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When genetic variants in a gene cluster are associated with a disease outcome, the causal pathway from the variants to the outcome can be difficult to disentangle. For example, the chemokine receptor gene cluster contains genetic variants associated with various cytokines. Associations between variants in this cluster and stroke risk may be driven by any of these cytokines. Multivariable Mendelian randomization is an extension of standard univariable Mendelian randomization to estimate the direct effects of related exposures with shared genetic predictors. However, when genetic variants are clustered, a Goldilocks dilemma arises: including too many highly-correlated variants in the analysis can lead to ill-conditioning, but pruning variants too aggressively can lead to imprecise estimates or even lack of identification. We propose multivariable methods that use principal component analysis to reduce many correlated genetic variants into a smaller number of orthogonal components that are used as instrumental variables. We show in simulations that these methods result in more precise estimates that are less sensitive to numerical instability due to both strong correlations and small changes in the input data. We apply the methods to demonstrate the most likely causal risk factor for stroke at the chemokine gene cluster is monocyte chemoattractant protein-1.

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Fast and reliable prediction of river flow velocities is important in many applications, including flood risk management. The shallow water equations (SWEs) are commonly used for this purpose. However, traditional numerical solvers of the SWEs are computationally expensive and require high-resolution riverbed profile measurement (bathymetry). In this work, we propose a two-stage process in which, first, using the principal component geostatistical approach (PCGA) we estimate the probability density function of the bathymetry from flow velocity measurements, and then use machine learning (ML) algorithms to obtain a fast solver for the SWEs. The fast solver uses realizations from the posterior bathymetry distribution and takes as input the prescribed range of BCs. The first stage allows us to predict flow velocities without direct measurement of the bathymetry. Furthermore, we augment the bathymetry posterior distribution to a more general class of distributions before providing them as inputs to ML algorithm in the second stage. This allows the solver to incorporate future direct bathymetry measurements into the flow velocity prediction for improved accuracy, even if the bathymetry changes over time compared to its original indirect estimation. We propose and benchmark three different solvers, referred to as PCA-DNN (principal component analysis-deep neural network), SE (supervised encoder), and SVE (supervised variational encoder), and validate them on the Savannah river, Augusta, GA. Our results show that the fast solvers are capable of predicting flow velocities for different bathymetry and BCs with good accuracy, at a computational cost that is significantly lower than the cost of solving the full boundary value problem with traditional methods.

Producing diverse and realistic images with generative models such as GANs typically requires large scale training with vast amount of images. GANs trained with extremely limited data can easily overfit to few training samples and display undesirable properties like "stairlike" latent space where transitions in latent space suffer from discontinuity, occasionally yielding abrupt changes in outputs. In this work, we consider the situation where neither large scale dataset of our interest nor transferable source dataset is available, and seek to train existing generative models with minimal overfitting and mode collapse. We propose latent mixup-based distance regularization on the feature space of both a generator and the counterpart discriminator that encourages the two players to reason not only about the scarce observed data points but the relative distances in the feature space they reside. Qualitative and quantitative evaluation on diverse datasets demonstrates that our method is generally applicable to existing models to enhance both fidelity and diversity under the constraint of limited data. Code will be made public.

Conventional supervised learning methods, especially deep ones, are found to be sensitive to out-of-distribution (OOD) examples, largely because the learned representation mixes the semantic factor with the variation factor due to their domain-specific correlation, while only the semantic factor causes the output. To address the problem, we propose a Causal Semantic Generative model (CSG) based on a causal reasoning so that the two factors are modeled separately, and develop methods for OOD prediction from a single training domain, which is common and challenging. The methods are based on the causal invariance principle, with a novel design for both efficient learning and easy prediction. Theoretically, we prove that under certain conditions, CSG can identify the semantic factor by fitting training data, and this semantic-identification guarantees the boundedness of OOD generalization error and the success of adaptation. Empirical study shows improved OOD performance over prevailing baselines.

Leveraging biased click data for optimizing learning to rank systems has been a popular approach in information retrieval. Because click data is often noisy and biased, a variety of methods have been proposed to construct unbiased learning to rank (ULTR) algorithms for the learning of unbiased ranking models. Among them, automatic unbiased learning to rank (AutoULTR) algorithms that jointly learn user bias models (i.e., propensity models) with unbiased rankers have received a lot of attention due to their superior performance and low deployment cost in practice. Despite their differences in theories and algorithm design, existing studies on ULTR usually use uni-variate ranking functions to score each document or result independently. On the other hand, recent advances in context-aware learning-to-rank models have shown that multivariate scoring functions, which read multiple documents together and predict their ranking scores jointly, are more powerful than uni-variate ranking functions in ranking tasks with human-annotated relevance labels. Whether such superior performance would hold in ULTR with noisy data, however, is mostly unknown. In this paper, we investigate existing multivariate scoring functions and AutoULTR algorithms in theory and prove that permutation invariance is a crucial factor that determines whether a context-aware learning-to-rank model could be applied to existing AutoULTR framework. Our experiments with synthetic clicks on two large-scale benchmark datasets show that AutoULTR models with permutation-invariant multivariate scoring functions significantly outperform those with uni-variate scoring functions and permutation-variant multivariate scoring functions.

Graph convolution is the core of most Graph Neural Networks (GNNs) and usually approximated by message passing between direct (one-hop) neighbors. In this work, we remove the restriction of using only the direct neighbors by introducing a powerful, yet spatially localized graph convolution: Graph diffusion convolution (GDC). GDC leverages generalized graph diffusion, examples of which are the heat kernel and personalized PageRank. It alleviates the problem of noisy and often arbitrarily defined edges in real graphs. We show that GDC is closely related to spectral-based models and thus combines the strengths of both spatial (message passing) and spectral methods. We demonstrate that replacing message passing with graph diffusion convolution consistently leads to significant performance improvements across a wide range of models on both supervised and unsupervised tasks and a variety of datasets. Furthermore, GDC is not limited to GNNs but can trivially be combined with any graph-based model or algorithm (e.g. spectral clustering) without requiring any changes to the latter or affecting its computational complexity. Our implementation is available online.

Clustering is one of the most fundamental and wide-spread techniques in exploratory data analysis. Yet, the basic approach to clustering has not really changed: a practitioner hand-picks a task-specific clustering loss to optimize and fit the given data to reveal the underlying cluster structure. Some types of losses---such as k-means, or its non-linear version: kernelized k-means (centroid based), and DBSCAN (density based)---are popular choices due to their good empirical performance on a range of applications. Although every so often the clustering output using these standard losses fails to reveal the underlying structure, and the practitioner has to custom-design their own variation. In this work we take an intrinsically different approach to clustering: rather than fitting a dataset to a specific clustering loss, we train a recurrent model that learns how to cluster. The model uses as training pairs examples of datasets (as input) and its corresponding cluster identities (as output). By providing multiple types of training datasets as inputs, our model has the ability to generalize well on unseen datasets (new clustering tasks). Our experiments reveal that by training on simple synthetically generated datasets or on existing real datasets, we can achieve better clustering performance on unseen real-world datasets when compared with standard benchmark clustering techniques. Our meta clustering model works well even for small datasets where the usual deep learning models tend to perform worse.

In one-class-learning tasks, only the normal case (foreground) can be modeled with data, whereas the variation of all possible anomalies is too erratic to be described by samples. Thus, due to the lack of representative data, the wide-spread discriminative approaches cannot cover such learning tasks, and rather generative models, which attempt to learn the input density of the foreground, are used. However, generative models suffer from a large input dimensionality (as in images) and are typically inefficient learners. We propose to learn the data distribution of the foreground more efficiently with a multi-hypotheses autoencoder. Moreover, the model is criticized by a discriminator, which prevents artificial data modes not supported by data, and enforces diversity across hypotheses. Our multiple-hypothesesbased anomaly detection framework allows the reliable identification of out-of-distribution samples. For anomaly detection on CIFAR-10, it yields up to 3.9% points improvement over previously reported results. On a real anomaly detection task, the approach reduces the error of the baseline models from 6.8% to 1.5%.

Despite huge success in the image domain, modern detection models such as Faster R-CNN have not been used nearly as much for video analysis. This is arguably due to the fact that detection models are designed to operate on single frames and as a result do not have a mechanism for learning motion representations directly from video. We propose a learning procedure that allows detection models such as Faster R-CNN to learn motion features directly from the RGB video data while being optimized with respect to a pose estimation task. Given a pair of video frames---Frame A and Frame B---we force our model to predict human pose in Frame A using the features from Frame B. We do so by leveraging deformable convolutions across space and time. Our network learns to spatially sample features from Frame B in order to maximize pose detection accuracy in Frame A. This naturally encourages our network to learn motion offsets encoding the spatial correspondences between the two frames. We refer to these motion offsets as DiMoFs (Discriminative Motion Features). In our experiments we show that our training scheme helps learn effective motion cues, which can be used to estimate and localize salient human motion. Furthermore, we demonstrate that as a byproduct, our model also learns features that lead to improved pose detection in still-images, and better keypoint tracking. Finally, we show how to leverage our learned model for the tasks of spatiotemporal action localization and fine-grained action recognition.

Importance sampling is one of the most widely used variance reduction strategies in Monte Carlo rendering. In this paper, we propose a novel importance sampling technique that uses a neural network to learn how to sample from a desired density represented by a set of samples. Our approach considers an existing Monte Carlo rendering algorithm as a black box. During a scene-dependent training phase, we learn to generate samples with a desired density in the primary sample space of the rendering algorithm using maximum likelihood estimation. We leverage a recent neural network architecture that was designed to represent real-valued non-volume preserving ('Real NVP') transformations in high dimensional spaces. We use Real NVP to non-linearly warp primary sample space and obtain desired densities. In addition, Real NVP efficiently computes the determinant of the Jacobian of the warp, which is required to implement the change of integration variables implied by the warp. A main advantage of our approach is that it is agnostic of underlying light transport effects, and can be combined with many existing rendering techniques by treating them as a black box. We show that our approach leads to effective variance reduction in several practical scenarios.

In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data is available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm by experiments on synthetic and real data.

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