Advances in Feature Selection with Mutual Information

The selection of features that are relevant for a prediction or classification problem is an important problem in many domains involving high-dimensional data. Selecting features helps fighting the curse of dimensionality, improving the performances of prediction or classification methods, and interpreting the application. In a nonlinear context, the mutual information is widely used as relevance criterion for features and sets of features. Nevertheless, it suffers from at least three major limitations: mutual information estimators depend on smoothing parameters, there is no theoretically justified stopping criterion in the feature selection greedy procedure, and the estimation itself suffers from the curse of dimensionality. This chapter shows how to deal with these problems. The two first ones are addressed by using resampling techniques that provide a statistical basis to select the estimator parameters and to stop the search procedure. The third one is addressed by modifying the mutual information criterion into a measure of how features are complementary (and not only informative) for the problem at hand

Evaluation of clustering results and novel cluster algorithms

Cluster analysis is frequently performed in many application fields to find groups in data. For example, in medicine, researchers have used gene expression data to cluster patients suffering from a particular disease (e.g., breast cancer), in order to detect new disease subtypes. Many cluster algorithms and methods for cluster validation, i.e., methods for evaluating the quality of cluster analysis results, have been proposed in the literature. However, open questions about the evaluation of both clustering results and novel cluster algorithms remain. It has rarely been discussed whether a) interesting clustering results or b) promising performance evaluations of newly presented cluster algorithms might be over-optimistic, in the sense that these good results cannot be replicated on new data or in other settings. Such questions are relevant in light of the so-called "replication crisis"; in various research disciplines such as medicine, biology, psychology, and economics, many results have turned out to be non-replicable, casting doubt on the trustworthiness and reliability of scientific findings. This crisis has led to increasing popularity of "metascience". Metascientific studies analyze problems that have contributed to the replication crisis (e.g., questionable research practices), and propose and evaluate possible solutions. So far, metascientific studies have mainly focused on issues related to significance testing. In contrast, this dissertation addresses the reliability of a) clustering results in applied research and b) results concerning newly presented cluster algorithms in the methodological literature. Different aspects of this topic are discussed in three Contributions. The first Contribution presents a framework for validating clustering results on validation data. Using validation data is vital to examine the replicability and generalizability of results. While applied researchers sometimes use validation data to check their clustering results, our article is the first to review the different approaches in the literature and to structure them in a systematic manner. We demonstrate that many classical cluster validation techniques, such as internal and external validation, can be combined with validation data. Our framework provides guidance to applied researchers who wish to evaluate their own clustering results or the results of other teams on new data. The second Contribution applies the framework from Contribution 1 to quantify over-optimistic bias in the context of a specific application field, namely unsupervised microbiome research. We analyze over-optimism effects which result from the multiplicity of analysis strategies for cluster analysis and network learning. The plethora of possible analysis strategies poses a challenge for researchers who are often uncertain about which method to use. Researchers might be tempted to try different methods on their dataset and look for the method yielding the "best" result. If only the "best" result is selectively reported, this may cause "overfitting" of the method to the dataset and the result might not be replicable on validation data. We quantify such over-optimism effects for four illustrative types of unsupervised research tasks (clustering of bacterial genera, hub detection in microbial association networks, differential network analysis, and clustering of samples). Contributions 1 and 2 consider the evaluation of clustering results and thus adopt a metascientific perspective on applied research. In contrast, the third Contribution is a metascientific study about methodological research on the development of new cluster algorithms. This Contribution analyzes the over-optimistic evaluation and reporting of novel cluster algorithms. As an illustrative example, we consider the recently proposed cluster algorithm "Rock"; initially deemed promising, it later turned out to be not generally better than its competitors. We demonstrate how Rock can nevertheless appear to outperform competitors via optimization of the evaluation design, namely the used data types, data characteristics, the algorithm’s parameters, and the choice of competing algorithms. The study is a cautionary tale that illustrates how easy it can be for researchers to claim apparent "superiority" of a new cluster algorithm. This, in turn, stresses the importance of strategies for avoiding the problems of over-optimism, such as neutral benchmark studies

Classification algorithms for Big Data with applications in the urban security domain

A classification algorithm is a versatile tool, that can serve as a predictor for the future or as an analytical tool to understand the past. Several obstacles prevent classification from scaling to a large Volume, Velocity, Variety or Value. The aim of this thesis is to scale distributed classification algorithms beyond current limits, assess the state-of-practice of Big Data machine learning frameworks and validate the effectiveness of a data science process in improving urban safety. We found in massive datasets with a number of large-domain categorical features a difficult challenge for existing classification algorithms. We propose associative classification as a possible answer, and develop several novel techniques to distribute the training of an associative classifier among parallel workers and improve the final quality of the model. The experiments, run on a real large-scale dataset with more than 4 billion records, confirmed the quality of the approach. To assess the state-of-practice of Big Data machine learning frameworks and streamline the process of integration and fine-tuning of the building blocks, we developed a generic, self-tuning tool to extract knowledge from network traffic measurements. The result is a system that offers human-readable models of the data with minimal user intervention, validated by experiments on large collections of real-world passive network measurements. A good portion of this dissertation is dedicated to the study of a data science process to improve urban safety. First, we shed some light on the feasibility of a system to monitor social messages from a city for emergency relief. We then propose a methodology to mine temporal patterns in social issues, like crimes. Finally, we propose a system to integrate the findings of Data Science on the citizenry’s perception of safety and communicate its results to decision makers in a timely manner. We applied and tested the system in a real Smart City scenario, set in Turin, Italy

Relevance-based language models : new estimations and applications

[Abstratc] Relevance-Based Language Models introduced in the Language Modelling framework the concept of relevance, which is explicit in other retrieval models such as the Probabilistic models. Relevance Models have been mainly used for a specific task within Information Retrieval called Pseudo-Relevance Feedback, a kind of local query expansion technique where relevance is assumed over a top of documents from the initial retrieval and where those documents are used to select expansion terms for the original query and produce a, hopefully more effective, second retrieval. In this thesis we investigate some new estimations for Relevance Models for both Pseudo-Relevance Feedback and other tasks beyond retrieval, particularly, constrained text clustering and item recommendation in Recommender Systems. We study the benefits of our proposals for those tasks in comparison with existing estimations. This new modellings are able not only to improve the effectiveness of the existing estimations and methods but also to outperform their robustness, a critical factor when dealing with Pseudo-Relevance Feedback methods. These objectives are pursued by different means: promoting divergent terms in the estimation of the Relevance Models, presenting new cluster-based retrieval models, introducing new methods for automatically determine the size of the pseudo-relevant set on a query-basis, and originally producing new modellings under the Relevance-Based Language Modelling framework for the constrained text clustering and the item recommendation problems

Making music through real-time voice timbre analysis: machine learning and timbral control

PhDPeople can achieve rich musical expression through vocal sound { see for example human beatboxing, which achieves a wide timbral variety through a range of extended techniques. Yet the vocal modality is under-exploited as a controller for music systems. If we can analyse a vocal performance suitably in real time, then this information could be used to create voice-based interfaces with the potential for intuitive and ful lling levels of expressive control. Conversely, many modern techniques for music synthesis do not imply any particular interface. Should a given parameter be controlled via a MIDI keyboard, or a slider/fader, or a rotary dial? Automatic vocal analysis could provide a fruitful basis for expressive interfaces to such electronic musical instruments. The principal questions in applying vocal-based control are how to extract musically meaningful information from the voice signal in real time, and how to convert that information suitably into control data. In this thesis we address these questions, with a focus on timbral control, and in particular we develop approaches that can be used with a wide variety of musical instruments by applying machine learning techniques to automatically derive the mappings between expressive audio input and control output. The vocal audio signal is construed to include a broad range of expression, in particular encompassing the extended techniques used in human beatboxing. The central contribution of this work is the application of supervised and unsupervised machine learning techniques to automatically map vocal timbre to synthesiser timbre and controls. Component contributions include a delayed decision-making strategy for low-latency sound classi cation, a regression-tree method to learn associations between regions of two unlabelled datasets, a fast estimator of multidimensional di erential entropy and a qualitative method for evaluating musical interfaces based on discourse analysis

Robust speaker diarization for meetings

Aquesta tesi doctoral mostra la recerca feta en l'àrea de la diarització de locutor per a sales de reunions. En la present s'estudien els algorismes i la implementació d'un sistema en diferit de segmentació i aglomerat de locutor per a grabacions de reunions a on normalment es té accés a més d'un micròfon per al processat. El bloc més important de recerca s'ha fet durant una estada al International Computer Science Institute (ICSI, Berkeley, Caligornia) per un període de dos anys.La diarització de locutor s'ha estudiat força per al domini de grabacions de ràdio i televisió. La majoria dels sistemes proposats utilitzen algun tipus d'aglomerat jeràrquic de les dades en grups acústics a on de bon principi no se sap el número de locutors òptim ni tampoc la seva identitat. Un mètode molt comunment utilitzat s'anomena "bottom-up clustering" (aglomerat de baix-a-dalt), amb el qual inicialment es defineixen molts grups acústics de dades que es van ajuntant de manera iterativa fins a obtenir el nombre òptim de grups tot i acomplint un criteri de parada. Tots aquests sistemes es basen en l'anàlisi d'un canal d'entrada individual, el qual no permet la seva aplicació directa per a reunions. A més a més, molts d'aquests algorisms necessiten entrenar models o afinar els parameters del sistema usant dades externes, el qual dificulta l'aplicabilitat d'aquests sistemes per a dades diferents de les usades per a l'adaptació.La implementació proposada en aquesta tesi es dirigeix a solventar els problemes mencionats anteriorment. Aquesta pren com a punt de partida el sistema existent al ICSI de diarització de locutor basat en l'aglomerat de "baix-a-dalt". Primer es processen els canals de grabació disponibles per a obtindre un sol canal d'audio de qualitat major, a més dínformació sobre la posició dels locutors existents. Aleshores s'implementa un sistema de detecció de veu/silenci que no requereix de cap entrenament previ, i processa els segments de veu resultant amb una versió millorada del sistema mono-canal de diarització de locutor. Aquest sistema ha estat modificat per a l'ús de l'informació de posició dels locutors (quan es tingui) i s'han adaptat i creat nous algorismes per a que el sistema obtingui tanta informació com sigui possible directament del senyal acustic, fent-lo menys depenent de les dades de desenvolupament. El sistema resultant és flexible i es pot usar en qualsevol tipus de sala de reunions pel que fa al nombre de micròfons o la seva posició. El sistema, a més, no requereix en absolute dades d´entrenament, sent més senzill adaptar-lo a diferents tipus de dades o dominis d'aplicació. Finalment, fa un pas endavant en l'ús de parametres que siguin mes robusts als canvis en les dades acústiques. Dos versions del sistema es van presentar amb resultats excel.lents a les evaluacions de RT05s i RT06s del NIST en transcripció rica per a reunions, a on aquests es van avaluar amb dades de dos subdominis diferents (conferencies i reunions). A més a més, es fan experiments utilitzant totes les dades disponibles de les evaluacions RT per a demostrar la viabilitat dels algorisms proposats en aquesta tasca.This thesis shows research performed into the topic of speaker diarization for meeting rooms. It looks into the algorithms and the implementation of an offline speaker segmentation and clustering system for a meeting recording where usually more than one microphone is available. The main research and system implementation has been done while visiting the International Computes Science Institute (ICSI, Berkeley, California) for a period of two years. Speaker diarization is a well studied topic on the domain of broadcast news recordings. Most of the proposed systems involve some sort of hierarchical clustering of the data into clusters, where the optimum number of speakers of their identities are unknown a priory. A very commonly used method is called bottom-up clustering, where multiple initial clusters are iteratively merged until the optimum number of clusters is reached, according to some stopping criterion. Such systems are based on a single channel input, not allowing a direct application for the meetings domain. Although some efforts have been done to adapt such systems to multichannel data, at the start of this thesis no effective implementation had been proposed. Furthermore, many of these speaker diarization algorithms involve some sort of models training or parameter tuning using external data, which impedes its usability with data different from what they have been adapted to.The implementation proposed in this thesis works towards solving the aforementioned problems. Taking the existing hierarchical bottom-up mono-channel speaker diarization system from ICSI, it first uses a flexible acoustic beamforming to extract speaker location information and obtain a single enhanced signal from all available microphones. It then implements a train-free speech/non-speech detection on such signal and processes the resulting speech segments with an improved version of the mono-channel speaker diarization system. Such system has been modified to use speaker location information (then available) and several algorithms have been adapted or created new to adapt the system behavior to each particular recording by obtaining information directly from the acoustics, making it less dependent on the development data.The resulting system is flexible to any meetings room layout regarding the number of microphones and their placement. It is train-free making it easy to adapt to different sorts of data and domains of application. Finally, it takes a step forward into the use of parameters that are more robust to changes in the acoustic data. Two versions of the system were submitted with excellent results in RT05s and RT06s NIST Rich Transcription evaluations for meetings, where data from two different subdomains (lectures and conferences) was evaluated. Also, experiments using the RT datasets from all meetings evaluations were used to test the different proposed algorithms proving their suitability to the task.Postprint (published version

Identifying Structure Transitions Using Machine Learning Methods

Methodologies from data science and machine learning, both new and old, provide an exciting opportunity to investigate physical systems using extremely expressive statistical modeling techniques. Physical transitions are of particular interest, as they are accompanied by pattern changes in the configurations of the systems. Detecting and characterizing pattern changes in data happens to be a particular strength of statistical modeling in data science, especially with the highly expressive and flexible neural network models that have become increasingly computationally accessible in recent years through performance improvements in both hardware and algorithmic implementations. Conceptually, the machine learning approach can be regarded as one that employing algorithms that eschew explicit instructions in favor of strategies based around pattern extraction and inference driven by statistical analysis and large complex data sets. This allows for the investigation of physical systems using only raw configurational information to make inferences instead of relying on physical information obtained from a priori knowledge of the system. This work focuses on the extraction of useful compressed representations of physical configurations from systems of interest to automate phase classification tasks in addition to the identification of critical points and crossover regions