Genetic optimization of training sets for improved machine learning models of molecular properties

The training of molecular models of quantum mechanical properties based on statistical machine learning requires large datasets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of training examples is often difficult or impossible to achieve as prior knowledge may be sparse or unavailable. Ordinarily representative selection of training molecules from such datasets is achieved through random sampling. We use genetic algorithms for the optimization of training set composition consisting of tens of thousands of small organic molecules. The resulting machine learning models are considerably more accurate with respect to small randomly selected training sets: mean absolute errors for out-of-sample predictions are reduced to ~25% for enthalpies, free energies, and zero-point vibrational energy, to ~50% for heat-capacity, electron-spread, and polarizability, and by more than ~20% for electronic properties such as frontier orbital eigenvalues or dipole-moments. We discuss and present optimized training sets consisting of 10 molecular classes for all molecular properties studied. We show that these classes can be used to design improved training sets for the generation of machine learning models of the same properties in similar but unrelated molecular sets.Comment: 9 pages, 6 figure

The influence of negative training set size on machine learning-based virtual screening

BACKGROUND: The paper presents a thorough analysis of the influence of the number of negative training examples on the performance of machine learning methods. RESULTS: The impact of this rather neglected aspect of machine learning methods application was examined for sets containing a fixed number of positive and a varying number of negative examples randomly selected from the ZINC database. An increase in the ratio of positive to negative training instances was found to greatly influence most of the investigated evaluating parameters of ML methods in simulated virtual screening experiments. In a majority of cases, substantial increases in precision and MCC were observed in conjunction with some decreases in hit recall. The analysis of dynamics of those variations let us recommend an optimal composition of training data. The study was performed on several protein targets, 5 machine learning algorithms (SMO, Naïve Bayes, Ibk, J48 and Random Forest) and 2 types of molecular fingerprints (MACCS and CDK FP). The most effective classification was provided by the combination of CDK FP with SMO or Random Forest algorithms. The Naïve Bayes models appeared to be hardly sensitive to changes in the number of negative instances in the training set. CONCLUSIONS: In conclusion, the ratio of positive to negative training instances should be taken into account during the preparation of machine learning experiments, as it might significantly influence the performance of particular classifier. What is more, the optimization of negative training set size can be applied as a boosting-like approach in machine learning-based virtual screening

Modeling with the Crowd: Optimizing the Human-Machine Partnership with Zooniverse

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.Comment: 5 pages, 1 figure. To appear in Proceedings of the International Astronomical Unio

A meta-heuristic approach for developing PROAFTN with decision tree

© 2016 IEEE. Machine learning algorithms known for their performance in using historical data and examples to predict and classify unknown instances. Decision tree is an efficient machine learning approach that can use data only without the involvement of decision maker to improve the decision making process. Multi-Criteria Decision Analysis (MCDA)is another paradigm used for data classification. In this paper, we propose a new fuzzy classification method based on MCDA called PROAFTN. To use PROAFTN, a set of parameters need to be established from data. The proposed approach uses data pre-processing and canonical genetic algorithm (GA) for obtaining these parameters from data. The generated models have been applied on popular data selected from several application domain, health, economy, etc. According to our experimental study, the new model performs significantly better than decision trees according in terms of accuracy and the interpretation of the decision rules

MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method

BACKGROUND: Machine learning based miRNA-target prediction algorithms often fail to obtain a balanced prediction accuracy in terms of both sensitivity and specificity due to lack of the gold standard of negative examples, miRNA-targeting site context specific relevant features and efficient feature selection process. Moreover, all the sequence, structure and machine learning based algorithms are unable to distribute the true positive predictions preferentially at the top of the ranked list; hence the algorithms become unreliable to the biologists. In addition, these algorithms fail to obtain considerable combination of precision and recall for the target transcripts that are translationally repressed at protein level. METHODOLOGY/PRINCIPAL FINDING: In the proposed article, we introduce an efficient miRNA-target prediction system MultiMiTar, a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. CONCLUSIONS/SIGNIFICANCE: MultiMiTar is found to achieve much higher Matthew's correlation coefficient (MCC) of 0.583 and average class-wise accuracy (ACA) of 0.8 compared to the others target prediction methods for a completely independent test data set. The obtained MCC and ACA values of these algorithms range from -0.269 to 0.155 and 0.321 to 0.582, respectively. Moreover, it shows a more balanced result in terms of precision and sensitivity (recall) for the translationally repressed data set as compared to all the other existing methods. An important aspect is that the true positive predictions are distributed preferentially at the top of the ranked list that makes MultiMiTar reliable for the biologists. MultiMiTar is now available as an online tool at www.isical.ac.in/~bioinfo_miu/multimitar.htm. MultiMiTar software can be downloaded from www.isical.ac.in/~bioinfo_miu/multimitar-download.htm

A survey of cost-sensitive decision tree induction algorithms

The past decade has seen a significant interest on the problem of inducing decision trees that take account of costs of misclassification and costs of acquiring the features used for decision making. This survey identifies over 50 algorithms including approaches that are direct adaptations of accuracy based methods, use genetic algorithms, use anytime methods and utilize boosting and bagging. The survey brings together these different studies and novel approaches to cost-sensitive decision tree learning, provides a useful taxonomy, a historical timeline of how the field has developed and should provide a useful reference point for future research in this field

Machine Learning in Adversarial Environments

Machine Learning, especially Deep Neural Nets (DNNs), has achieved great success in a variety of applications. Unlike classical algorithms that could be formally analyzed, there is less understanding of neural network-based learning algorithms. This lack of understanding through either formal methods or empirical observations results in potential vulnerabilities that could be exploited by adversaries. This also hinders the deployment and adoption of learning methods in security-critical systems. Recent works have demonstrated that DNNs are vulnerable to carefully crafted adversarial perturbations. We refer to data instances with added adversarial perturbations as “adversarial examples”. Such adversarial examples can mislead DNNs to produce adversary-selected results. Furthermore, it can cause a DNN system to misbehavior in unexpected and potentially dangerous ways. In this context, in this thesis, we focus on studying the security problem of current DNNs from the viewpoints of both attack and defense. First, we explore the space of attacks against DNNs during the test time. We revisit the integrity of Lp regime and propose a new and rigorous threat model of adversarial examples. Based on this new threat model, we present the technique to generate adversarial examples in the digital space. Second, we study the physical consequence of adversarial examples in the 3D and physical spaces. We first study the vulnerabilities of various vision systems by simulating the photo0taken process by using the physical renderer. To further explore the physical consequence in the real world, we select the safety-critical application of autonomous driving as the target system and study the vulnerability of the LiDAR-perceptual module. These studies show the potentially severe consequences of adversarial examples and raise awareness on its risks. Last but not least, we develop solutions to defend against adversarial examples. We propose a consistency-check based method to detect adversarial examples by leveraging property of either the learning model or the data. We show two examples in the segmentation task (leveraging learning model) and video data (leveraging the data), respectively.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162944/1/xiaocw_1.pd