Data-driven recipe completion using machine learning methods

Small Stochastic Data Compactification Concept Justified in the Entropy Basis

Measurement is a typical way of gathering information about an investigated object, generalized by a finite set of characteristic parameters. The result of each iteration of the measurement is an instance of the class of the investigated object in the form of a set of values of characteristic parameters. An ordered set of instances forms a collection whose dimensionality for a real object is a factor that cannot be ignored. Managing the dimensionality of data collections, as well as classification, regression, and clustering, are fundamental problems for machine learning. Compactification is the approximation of the original data collection by an equivalent collection (with a reduced dimension of characteristic parameters) with the control of accompanying information capacity losses. Related to compactification is the data completeness verifying procedure, which is characteristic of the data reliability assessment. If there are stochastic parameters among the initial data collection characteristic parameters, the compactification procedure becomes more complicated. To take this into account, this study proposes a model of a structured collection of stochastic data defined in terms of relative entropy. The compactification of such a data model is formalized by an iterative procedure aimed at maximizing the relative entropy of sequential implementation of direct and reverse projections of data collections, taking into account the estimates of the probability distribution densities of their attributes. The procedure for approximating the relative entropy function of compactification to reduce the computational complexity of the latter is proposed. To qualitatively assess compactification this study undertakes a formal analysis that uses data collection information capacity and the absolute and relative share of information losses due to compaction as its metrics. Taking into account the semantic connection of compactification and completeness, the proposed metric is also relevant for the task of assessing data reliability. Testing the proposed compactification procedure proved both its stability and efficiency in comparison with previously used analogues, such as the principal component analysis method and the random projection method.

Utilization of text mining as a big data analysis tool for food science and nutrition

Big data analysis has found applications in many industries due to its ability to turn huge amounts of data into insights for informed business and operational decisions. Advanced data mining techniques have been applied in many sectors of supply chains in the food industry. However, the previous work has mainly focused on the analysis of instrument-generated data such as those from hyperspectral imaging, spectroscopy, and biometric receptors. The importance of digital text data in the food and nutrition has only recently gained attention due to advancements in big data analytics. The purpose of this review is to provide an overview of the data sources, computational methods, and applications of text data in the food industry. Text mining techniques such as word-level analysis (e.g., frequency analysis), word association analysis (e.g., network analysis), and advanced techniques (e.g., text classification, text clustering, topic modeling, information retrieval, and sentiment analysis) will be discussed. Applications of text data analysis will be illustrated with respect to food safety and food fraud surveillance, dietary pattern characterization, consumer-opinion mining, new-product development, food knowledge discovery, food supply-chain management, and online food services. The goal is to provide insights for intelligent decision-making to improve food production, food safety, and human nutrition.

Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Supervised machine learning techniques have traditionally been very successful at reconstructing biological networks, such as protein-ligand interaction, protein-protein interaction and gene regulatory networks. Many supervised techniques for network prediction use linear models on a possibly nonlinear pairwise feature representation of edges. Recently, much emphasis has been placed on the correct evaluation of such supervised models. It is vital to distinguish between using a model to either predict new interactions in a given network or to predict interactions for a new vertex not present in the original network. This distinction matters because (i) the performance might dramatically differ between the prediction settings and (ii) tuning the model hyperparameters to obtain the best possible model depends on the setting of interest. Specific cross-validation schemes need to be used to assess the performance in such different prediction settings.In this work we discuss a state-of-the-art kernel-based network inference technique called two-step kernel ridge regression. We show that this regression model can be trained efficiently, with a time complexity scaling with the number of vertices rather than the number of edges. Furthermore, this framework leads to a series of cross-validation shortcuts that allow one to rapidly estimate the model performance for any relevant network prediction setting. This allows computational biologists to fully assess the capabilities of their models. The machine learning techniques with the algebraic shortcuts are implemented in the RLScore software package: https://github.com/aatapa/RLScore.