textual online content. The baseline supervised learning techniques such as SVM, etc., have been firstly implemented with the traditional tf-idf model and then with the novel feature optimization model. Benchmark Kaggle dataset, which includes a collection of tweets is considered to report the results. The results are assessed on the basis of performance accuracy. Empirical analysis validates that the proposed implementation of a binary cuckoo search for feature selection optimization in a sentiment analysis task outperforms the elementary supervised algorithms based on the conventional tf-idf score.