Finding Rule-Interpretable Non-Negative Data Representation

Non-negative Matrix Factorization (NMF) is an intensively used technique for obtaining parts-based, lower dimensional and non-negative representation of non-negative data. It is a popular method in different research fields. Scientists performing research in the fields of biology, medicine and pharmacy often prefer NMF over other dimensionality reduction approaches (such as PCA) because the non-negativity of the approach naturally fits the characteristics of the domain problem and its result is easier to analyze and understand. Despite these advantages, it still can be hard to get exact characterization and interpretation of the NMF's resulting latent factors due to their numerical nature. On the other hand, rule-based approaches are often considered more interpretable but lack the parts-based interpretation. In this work, we present a version of the NMF approach that merges rule-based descriptions with advantages of part-based representation offered by the NMF approach. Given the numerical input data with non-negative entries and a set of rules with high entity coverage, the approach creates the lower-dimensional non-negative representation of the input data in such a way that its factors are described by the appropriate subset of the input rules. In addition to revealing important attributes for latent factors, it allows analyzing relations between these attributes and provides the exact numerical intervals or categorical values they take. The proposed approach provides numerous advantages in tasks such as focused embedding or performing supervised multi-label NMF.

Multi-view redescription mining using tree-based multi-target prediction models

The task of redescription mining is concerned with re-describing different subsets of entities contained in a dataset and revealing non-trivial associations between different subsets of attributes, called views. This interesting and challenging task is encountered in different scientific fields, and is addressed by a number of approaches that obtain redescriptions and allow for the exploration and analysis of attribute associations. The main limitation of existing approaches to this task is their inability to use more than two views. Our work alleviates this drawback. We present a memory efficient, extensible multi-view redescription mining framework that can be used to relate multiple, i.e. more than two views, disjoint sets of attributes describing one set of entities. The framework includes: a) the use of random forest of Predictive Clustering trees, with and without random output selection, and random forests of Extra Predictive Clustering trees, b) using Extra Predictive Clustering trees as a main rule generation mechanism in the framework and c) using random view subset projections. We provide multiple performance analyses of the proposed framework and demonstrate its usefulness in increasing the understanding of different machine learning models, which has become a topic of growing importance in machine learning and especially in the field of computer science called explainable data science.

Using Redescription Mining to Relate Clinical and Biological Characteristics of Cognitively Impaired and Alzheimer's Disease Patients

We used redescription mining to find interpretable rules revealing associations between those determinants that provide insights about the Alzheimer's disease (AD). We extended the CLUS-RM redescription mining algorithm to a constraint-based redescription mining (CBRM) setting, which enables several modes of targeted exploration of specific, user-constrained associations. Redescription mining enabled finding specific constructs of clinical and biological attributes that describe many groups of subjects of different size, homogeneity and levels of cognitive impairment. We confirmed some previously known findings. However, in some instances, as with the attributes: testosterone, the imaging attribute Spatial Pattern of Abnormalities for Recognition of Early AD, as well as the levels of leptin and angiopoietin-2 in plasma, we corroborated previously debatable findings or provided additional information about these variables and their association with AD pathogenesis. Applying redescription mining on ADNI data resulted with the discovery of one largely unknown attribute: the Pregnancy-Associated Protein-A (PAPP-A), which we found highly associated with cognitive impairment in AD. Statistically significant correlations (p <= 0.01) were found between PAPP-A and various different clinical tests. The high importance of this finding lies in the fact that PAPP-A is a metalloproteinase, known to cleave insulin-like growth factor binding proteins. Since it also shares similar substrates with A Disintegrin and the Metalloproteinase family of enzymes that act as {\alpha}-secretase to physiologically cleave amyloid precursor protein (APP) in the non-amyloidogenic pathway, it could be directly involved in the metabolism of APP very early during the disease course. Therefore, further studies should investigate the role of PAPP-A in the development of AD more thoroughly.

A framework for redescription set construction

Redescription mining is a field of knowledge discovery that aims at finding different descriptions of similar subsets of instances in the data. These descriptions are represented as rules inferred from one or more disjoint sets of attributes, called views. As such, they support knowledge discovery process and help domain experts in formulating new hypotheses or constructing new knowledge bases and decision support systems. In contrast to previous approaches that typically create one smaller set of redescriptions satisfying a pre-defined set of constraints, we introduce a framework that creates large and heterogeneous redescription set from which user/expert can extract compact sets of differing properties, according to its own preferences. Construction of large and heterogeneous redescription set relies on CLUS-RM algorithm and a novel, conjunctive refinement procedure that facilitates generation of larger and more accurate redescription sets. The work also introduces the variability of redescription accuracy when missing values are present in the data, which significantly extends applicability of the method. Crucial part of the framework is the redescription set extraction based on heuristic multi-objective optimization procedure that allows user to define importance levels towards one or more redescription quality criteria. We provide both theoretical and empirical comparison of the novel framework against current state of the art redescription mining algorithms and show that it represents more efficient and versatile approach for mining redescriptions from data.