Linear filtering reveals false negatives in species interaction data

Species interaction datasets, often represented as sparse matrices, are usually collected through observation studies targeted at identifying species interactions. Due to the extensive required sampling effort, species interaction datasets usually contain many false negatives, often leading to bias in derived descriptors. We show that a simple linear filter can be used to detect false negatives by scoring interactions based on the structure of the interaction matrices. On 180 different datasets of various sizes, sparsities and ecological interaction types, we found that on average in about 75% of the cases, a false negative interaction got a higher score than a true negative interaction. Furthermore, we show that this filter is very robust, even when the interaction matrix contains a very large number of false negatives. Our results demonstrate that unobserved interactions can be detected in species interaction datasets, even without resorting to information about the species involved

Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models

Many complex multi-target prediction problems that concern large target spaces are characterised by a need for efficient prediction strategies that avoid the computation of predictions for all targets explicitly. Examples of such problems emerge in several subfields of machine learning, such as collaborative filtering, multi-label classification, dyadic prediction and biological network inference. In this article we analyse efficient and exact algorithms for computing the top-$K$ predictions in the above problem settings, using a general class of models that we refer to as separable linear relational models. We show how to use those inference algorithms, which are modifications of well-known information retrieval methods, in a variety of machine learning settings. Furthermore, we study the possibility of scoring items incompletely, while still retaining an exact top-K retrieval. Experimental results in several application domains reveal that the so-called threshold algorithm is very scalable, performing often many orders of magnitude more efficiently than the naive approach

Predicting pharmaceutical particle size distributions using kernel mean embedding

In the pharmaceutical industry, the transition to continuous manufacturing of solid dosage forms is adopted by more and more companies. For these continuous processes, high-quality process models are needed. In pharmaceutical wet granulation, a unit operation in the ConsiGmaTM-25 continuous powder-to-tablet system (GEA Pharma systems, Collette, Wommelgem, Belgium), the product under study presents itself as a collection of particles that differ in shape and size. The measurement of this collection results in a particle size distribution. However, the theoretical basis to describe the physical phenomena leading to changes in this particle size distribution is lacking. It is essential to understand how the particle size distribution changes as a function of the unit operation's process settings, as it has a profound effect on the behavior of the fluid bed dryer. Therefore, we suggest a data-driven modeling framework that links the machine settings of the wet granulation unit operation and the output distribution of granules. We do this without making any assumptions on the nature of the distributions under study. A simulation of the granule size distribution could act as a soft sensor when in-line measurements are challenging to perform. The method of this work is a two-step procedure: first, the measured distributions are transformed into a high-dimensional feature space, where the relation between the machine settings and the distributions can be learnt. Second, the inverse transformation is performed, allowing an interpretation of the results in the original measurement space. Further, a comparison is made with previous work, which employs a more mechanistic framework for describing the granules. A reliable prediction of the granule size is vital in the assurance of quality in the production line, and is needed in the assessment of upstream (feeding) and downstream (drying, milling, and tableting) issues. Now that a validated data-driven framework for predicting pharmaceutical particle size distributions is available, it can be applied in settings such as model-based experimental design and, due to its fast computation, there is potential in real-time model predictive control

Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data

In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance

A Comparative Study of Pairwise Learning Methods based on Kernel Ridge Regression

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction or network inference problems. During the last decade kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify existing kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency and spectral filtering properties. Our theoretical results provide valuable insights in assessing the advantages and limitations of existing pairwise learning methods.Comment: arXiv admin note: text overlap with arXiv:1606.0427

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

A kernel-based framework for learning graded relations from data

Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are often expressed in a graded manner in real-world applications. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and graded relations are considered, and it unifies existing approaches because different types of graded relations can be modeled, including symmetric and reciprocal relations. This framework establishes important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated through various experiments on synthetic and real-world data.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl