6,410 research outputs found
A supervised clustering approach for fMRI-based inference of brain states
We propose a method that combines signals from many brain regions observed in
functional Magnetic Resonance Imaging (fMRI) to predict the subject's behavior
during a scanning session. Such predictions suffer from the huge number of
brain regions sampled on the voxel grid of standard fMRI data sets: the curse
of dimensionality. Dimensionality reduction is thus needed, but it is often
performed using a univariate feature selection procedure, that handles neither
the spatial structure of the images, nor the multivariate nature of the signal.
By introducing a hierarchical clustering of the brain volume that incorporates
connectivity constraints, we reduce the span of the possible spatial
configurations to a single tree of nested regions tailored to the signal. We
then prune the tree in a supervised setting, hence the name supervised
clustering, in order to extract a parcellation (division of the volume) such
that parcel-based signal averages best predict the target information.
Dimensionality reduction is thus achieved by feature agglomeration, and the
constructed features now provide a multi-scale representation of the signal.
Comparisons with reference methods on both simulated and real data show that
our approach yields higher prediction accuracy than standard voxel-based
approaches. Moreover, the method infers an explicit weighting of the regions
involved in the regression or classification task
Task-Driven Dictionary Learning
Modeling data with linear combinations of a few elements from a learned
dictionary has been the focus of much recent research in machine learning,
neuroscience and signal processing. For signals such as natural images that
admit such sparse representations, it is now well established that these models
are well suited to restoration tasks. In this context, learning the dictionary
amounts to solving a large-scale matrix factorization problem, which can be
done efficiently with classical optimization tools. The same approach has also
been used for learning features from data for other purposes, e.g., image
classification, but tuning the dictionary in a supervised way for these tasks
has proven to be more difficult. In this paper, we present a general
formulation for supervised dictionary learning adapted to a wide variety of
tasks, and present an efficient algorithm for solving the corresponding
optimization problem. Experiments on handwritten digit classification, digital
art identification, nonlinear inverse image problems, and compressed sensing
demonstrate that our approach is effective in large-scale settings, and is well
suited to supervised and semi-supervised classification, as well as regression
tasks for data that admit sparse representations.Comment: final draft post-refereein
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
Supervised machine learning techniques have traditionally been very successful at reconstructing biological networks, such as protein-ligand interaction, protein-protein interaction and gene regulatory networks. Many supervised techniques for network prediction use linear models on a possibly nonlinear pairwise feature representation of edges. Recently, much emphasis has been placed on the correct evaluation of such supervised models. It is vital to distinguish between using a model to either predict new interactions in a given network or to predict interactions for a new vertex not present in the original network. This distinction matters because (i) the performance might dramatically differ between the prediction settings and (ii) tuning the model hyperparameters to obtain the best possible model depends on the setting of interest. Specific cross-validation schemes need to be used to assess the performance in such different prediction settings. In this work we discuss a state-of-the-art kernel-based network inference technique called two-step kernel ridge regression. We show that this regression model can be trained efficiently, with a time complexity scaling with the number of vertices rather than the number of edges. Furthermore, this framework leads to a series of cross-validation shortcuts that allow one to rapidly estimate the model performance for any relevant network prediction setting. This allows computational biologists to fully assess the capabilities of their models
Semi-Supervised Kernel PCA
We present three generalisations of Kernel Principal Components Analysis
(KPCA) which incorporate knowledge of the class labels of a subset of the data
points. The first, MV-KPCA, penalises within class variances similar to Fisher
discriminant analysis. The second, LSKPCA is a hybrid of least squares
regression and kernel PCA. The final LR-KPCA is an iteratively reweighted
version of the previous which achieves a sigmoid loss function on the labeled
points. We provide a theoretical risk bound as well as illustrative experiments
on real and toy data sets
API design for machine learning software: experiences from the scikit-learn project
Scikit-learn is an increasingly popular machine learning li- brary. Written
in Python, it is designed to be simple and efficient, accessible to
non-experts, and reusable in various contexts. In this paper, we present and
discuss our design choices for the application programming interface (API) of
the project. In particular, we describe the simple and elegant interface shared
by all learning and processing units in the library and then discuss its
advantages in terms of composition and reusability. The paper also comments on
implementation details specific to the Python ecosystem and analyzes obstacles
faced by users and developers of the library
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