Advances in pre-processing and model generation for mass spectrometric data analysis

The analysis of complex signals as obtained by mass spectrometric measurements is complicated and needs an appropriate representation of the data. Thereby the kind of preprocessing, feature extraction as well as the used similarity measure are of particular importance. Focusing on biomarker analysis and taking the functional nature of the data into account this task is even more complicated. A new mass spectrometry tailored data preprocessing is shown, discussed and analyzed in a clinical proteom study compared to a standard setting

HCF-CRS: A Hybrid Content based Fuzzy Conformal Recommender System for providing recommendations with confidence

A Recommender System (RS) is an intelligent system that assists users in finding the items of their interest (e.g. books, movies, music) by preventing them to go through huge piles of data available online. In an effort to overcome the data sparsity issue in recommender systems, this research incorporates a content based filtering technique with fuzzy inference system and a conformal prediction approach introducing a new framework called Hybrid Content based Fuzzy Conformal Recommender System (HCF-CRS). The proposed framework is implemented to be used in the domain of movies and it provides quality recommendations to users with a confidence level and an improved accuracy. In our proposed framework, first, a Content Based Filtering (CBF) technique is applied to create a user profile by considering the history of each user. CBF is useful in the situations like: lack of demographic information and the data sparsity problems. Second, a Fuzzy based technique is incorporated to find the similarities and differences between the user profile and the movies in the dataset using a set of fuzzy rules to get a predicted rating for each movie. Third, a Conformal prediction algorithm is implemented to calculate the non-conformity measure between the predicted ratings produced by fuzzy system and the actual ratings from the dataset. A p-value (confidence measure) is computed to give a level of confidence to each recommended item and a bound is set on the confidence level called a significance level ε, according to which the movies only above the specified significance level are recommended to user. By building a confidence centric hybrid conformal recommender system using the content based filtering approach with fuzzy logic and conformal prediction algorithm, the reliability and the accuracy of the system is considerably enhanced. The experiments are evaluated on MovieLens and Movie Tweetings datasets for recommending movies to the users and they are compared with other state-of-the-art recommender systems. Finally, the results confirm that the proposed algorithms perform better than the traditional ones

Adaptive conformal semi-supervised vector quantization for dissimilarity data

Zhu X, Schleif F-M, Hammer B. Adaptive Conformal Semi-Supervised Vector Quantization for Dissimilarity Data. Pattern Recognition Letters. 2014;49:138-145

Adaptive prototype-based dissimilarity learning

Zhu X. Adaptive prototype-based dissimilarity learning. Bielefeld: Universitätsbibliothek Bielefeld; 2015.In this thesis we focus on prototype-based learning techniques, namely three unsuper- vised techniques: generative topographic mapping (GTM), neural gas (NG) and affinity propagation (AP), and two supervised techniques: generalized learning vector quantiza- tion (GLVQ) and robust soft learning vector quantization (RSLVQ). We extend their abilities with respect to the following central aspects: • Applicability on dissimilarity data: Due to the increased complexity of data, in many cases data are only available in form of (dis)similarities which describe the relations between objects. Classical methods can not directly deal with this kind of data. For unsupervised methods this problem has been studied, here we transfer the same idea to the two supervised prototype-based techniques such that they can directly deal with dissimilarities without an explicit embedding into a vector space. • Quadratic complexity issue: For dealing with dissimilarity data, due to the need of the full dissimilarity matrix, the complexity becomes quadratic which is infeasible for large data sets. In this thesis we investigate two linear approximation techniques: Nyström approximation and patch processing, and integrate them into unsupervised and supervised prototype-based techniques. • Reliability of prototype-based classifiers: In practical applications, a relia- bility measure is beneficial for evaluating the classification quality expected by the end users. Here we adopt concepts from conformal prediction (CP), which provides point-wise confidence measure of the prediction, and we combine those with supervised prototype-based techniques. • Model complexity: By means of the confidence values provided by CP, the model complexity can be automatically adjusted by adding new prototypes to cover low confidence data space. • Extendability to semi-supervised problems: Besides its ability to evaluate a classifier, conformal prediction can also be considered as a classifier. This opens a way that supervised techniques can be easily extended for semi-supervised settings by means of a self-training approach

A Saliency-based Clustering Framework for Identifying Aberrant Predictions

In machine learning, classification tasks serve as the cornerstone of a wide range of real-world applications. Reliable, trustworthy classification is particularly intricate in biomedical settings, where the ground truth is often inherently uncertain and relies on high degrees of human expertise for labeling. Traditional metrics such as precision and recall, while valuable, are insufficient for capturing the nuances of these ambiguous scenarios. Here we introduce the concept of aberrant predictions, emphasizing that the nature of classification errors is as critical as their frequency. We propose a novel, efficient training methodology aimed at both reducing the misclassification rate and discerning aberrant predictions. Our framework demonstrates a substantial improvement in model performance, achieving a 20\% increase in precision. We apply this methodology to the less-explored domain of veterinary radiology, where the stakes are high but have not been as extensively studied compared to human medicine. By focusing on the identification and mitigation of aberrant predictions, we enhance the utility and trustworthiness of machine learning classifiers in high-stakes, real-world scenarios, including new applications in the veterinary world

Improved one-class SVM classifier for sounds classification

©2007 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.International audienceThis paper proposes to apply optimized One-Class Support Vector Machines (1-SVMs) as a discriminative framework in order to address a specific audio classification problem. First, since SVM-based classifier with gaussian RBF kernel is sensitive to the kernel width, the width will be scaled in a distribution-dependent way permitting to avoid underfitting and over-fitting problems. Moreover, an advanced dissimilarity measure will be introduced. We illustrate the performance of these methods on an audio database containing environmental sounds that may be of great importance for surveillance and security applications. The experiments conducted on a multi-class problem show that by choosing adequately the SVM parameters, we can efficiently address a sounds classification problem characterized by complex real-world datasets

Using Predicted Bioactivity Profiles to Improve Predictive Modeling

Predictive modeling is a cornerstone in early drug development. Using information for multiple domains or across prediction tasks has the potential to improve the performance of predictive modeling. However, aggregating data often leads to incomplete data matrices that might be limiting for modeling. In line with previous studies, we show that by generating predicted bioactivity profiles, and using these as additional features, prediction accuracy of biological endpoints can be improved. Using conformal prediction, a type of confidence predictor, we present a robust framework for the calculation of these profiles and the evaluation of their impact. We report on the outcomes from several approaches to generate the predicted profiles on 16 datasets in cytotoxicity and bioactivity and show that efficiency is improved the most when including the p-values from conformal prediction as bioactivity profiles

A transient boundary element method model of Schroeder diffuser scattering using well mouth impedance

Room acoustic diffusers can be used to treat critical listening environments to improve sound quality. One popular class is Schroeder diffusers, which comprise wells of varying depth separated by thin fins. This paper concerns a new approach to enable the modelling of these complex surfaces in the time domain. Mostly, diffuser scattering is predicted using steady-state, single frequency methods. A popular approach is to use a frequency domain Boundary Element Method (BEM) model of a box containing the diffuser, where the mouth of each well is replaced by a compliant surface with appropriate surface impedance. The best way of representing compliant surfaces in time domain prediction models, such as the transient BEM is, however, currently unresolved. A representation based on surface impedance yields convolution kernels which involve future sound, so is not compatible with the current generation of time-marching transient BEM solvers. Consequently, this paper proposes the use of a surface reflection kernel for modelling well behaviour and this is tested in a time domain BEM implementation. The new algorithm is verified on two surfaces including a Schroeder diffuser model and accurate results are obtained. It is hoped that this representation may be extended to arbitrary compliant locally reacting materials