Motivation: Liquid chromatography is frequently used as a means to reduce the complexity of peptide-mixtures in shotgun proteomics. For such systems, the time when a peptide is released from a chromatography column and registered in the mass spectrometer is referred to as the peptide's retention time . Using heuristics or machine learning techniques, previous studies have demonstrated that it is possible to predict the retention time of a peptide from its amino acid sequence. In this paper, we are applying Gaussian Process Regression to the feature representation of a previously described predictor E lude . Using this framework, we demonstrate that it is possible to estimate the uncertainty of the prediction made by the model. Here we show how this uncertainty relates to the actual error of the prediction. Results: In our experiments, we observe a strong correlation between the estimated uncertainty provided by Gaussian Process Regression and the actual prediction error. This relation provides us with new means for assessment of the predictions. We demonstrate how a subset of the peptides can be selected with lower prediction error compared to the whole set. We also demonstrate how such predicted standard deviations can be used for designing adaptive windowing strategies. Contact: [email protected]. Availability and Implementation: Our software and the data used in our experiments is publicly available and can be downloaded from https://github.com/statisticalbiotechnology/GPTime .

We discuss the properties of a class of latent variable models that assumes each labeled sample is associated with a set of different features, with no prior knowledge of which feature is the most relevant feature to be used. Deformable-Part Models (DPM) can be seen as good examples of such models. These models are usually considered to be expensive to train and very sensitive to the initialization. In this paper, we focus on the learning of such models by introducing a topological framework and show how it is possible to both reduce the learning complexity and produce more robust decision boundaries. We will also argue how our framework can be used for producing robust decision boundaries without exploiting the dataset bias or relying on accurate annotations. To experimentally evaluate our method and compare with previously published frameworks, we focus on the problem of image classification with object localization. In this problem, the correct location of the objects is unknown, during both training and testing stages, and is considered as a latent variable.

In this paper, we discuss the properties of a class of latent variable models that assumes each labeled sample is associated with set of different features, with no prior knowledge of which feature is the most relevant feature to be used. Deformable-Part Models (DPM) can be seen as good example of such models. While Latent SVM framework (LSVM) has proven to be an efficient tool for solving these models, we will argue that the solution found by this tool is very sensitive to the initialization. To decrease this dependency, we propose a novel clustering procedure, for these problems, to find cluster centers that are shared by several sample sets while ignoring the rest of the cluster centers. As we will show, these cluster centers will provide a robust initialization for the LSVM framework.

In this paper, we propose a framework to gradually improve the quality of an already existing image descriptor. The descriptor used in this paper \cite{Afkham:wf} uses the response of a series of discriminative components for summarizing each image. As we will show, this descriptor has an ideal form in which all categories become linearly separable. While, reaching this form is not feasible, we will argue by replacing a small fraction of the components, it is possible to obtain a descriptor which is, on average, closer to this ideal form. To do so, we identify which components do not contribute to the quality of the descriptor and replace them with more robust components. Here, a joint feature selection method is used to find more robust components. As our experiments show, this change directly reflects in the capability of the resulting descriptor in discriminating between different categories.

Most object classes share a considerable amount of local appearance and often only a small number of features are discriminative. The traditional approach to represent an object is based on a summarization of the local characteristics by counting the number of feature occurrences. In this paper we propose the use of a recently developed technique for summarizations that, rather than looking into the quantity of features, encodes their quality to learn a description of an object. Our approach is based on extracting and aggregating only the essential characteristics of an object class for a task. We show how the proposed method significantly improves on previous work in 3D object categorization. We discuss the benefits of the method in other scenarios such as robot grasping. We provide extensive quantitative and qualitative experiments comparing our approach to the state of the art to justify the described approach.

This paper presents a method for visual object categorization based on encoding the joint textural information in objects and the surrounding background, and requiring no segmentation during recognition. The framework can be used together with various learning techniques and model representations. Here we use this framework with simple probabilistic models and more complex representations obtained using Support Vector Machines. We prove that our approach provides good recognition performance for complex problems for which some of the existing methods have difficulties. Additionally, we introduce a new extensive database containing realistic images of animals in complex natural environments. We assess the database in a set of experiments in which we compare the performance of our approach with a recently proposed method.