Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods

ChemPhysChem ◽  
2020 ◽  
Vol 21 (23) ◽  
pp. 2599-2604
Author(s):  
Jindřich Fanfrlík ◽  
Adam Pecina ◽  
Jan Řezáč ◽  
Martin Lepšík ◽  
Menyhárt B. Sárosi ◽  
...  
Keyword(s):  
Computational Methods ◽  
Data Sets ◽  
Boron Cluster ◽  
Benchmark Data ◽  
Dihydrogen Bonding

The Computational Models of Drug-target Interaction Prediction

2020 ◽  
Vol 27 (5) ◽  
pp. 348-358 ◽  
Author(s):  
Yijie Ding ◽  
Jijun Tang ◽  
Fei Guo
Keyword(s):  
Machine Learning ◽  
Computational Methods ◽  
Drug Target ◽  
Computational Models ◽  
Data Sets ◽  
Target Interaction ◽  
Interaction Prediction ◽  
The Past ◽  
Benchmark Data ◽  
Precision Recall Curve

:The identification of Drug-Target Interactions (DTIs) is an important process in drug discovery and medical research. However, the tradition experimental methods for DTIs identification are still time consuming, extremely expensive and challenging. In the past ten years, various computational methods have been developed to identify potential DTIs. In this paper, the identification methods of DTIs are summarized. What's more, several state-of-the-art computational methods are mainly introduced, containing network-based method and machine learning-based method. In particular, for machine learning-based methods, including the supervised and semisupervised models, have essential differences in the approach of negative samples. Although these effective computational models in identification of DTIs have achieved significant improvements, network-based and machine learning-based methods have their disadvantages, respectively. These computational methods are evaluated on four benchmark data sets via values of Area Under the Precision Recall curve (AUPR).

Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

2021 ◽  
Vol 17 (3) ◽  
pp. 1548-1561
Author(s):  
Kristian Kříž ◽  
Martin Nováček ◽  
Jan Řezáč
Keyword(s):  
Data Sets ◽  
Benchmark Data ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Bayesian Trigonometric Support Vector Classifier

2003 ◽  
Vol 15 (9) ◽  
pp. 2227-2254 ◽  
Author(s):  
Wei Chu ◽  
S. Sathiya Keerthi ◽  
Chong Jin Ong
Keyword(s):  
Loss Function ◽  
Gaussian Processes ◽  
Likelihood Function ◽  
Support Vector ◽  
Data Sets ◽  
Model Adaptation ◽  
Bayesian Techniques ◽  
Benchmark Data ◽  
Support Vector Classifier ◽  
Set Up

This letter describes Bayesian techniques for support vector classification. In particular, we propose a novel differentiable loss function, called the trigonometric loss function, which has the desirable characteristic of natural normalization in the likelihood function, and then follow standard gaussian processes techniques to set up a Bayesian framework. In this framework, Bayesian inference is used to implement model adaptation, while keeping the merits of support vector classifier, such as sparseness and convex programming. This differs from standard gaussian processes for classification. Moreover, we put forward class probability in making predictions. Experimental results on benchmark data sets indicate the usefulness of this approach.

scholarly journals AA-HMM: An Anti-Adversarial Hidden Markov Model for Network-Based Intrusion Detection

2018 ◽  
Vol 8 (12) ◽  
pp. 2421 ◽  
Author(s):  
Chongya Song ◽  
Alexander Pons ◽  
Kang Yen
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Performance Metrics ◽  
Hidden Markov ◽  
Data Sets ◽  
Learning Abilities ◽  
Benchmark Data ◽  
Malicious Behavior ◽  
Network Intrusion ◽  
The Common

In the field of network intrusion, malware usually evades anomaly detection by disguising malicious behavior as legitimate access. Therefore, detecting these attacks from network traffic has become a challenge in this an adversarial setting. In this paper, an enhanced Hidden Markov Model, called the Anti-Adversarial Hidden Markov Model (AA-HMM), is proposed to effectively detect evasion pattern, using the Dynamic Window and Threshold techniques to achieve adaptive, anti-adversarial, and online-learning abilities. In addition, a concept called Pattern Entropy is defined and acts as the foundation of AA-HMM. We evaluate the effectiveness of our approach employing two well-known benchmark data sets, NSL-KDD and CTU-13, in terms of the common performance metrics and the algorithm’s adaptation and anti-adversary abilities.

Deep Learning for Biometric Face Recognition: Experimental Study on Benchmark Data Sets

2020 ◽  
pp. 71-97
Author(s):  
Natalya Selitskaya ◽  
S. Sielicki ◽  
L. Jakaite ◽  
V. Schetinin ◽  
F. Evans ◽  
...  
Keyword(s):  
Experimental Study ◽  
Deep Learning ◽  
Face Recognition ◽  
Data Sets ◽  
Benchmark Data

scholarly journals CAMISIM: Simulating metagenomes and microbial communities

2018 ◽  
Author(s):  
Adrian Fritz ◽  
Peter Hofmann ◽  
Stephan Majda ◽  
Eik Dahms ◽  
Johannes Dröge ◽  
...  
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Real Data ◽  
Small Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Taxonomic Profiling ◽  
Benchmark Data ◽  
Sequencing Technologies ◽  
Wide Range

Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Here, we describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series and differential abundance studies, includes real and simulated strain-level diversity, and generates second and third generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with truth standards for method evaluation. All data sets and the software are freely available at: https://github.com/CAMI-challenge/CAMISIM

Validation-Based Sparse Gaussian Process Classifier Design

2009 ◽  
Vol 21 (7) ◽  
pp. 2082-2103 ◽  
Author(s):  
Shirish Shevade ◽  
S. Sundararajan
Keyword(s):  
Bayesian Methods ◽  
Real World ◽  
Basis Vector ◽  
Data Sets ◽  
Training Set ◽  
Classifier Design ◽  
Set Size ◽  
Benchmark Data ◽  
Regression Problems ◽  
Classification And Regression

Gaussian processes (GPs) are promising Bayesian methods for classification and regression problems. Design of a GP classifier and making predictions using it is, however, computationally demanding, especially when the training set size is large. Sparse GP classifiers are known to overcome this limitation. In this letter, we propose and study a validation-based method for sparse GP classifier design. The proposed method uses a negative log predictive (NLP) loss measure, which is easy to compute for GP models. We use this measure for both basis vector selection and hyperparameter adaptation. The experimental results on several real-world benchmark data sets show better or comparable generalization performance over existing methods.

SeisBench: A toolbox for benchmarking and applying machine learning in seismology.

2021 ◽  
Author(s):  
Jack Woollam ◽  
Jannes Münchmeyer ◽  
Carlo Giunchi ◽  
Dario Jozinovic ◽  
Tobias Diehl ◽  
...  
Keyword(s):  
Machine Learning ◽  
Model Comparison ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Quality Data ◽  
Data Sets ◽  
Waveform Data ◽  
Detection Techniques ◽  
Benchmark Data

<p>Machine learning methods have seen widespread adoption within the seismological community in recent years due to their ability to effectively process large amounts of data, while equalling or surpassing the performance of human analysts or classic algorithms. In the wider machine learning world, for example in imaging applications, the open availability of extensive high-quality datasets for training, validation, and the benchmarking of competing algorithms is seen as a vital ingredient to the rapid progress observed throughout the last decade. Within seismology, vast catalogues of labelled data are readily available, but collecting the waveform data for millions of records and assessing the quality of training examples is a time-consuming, tedious process. The natural variability in source processes and seismic wave propagation also presents a critical problem during training. The performance of models trained on different regions, distance and magnitude ranges are not easily comparable. The inability to easily compare and contrast state-of-the-art machine learning-based detection techniques on varying seismic data sets is currently a barrier to further progress within this emerging field. We present SeisBench, an extensible open-source framework for training, benchmarking, and applying machine learning algorithms. SeisBench provides access to various benchmark data sets and models from literature, along with pre-trained model weights, through a unified API. Built to be extensible, and modular, SeisBench allows for the simple addition of new models and data sets, which can be easily interchanged with existing pre-trained models and benchmark data. Standardising the access of varying quality data, and metadata simplifies comparison workflows, enabling the development of more robust machine learning algorithms. We initially focus on phase detection, identification and picking, but the framework is designed to be extended for other purposes, for example direct estimation of event parameters. Users will be able to contribute their own benchmarks and (trained) models. In the future, it will thus be much easier to compare both the performance of new algorithms against published machine learning models/architectures and to check the performance of established algorithms against new data sets. We hope that the ease of validation and inter-model comparison enabled by SeisBench will serve as a catalyst for the development of the next generation of machine learning techniques within the seismological community. The SeisBench source code will be published with an open license and explicitly encourages community involvement.</p>

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