61 research outputs found
Topological regression as an interpretable and efficient tool for quantitative structureactivity relationship modeling
Quantitative structure-activity relationship (QSAR)modeling is a powerful tool for drug discovery, yet the lack of interpretability of commonly used QSAR models hinders their application inmolecular design.We propose a similaritybased regression framework, topological regression (TR), that offers a statistically grounded, computationally fast, and interpretable technique to predict drug responses. We compare the predictive performance of TR on 530 ChEMBL human target activity datasets against the predictive performance of deep-learning-based QSAR models. Our results suggest that our sparse TR model can achieve equal, if not better, performance than the deep learningbased QSAR models and provide better intuitive interpretation by extracting an approximate isometry between the chemical space of the drugs and their activity space
Multi-view Metric Learning in Vector-valued Kernel Spaces
We consider the problem of metric learning for multi-view data and present a
novel method for learning within-view as well as between-view metrics in
vector-valued kernel spaces, as a way to capture multi-modal structure of the
data. We formulate two convex optimization problems to jointly learn the metric
and the classifier or regressor in kernel feature spaces. An iterative
three-step multi-view metric learning algorithm is derived from the
optimization problems. In order to scale the computation to large training
sets, a block-wise Nystr{\"o}m approximation of the multi-view kernel matrix is
introduced. We justify our approach theoretically and experimentally, and show
its performance on real-world datasets against relevant state-of-the-art
methods
DeepCoder: Semi-parametric Variational Autoencoders for Automatic Facial Action Coding
Human face exhibits an inherent hierarchy in its representations (i.e.,
holistic facial expressions can be encoded via a set of facial action units
(AUs) and their intensity). Variational (deep) auto-encoders (VAE) have shown
great results in unsupervised extraction of hierarchical latent representations
from large amounts of image data, while being robust to noise and other
undesired artifacts. Potentially, this makes VAEs a suitable approach for
learning facial features for AU intensity estimation. Yet, most existing
VAE-based methods apply classifiers learned separately from the encoded
features. By contrast, the non-parametric (probabilistic) approaches, such as
Gaussian Processes (GPs), typically outperform their parametric counterparts,
but cannot deal easily with large amounts of data. To this end, we propose a
novel VAE semi-parametric modeling framework, named DeepCoder, which combines
the modeling power of parametric (convolutional) and nonparametric (ordinal
GPs) VAEs, for joint learning of (1) latent representations at multiple levels
in a task hierarchy1, and (2) classification of multiple ordinal outputs. We
show on benchmark datasets for AU intensity estimation that the proposed
DeepCoder outperforms the state-of-the-art approaches, and related VAEs and
deep learning models.Comment: ICCV 2017 - accepte
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