Propositionalisation of multi-instance data using random forests

Multi-instance learning is a generalisation of attribute-value learning where examples for learning consist of labeled bags (i.e. multi-sets) of instances. This learning setting is more computationally challenging than attribute-value learning and a natural fit for important application areas of machine learning such as classification of molecules and image classification. One approach to solve multi-instance learning problems is to apply propositionalisation, where bags of data are converted into vectors of attribute-value pairs so that a standard propositional (i.e. attribute-value) learning algorithm can be applied. This approach is attractive because of the large number of propositional learning algorithms that have been developed and can thus be applied to the propositionalised data. In this paper, we empirically investigate a variant of an existing propositionalisation method called TLC. TLC uses a single decision tree to obtain propositionalised data. Our variant applies a random forest instead and is motivated by the potential increase in robustness that this may yield. We present results on synthetic and real-world data from the above two application domains showing that it indeed yields increased classification accuracy when applying boosting and support vector machines to classify the propositionalised data

Random Relational Rules

In the field of machine learning, methods for learning from single-table data have received much more attention than those for learning from multi-table, or relational data, which are generally more computationally complex. However, a significant amount of the world's data is relational. This indicates a need for algorithms that can operate efficiently on relational data and exploit the larger body of work produced in the area of single-table techniques. This thesis presents algorithms for learning from relational data that mitigate, to some extent, the complexity normally associated with such learning. All algorithms in this thesis are based on the generation of random relational rules. The assumption is that random rules enable efficient and effective relational learning, and this thesis presents evidence that this is indeed the case. To this end, a system for generating random relational rules is described, and algorithms using these rules are evaluated. These algorithms include direct classification, classification by propositionalisation, clustering, semi-supervised learning and generating random forests. The experimental results show that these algorithms perform competitively with previously published results for the datasets used, while often exhibiting lower runtime than other tested systems. This demonstrates that sufficient information for classification and clustering is retained in the rule generation process and that learning with random rules is efficient. Further applications of random rules are investigated. Propositionalisation allows single-table algorithms for classification and clustering to be applied to the resulting data, reducing the amount of relational processing required. Further results show that techniques for utilising additional unlabeled training data improve accuracy of classification in the semi-supervised setting. The thesis also develops a novel algorithm for building random forests by makingefficient use of random rules to generate trees and leaves in parallel

Sequence-based protein classification: binary Profile Hidden Markov Models and propositionalisation

Detecting similarity in biological sequences is a key element to understanding the mechanisms of life. Researchers infer potential structural, functional or evolutionary relationships from similarity. However, the concept of similarity is complex in biology. Sequences consist of different molecules with different chemical properties, have short and long distance interactions, form 3D structures and change through evolutionary processes. Amino acids are one of the key molecules of life. Most importantly, a sequence of amino acids constitutes the building block for proteins which play an essential role in cellular processes. This thesis investigates similarity amongst proteins. In this area of research there are two important and closely related classification tasks – the detection of similar proteins and the discrimination amongst them. Hidden Markov Models (HMMs) have been successfully applied to the detection task as they model sequence similarity very well. From a Machine Learning point of view these HMMs are essentially one-class classifiers trained solely on a small number of similar proteins neglecting the vast number of dissimilar ones. Our basic assumption is that integrating this neglected information will be highly beneficial to the classification task. Thus, we transform the problem representation from a one-class to a binary one. Equipped with the necessary sound understanding of Machine Learning, especially concerning problem representation and statistically significant evaluation, our work pursues and combines two different avenues on this aforementioned transformation. First, we introduce a binary HMM that discriminates significantly better than the standard one, even when only a fraction of the negative information is used. Second, we interpret the HMM as a structured graph of information. This information cannot be accessed by highly optimised standard Machine Learning classifiers as they expect a fixed length feature vector representation. Propositionalisation is a technique to transform the former representation into the latter. This thesis introduces new propositionalisation techniques. The change in representation changes the learning problem from a one-class, generative to a propositional, discriminative one. It is a common assumption that discriminative techniques are better suited for classification tasks, and our results validate this assumption. We suggest a new way to significantly improve on discriminative power and runtime by means of terminating the time-intense training of HMMs early, subsequently applying propositionalisation and classifying with a discriminative, binary learner

A Comparative Study of Machine Learning Models for Tabular Data Through Challenge of Monitoring Parkinson's Disease Progression Using Voice Recordings

People with Parkinson's disease must be regularly monitored by their physician to observe how the disease is progressing and potentially adjust treatment plans to mitigate the symptoms. Monitoring the progression of the disease through a voice recording captured by the patient at their own home can make the process faster and less stressful. Using a dataset of voice recordings of 42 people with early-stage Parkinson's disease over a time span of 6 months, we applied multiple machine learning techniques to find a correlation between the voice recording and the patient's motor UPDRS score. We approached this problem using a multitude of both regression and classification techniques. Much of this paper is dedicated to mapping the voice data to motor UPDRS scores using regression techniques in order to obtain a more precise value for unknown instances. Through this comparative study of variant machine learning methods, we realized some old machine learning methods like trees outperform cutting edge deep learning models on numerous tabular datasets.Comment: Accepted at "HIMS'20 - The 6th Int'l Conf on Health Informatics and Medical Systems"; https://americancse.org/events/csce2020/conferences/hims2

Reframing in context: A systematic approach for model reuse in machine learning

We describe a systematic approach called reframing, defined as the process of preparing a machine learning model (e.g., a classifier) to perform well over a range of operating contexts. One way to achieve this is by constructing a versatile model, which is not fitted to a particular context, and thus enables model reuse. We formally characterise reframing in terms of a taxonomy of context changes that may be encountered and distinguish it from model retraining and revision. We then identify three main kinds of reframing: input reframing, output reframing and structural reframing. We proceed by reviewing areas and problems where some notion of reframing has already been developed and shown useful, if under different names: re-optimising, adapting, tuning, thresholding, etc. This exploration of the landscape of reframing allows us to identify opportunities where reframing might be possible and useful. Finally, we describe related approaches in terms of the problems they address or the kind of solutions they obtain. The paper closes with a re-interpretation of the model development and deployment process with the use of reframing.We thank the anonymous reviewers for their comments, which have helped to improve this paper significantly. This work was supported by the REFRAME project, granted by the European Coordinated Research on Long-term Challenges in Information and Communication Sciences Technologies ERA-Net (CHIST-ERA), funded by their respective national funding agencies in the UK (EPSRC, EP/K018728), France and Spain (MINECO, PCIN-2013-037). It has also been partially supported by the EU (FEDER) and Spanish MINECO grant TIN2015-69175-C4-1-R and by Generalitat Valenciana PROMETEOII/2015/013.Hernández Orallo, J.; Martínez Usó, A.; Prudencio, RBC.; Kull, M.; Flach, P.; Ahmed, CF.; Lachiche, N. (2016). Reframing in context: A systematic approach for model reuse in machine learning. AI Communications. 29(5):551-566. https://doi.org/10.3233/AIC-160705S55156629