arXiv subjects

Samuel Kaski

Publications and source records attributed to Samuel Kaski.

At least 127 records · Page 7Linked to original sources

arXiv2021

Embarrassingly parallel MCMC using deep invertible transformations

While MCMC methods have become a main work-horse for Bayesian inference, scaling them to large distributed datasets is still a challenge. Embarrassingly parallel MCMC strategies take a divide-and-conquer stance to achieve this by writing the target posterior as a product of subposteriors, running MCMC for each of them in parallel and subsequently combining the results. The challenge then lies in devising efficient aggregation strategies. Current strategies trade-off between approximation quality, and costs of communication and computation. In this work, we introduce a novel method that addresses these issues simultaneously. Our key insight is to introduce a deep invertible transformation to approximate each of the subposteriors. These approximations can be made accurate even for complex distributions and serve as intermediate representations, keeping the total communication cost limited. Moreover, they enable us to sample from the product of the subposteriors using an efficient and stable importance sampling scheme. We demonstrate the approach outperforms available state-of-the-art methods in a range of challenging scenarios, including high-dimensional and heterogeneous subposteriors.

cs.LG↗

arXiv2021

Federated Stochastic Gradient Langevin Dynamics

Stochastic gradient MCMC methods, such as stochastic gradient Langevin dynamics (SGLD), employ fast but noisy gradient estimates to enable large-scale posterior sampling. Although we can easily extend SGLD to distributed settings, it suffers from two issues when applied to federated non-IID data. First, the variance of these estimates increases significantly. Second, delaying communication causes the Markov chains to diverge from the true posterior even for very simple models. To alleviate both these problems, we propose conducive gradients, a simple mechanism that combines local likelihood approximations to correct gradient updates. Notably, conducive gradients are easy to compute, and since we only calculate the approximations once, they incur negligible overhead. We apply conducive gradients to distributed stochastic gradient Langevin dynamics (DSGLD) and call the resulting method federated stochastic gradient Langevin dynamics (FSGLD). We demonstrate that our approach can handle delayed communication rounds, converging to the target posterior in cases where DSGLD fails. We also show that FSGLD outperforms DSGLD for non-IID federated data with experiments on metric learning and neural networks.

stat.ML↗

arXiv2021

DIVERSE: Bayesian Data IntegratiVE learning for precise drug ResponSE prediction

Detecting predictive biomarkers from multi-omics data is important for precision medicine, to improve diagnostics of complex diseases and for better treatments. This needs substantial experimental efforts that are made difficult by the heterogeneity of cell lines and huge cost. An effective solution is to build a computational model over the diverse omics data, including genomic, molecular, and environmental information. However, choosing informative and reliable data sources from among the different types of data is a challenging problem. We propose DIVERSE, a framework of Bayesian importance-weighted tri- and bi-matrix factorization(DIVERSE3 or DIVERSE2) to predict drug responses from data of cell lines, drugs, and gene interactions. DIVERSE integrates the data sources systematically, in a step-wise manner, examining the importance of each added data set in turn. More specifically, we sequentially integrate five different data sets, which have not all been combined in earlier bioinformatic methods for predicting drug responses. Empirical experiments show that DIVERSE clearly outperformed five other methods including three state-of-the-art approaches, under cross-validation, particularly in out-of-matrix prediction, which is closer to the setting of real use cases and more challenging than simpler in-matrix prediction. Additionally, case studies for discovering new drugs further confirmed the performance advantage of DIVERSE.

q-bio.QM↗

arXiv2021

Affine Transport for Sim-to-Real Domain Adaptation

Sample-efficient domain adaptation is an open problem in robotics. In this paper, we present affine transport -- a variant of optimal transport, which models the mapping between state transition distributions between the source and target domains with an affine transformation. First, we derive the affine transport framework; then, we extend the basic framework with Procrustes alignment to model arbitrary affine transformations. We evaluate the method in a number of OpenAI Gym sim-to-sim experiments with simulation environments, as well as on a sim-to-real domain adaptation task of a robot hitting a hockeypuck such that it slides and stops at a target position. In each experiment, we evaluate the results when transferring between each pair of dynamics domains. The results show that affine transport can significantly reduce the model adaptation error in comparison to using the original, non-adapted dynamics model.

cs.RO↗

arXiv2021

Differentially Private Bayesian Inference for Generalized Linear Models

Generalized linear models (GLMs) such as logistic regression are among the most widely used arms in data analyst's repertoire and often used on sensitive datasets. A large body of prior works that investigate GLMs under differential privacy (DP) constraints provide only private point estimates of the regression coefficients, and are not able to quantify parameter uncertainty. In this work, with logistic and Poisson regression as running examples, we introduce a generic noise-aware DP Bayesian inference method for a GLM at hand, given a noisy sum of summary statistics. Quantifying uncertainty allows us to determine which of the regression coefficients are statistically significantly different from zero. We provide a previously unknown tight privacy analysis and experimentally demonstrate that the posteriors obtained from our model, while adhering to strong privacy guarantees, are close to the non-private posteriors.

cs.LG↗

arXiv2021

Privacy-preserving data sharing via probabilistic modelling

Differential privacy allows quantifying privacy loss resulting from accessing sensitive personal data. Repeated accesses to underlying data incur increasing loss. Releasing data as privacy-preserving synthetic data would avoid this limitation, but would leave open the problem of designing what kind of synthetic data. We propose formulating the problem of private data release through probabilistic modelling. This approach transforms the problem of designing the synthetic data into choosing a model for the data, allowing also including prior knowledge, which improves the quality of the synthetic data. We demonstrate empirically, in an epidemiological study, that statistical discoveries can be reliably reproduced from the synthetic data. We expect the method to have broad use in creating high-quality anonymized data twins of key data sets for research.

stat.ML↗

arXiv2021

Decision Rule Elicitation for Domain Adaptation

Human-in-the-loop machine learning is widely used in artificial intelligence (AI) to elicit labels for data points from experts or to provide feedback on how close the predicted results are to the target. This simplifies away all the details of the decision-making process of the expert. In this work, we allow the experts to additionally produce decision rules describing their decision-making; the rules are expected to be imperfect but to give additional information. In particular, the rules can extend to new distributions, and hence enable significantly improving performance for cases where the training and testing distributions differ, such as in domain adaptation. We apply the proposed method to lifelong learning and domain adaptation problems and discuss applications in other branches of AI, such as knowledge acquisition problems in expert systems. In simulated and real-user studies, we show that decision rule elicitation improves domain adaptation of the algorithm and helps to propagate expert's knowledge to the AI model.

cs.LG↗

arXiv2021

Informative Bayesian Neural Network Priors for Weak Signals

Encoding domain knowledge into the prior over the high-dimensional weight space of a neural network is challenging but essential in applications with limited data and weak signals. Two types of domain knowledge are commonly available in scientific applications: 1. feature sparsity (fraction of features deemed relevant); 2. signal-to-noise ratio, quantified, for instance, as the proportion of variance explained (PVE). We show how to encode both types of domain knowledge into the widely used Gaussian scale mixture priors with Automatic Relevance Determination. Specifically, we propose a new joint prior over the local (i.e., feature-specific) scale parameters that encodes knowledge about feature sparsity, and a Stein gradient optimization to tune the hyperparameters in such a way that the distribution induced on the model's PVE matches the prior distribution. We show empirically that the new prior improves prediction accuracy, compared to existing neural network priors, on several publicly available datasets and in a genetics application where signals are weak and sparse, often outperforming even computationally intensive cross-validation for hyperparameter tuning.

stat.ML↗

arXiv2020

Sample-efficient reinforcement learning using deep Gaussian processes

Reinforcement learning provides a framework for learning to control which actions to take towards completing a task through trial-and-error. In many applications observing interactions is costly, necessitating sample-efficient learning. In model-based reinforcement learning efficiency is improved by learning to simulate the world dynamics. The challenge is that model inaccuracies rapidly accumulate over planned trajectories. We introduce deep Gaussian processes where the depth of the compositions introduces model complexity while incorporating prior knowledge on the dynamics brings smoothness and structure. Our approach is able to sample a Bayesian posterior over trajectories. We demonstrate highly improved early sample-efficiency over competing methods. This is shown across a number of continuous control tasks, including the half-cheetah whose contact dynamics have previously posed an insurmountable problem for earlier sample-efficient Gaussian process based models.

stat.ML↗

arXiv2020

Scalable Bayesian neural networks by layer-wise input augmentation

We introduce implicit Bayesian neural networks, a simple and scalable approach for uncertainty representation in deep learning. Standard Bayesian approach to deep learning requires the impractical inference of the posterior distribution over millions of parameters. Instead, we propose to induce a distribution that captures the uncertainty over neural networks by augmenting each layer's inputs with latent variables. We present appropriate input distributions and demonstrate state-of-the-art performance in terms of calibration, robustness and uncertainty characterisation over large-scale, multi-million parameter image classification tasks.

stat.ML↗

arXiv2020

Rethinking pooling in graph neural networks

Graph pooling is a central component of a myriad of graph neural network (GNN) architectures. As an inheritance from traditional CNNs, most approaches formulate graph pooling as a cluster assignment problem, extending the idea of local patches in regular grids to graphs. Despite the wide adherence to this design choice, no work has rigorously evaluated its influence on the success of GNNs. In this paper, we build upon representative GNNs and introduce variants that challenge the need for locality-preserving representations, either using randomization or clustering on the complement graph. Strikingly, our experiments demonstrate that using these variants does not result in any decrease in performance. To understand this phenomenon, we study the interplay between convolutional layers and the subsequent pooling ones. We show that the convolutions play a leading role in the learned representations. In contrast to the common belief, local pooling is not responsible for the success of GNNs on relevant and widely-used benchmarks.

cs.LG↗

arXiv2020

Bayesian Inference for Optimal Transport with Stochastic Cost

In machine learning and computer vision, optimal transport has had significant success in learning generative models and defining metric distances between structured and stochastic data objects, that can be cast as probability measures. The key element of optimal transport is the so called lifting of an \emph{exact} cost (distance) function, defined on the sample space, to a cost (distance) between probability measures over the sample space. However, in many real life applications the cost is \emph{stochastic}: e.g., the unpredictable traffic flow affects the cost of transportation between a factory and an outlet. To take this stochasticity into account, we introduce a Bayesian framework for inferring the optimal transport plan distribution induced by the stochastic cost, allowing for a principled way to include prior information and to model the induced stochasticity on the transport plans. Additionally, we tailor an HMC method to sample from the resulting transport plan posterior distribution.

cs.LG↗

arXiv2020

Teaching to Learn: Sequential Teaching of Agents with Inner States

In sequential machine teaching, a teacher's objective is to provide the optimal sequence of inputs to sequential learners in order to guide them towards the best model. In this paper we extend this setting from current static one-data-set analyses to learners which change their learning algorithm or latent state to improve during learning, and to generalize to new datasets. We introduce a multi-agent formulation in which learners' inner state may change with the teaching interaction, which affects the learning performance in future tasks. In order to teach such learners, we propose an optimal control approach that takes the future performance of the learner after teaching into account. This provides tools for modelling learners having inner states, and machine teaching of meta-learning algorithms. Furthermore, we distinguish manipulative teaching, which can be done by effectively hiding data and also used for indoctrination, from more general education which aims to help the learner become better at generalization and learning in new datasets in the absence of a teacher.

cs.LG↗

arXiv2020

Likelihood-free inference by ratio estimation

We consider the problem of parametric statistical inference when likelihood computations are prohibitively expensive but sampling from the model is possible. Several so-called likelihood-free methods have been developed to perform inference in the absence of a likelihood function. The popular synthetic likelihood approach infers the parameters by modelling summary statistics of the data by a Gaussian probability distribution. In another popular approach called approximate Bayesian computation, the inference is performed by identifying parameter values for which the summary statistics of the simulated data are close to those of the observed data. Synthetic likelihood is easier to use as no measure of `closeness' is required but the Gaussianity assumption is often limiting. Moreover, both approaches require judiciously chosen summary statistics. We here present an alternative inference approach that is as easy to use as synthetic likelihood but not as restricted in its assumptions, and that, in a natural way, enables automatic selection of relevant summary statistic from a large set of candidates. The basic idea is to frame the problem of estimating the posterior as a problem of estimating the ratio between the data generating distribution and the marginal distribution. This problem can be solved by logistic regression, and including regularising penalty terms enables automatic selection of the summary statistics relevant to the inference task. We illustrate the general theory on canonical examples and employ it to perform inference for challenging stochastic nonlinear dynamical systems and high-dimensional summary statistics.

stat.ML↗

arXiv2020

Projective Preferential Bayesian Optimization

Bayesian optimization is an effective method for finding extrema of a black-box function. We propose a new type of Bayesian optimization for learning user preferences in high-dimensional spaces. The central assumption is that the underlying objective function cannot be evaluated directly, but instead a minimizer along a projection can be queried, which we call a projective preferential query. The form of the query allows for feedback that is natural for a human to give, and which enables interaction. This is demonstrated in a user experiment in which the user feedback comes in the form of optimal position and orientation of a molecule adsorbing to a surface. We demonstrate that our framework is able to find a global minimum of a high-dimensional black-box function, which is an infeasible task for existing preferential Bayesian optimization frameworks that are based on pairwise comparisons.

stat.ML↗

arXiv2020

A Decision-Theoretic Approach for Model Interpretability in Bayesian Framework

A salient approach to interpretable machine learning is to restrict modeling to simple models. In the Bayesian framework, this can be pursued by restricting the model structure and prior to favor interpretable models. Fundamentally, however, interpretability is about users' preferences, not the data generation mechanism; it is more natural to formulate interpretability as a utility function. In this work, we propose an interpretability utility, which explicates the trade-off between explanation fidelity and interpretability in the Bayesian framework. The method consists of two steps. First, a reference model, possibly a black-box Bayesian predictive model which does not compromise accuracy, is fitted to the training data. Second, a proxy model from an interpretable model family that best mimics the predictive behaviour of the reference model is found by optimizing the interpretability utility function. The approach is model agnostic -- neither the interpretable model nor the reference model are restricted to a certain class of models -- and the optimization problem can be solved using standard tools. Through experiments on real-word data sets, using decision trees as interpretable models and Bayesian additive regression models as reference models, we show that for the same level of interpretability, our approach generates more accurate models than the alternative of restricting the prior. We also propose a systematic way to measure stability of interpretabile models constructed by different interpretability approaches and show that our proposed approach generates more stable models.

cs.LG↗

arXiv2020

Differentially private cross-silo federated learning

Strict privacy is of paramount importance in distributed machine learning. Federated learning, with the main idea of communicating only what is needed for learning, has been recently introduced as a general approach for distributed learning to enhance learning and improve security. However, federated learning by itself does not guarantee any privacy for data subjects. To quantify and control how much privacy is compromised in the worst-case, we can use differential privacy. In this paper we combine additively homomorphic secure summation protocols with differential privacy in the so-called cross-silo federated learning setting. The goal is to learn complex models like neural networks while guaranteeing strict privacy for the individual data subjects. We demonstrate that our proposed solutions give prediction accuracy that is comparable to the non-distributed setting, and are fast enough to enable learning models with millions of parameters in a reasonable time. To enable learning under strict privacy guarantees that need privacy amplification by subsampling, we present a general algorithm for oblivious distributed subsampling. However, we also argue that when malicious parties are present, a simple approach using distributed Poisson subsampling gives better privacy. Finally, we show that by leveraging random projections we can further scale-up our approach to larger models while suffering only a modest performance loss.

cs.CR↗

arXiv2020

Human Strategic Steering Improves Performance of Interactive Optimization

A central concern in an interactive intelligent system is optimization of its actions, to be maximally helpful to its human user. In recommender systems for instance, the action is to choose what to recommend, and the optimization task is to recommend items the user prefers. The optimization is done based on earlier user's feedback (e.g. "likes" and "dislikes"), and the algorithms assume the feedback to be faithful. That is, when the user clicks "like," they actually prefer the item. We argue that this fundamental assumption can be extensively violated by human users, who are not passive feedback sources. Instead, they are in control, actively steering the system towards their goal. To verify this hypothesis, that humans steer and are able to improve performance by steering, we designed a function optimization task where a human and an optimization algorithm collaborate to find the maximum of a 1-dimensional function. At each iteration, the optimization algorithm queries the user for the value of a hidden function $f$ at a point $x$, and the user, who sees the hidden function, provides an answer about $f(x)$. Our study on 21 participants shows that users who understand how the optimization works, strategically provide biased answers (answers not equal to $f(x)$), which results in the algorithm finding the optimum significantly faster. Our work highlights that next-generation intelligent systems will need user models capable of helping users who steer systems to pursue their goals.

cs.HC↗