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Samuel Kaski

Samuel Kaski appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningInformation RetrievalArtificial IntelligenceApplicationsMethodologyGenomicsHuman-Computer InteractionQuantitative MethodsComputational Engineering, Finance, and ScienceCryptography and SecurityBiomoleculesComputationMultiagent SystemsDistributed, Parallel, and Cluster ComputingMathematical SoftwareMolecular Networks

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Published work

58 published item(s)

preprint2026arXiv

Decoupled Conformal Optimisation: Efficient Prediction Sets via Independent Tuning and Calibration

Bayesian conformal optimisation methods often use the same held-out data both to search for efficient prediction sets and to certify coverage or risk. This coupling is natural for high-probability risk-control guarantees, but it is not necessary when the target is standard finite-sample marginal conformal coverage. We propose Decoupled Conformal Optimisation (DCO), a train-tune-calibrate design principle that uses an independent tuning split for efficiency-oriented structural selection and a fresh calibration split for the final conformal quantile. Conditional on the tuned structure, standard split-conformal exchangeability yields finite-sample marginal coverage for any candidate class, without a confidence parameter or multiple-testing correction. DCO therefore targets a different finite-sample guarantee from PAC-style methods: marginal conformal coverage rather than high-probability risk control. Under consistency assumptions on the coupled risk bound, the two approaches nevertheless converge to the same population threshold. Across classification and regression benchmarks, including ImageNet-A, CIFAR-100, Diabetes, California Housing, and Concrete, DCO tracks the nominal coverage level closely while often reducing average prediction-set size or interval width relative to PAC-style calibration. On ImageNet-A, for example, the average set size decreases from $26.52$ to $25.26$ and the 95th-percentile set size from $58.95$ to $53.73$; on Diabetes, the average interval width decreases from $2.098$ to $1.914$.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Elicitation-Augmented Bayesian Optimization

Human-in-the-loop Bayesian optimization (HITL BO) methods utilize human expertise to improve the sample-efficiency of BO. Most HITL BO methods assume that a domain expert can quantify their knowledge, for instance by pinpointing query locations or specifying their prior beliefs about the location of the maximum as a probability distribution. However, since human expertise is often tacit and cannot be explicitly quantified, we consider a setting where domain knowledge of an expert is elicited via pairwise comparisons of designs. We interpret the expert's pairwise judgements as noisy evidence about the values of the observable objective function and develop a principled method for combining the information obtained via direct observations and pairwise queries. Specifically, we derive a cost-aware value-of-information acquisition function that balances direct observations against pairwise queries. The proposed method approaches the convex hull of the trajectories of the individual information sources: when pairwise queries are cheap it substantially improves sample-efficiency over observation-only BO, and when pairwise queries are costly or noisy, it recovers the performance of standard BO by relying on direct observations alone.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

In-Context Black-Box Optimization with Unreliable Feedback

Black-box optimization in science and engineering often comes with side information: experts, simulators, pretrained predictors, or heuristics can suggest which candidates look promising. This information can accelerate search, but it can also be biased, input-dependent, or misleading. Feedback-aware BO methods typically handle one task at a time, limiting their ability to generalize over multiple sources of feedback. In-context optimizers address cross-task adaptation, but usually assume that optimization history is the only available signal at test time. We study feedback-informed in-context black-box optimization (FICBO), where a pretrained optimizer conditions on both the observed history and cheap auxiliary feedback for the current candidate set. We introduce a structured feedback prior that models how feedback sources vary in their access, relevance, and distortion relative to the true objective, and use it to pretrain a feedback-aware transformer. At test time, the model estimates source reliability in context by comparing observed objective values with auxiliary signals, improving query selection. On synthetic and real-world tasks, FICBO effectively exploits informative feedback while remaining robust to weak or misleading sources, improving over other baselines. Empirical investigations further illustrate how the model perceives test-time sources, offering insights into its interpretability and decision-making process.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Online Sharp-Calibrated Bayesian Optimization

Bayesian optimization (BO) is a widely used framework for optimizing expensive black-box functions, commonly based on Gaussian process (GP) surrogate models. Its effectiveness relies on uncertainty quantification that is both sharp (informative) and well-calibrated along the BO trajectory. In practice, GP kernel hyperparameters are unknown and are refit online from sequentially collected (non-i.i.d.) data, which can yield miscalibrated or overly conservative uncertainty and lies outside the fixed-kernel assumptions of standard BO regret theory. We propose Online Sharp-Calibrated Bayesian Optimization (OSCBO), a BO algorithm that adaptively balances GP sharpness and calibration by casting hyperparameter selection as a constrained online-learning problem. We also show that OSCBO preserves sublinear regret bounds by leveraging the theoretical guarantees of the underlying online learning algorithm. Empirically, OSCBO performs competitively across synthetic and real-world benchmarks, ranking among the strongest methods in final simple regret while maintaining robust cumulative-regret behavior.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

Robust and Computation-Aware Gaussian Processes

Gaussian processes (GPs) are widely used for regression and optimization tasks such as Bayesian optimization (BO) due to their expressiveness and principled uncertainty estimates. However, in settings with large datasets corrupted by outliers, standard GPs and their sparse approximations struggle with computational tractability and robustness. We introduce Robust Computation-aware Gaussian Process (RCaGP), a novel GP model that jointly addresses these challenges by combining a principled treatment of approximation-induced uncertainty with robust generalized Bayesian updating. The key insight is that robustness and approximation-awareness are not orthogonal but intertwined: approximations can exacerbate the impact of outliers, and mitigating one without the other is insufficient. Unlike previous work that focuses narrowly on either robustness or approximation quality, RCaGP combines both in a principled and scalable framework, thus effectively managing both outliers and computational uncertainties introduced by approximations such as low-rank matrix multiplications. Our model ensures more conservative and reliable uncertainty estimates, a property we rigorously demonstrate. Additionally, we establish a robustness property and show that the mean function is key to preserving it, motivating a tailored model selection scheme for robust mean functions. Empirical results confirm that solving these challenges jointly leads to superior performance across both clean and outlier-contaminated settings, both on regression and high-throughput Bayesian optimization benchmarks.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Approximate Bayesian Computation with Domain Expert in the Loop

Approximate Bayesian computation (ABC) is a popular likelihood-free inference method for models with intractable likelihood functions. As ABC methods usually rely on comparing summary statistics of observed and simulated data, the choice of the statistics is crucial. This choice involves a trade-off between loss of information and dimensionality reduction, and is often determined based on domain knowledge. However, handcrafting and selecting suitable statistics is a laborious task involving multiple trial-and-error steps. In this work, we introduce an active learning method for ABC statistics selection which reduces the domain expert's work considerably. By involving the experts, we are able to handle misspecified models, unlike the existing dimension reduction methods. Moreover, empirical results show better posterior estimates than with existing methods, when the simulation budget is limited.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Bayesian Optimization Augmented with Actively Elicited Expert Knowledge

Bayesian optimization (BO) is a well-established method to optimize black-box functions whose direct evaluations are costly. In this paper, we tackle the problem of incorporating expert knowledge into BO, with the goal of further accelerating the optimization, which has received very little attention so far. We design a multi-task learning architecture for this task, with the goal of jointly eliciting the expert knowledge and minimizing the objective function. In particular, this allows for the expert knowledge to be transferred into the BO task. We introduce a specific architecture based on Siamese neural networks to handle the knowledge elicitation from pairwise queries. Experiments on various benchmark functions with both simulated and actual human experts show that the proposed method significantly speeds up BO even when the expert knowledge is biased compared to the objective function.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Best-Response Bayesian Reinforcement Learning with Bayes-adaptive POMDPs for Centaurs

Centaurs are half-human, half-AI decision-makers where the AI's goal is to complement the human. To do so, the AI must be able to recognize the goals and constraints of the human and have the means to help them. We present a novel formulation of the interaction between the human and the AI as a sequential game where the agents are modelled using Bayesian best-response models. We show that in this case the AI's problem of helping bounded-rational humans make better decisions reduces to a Bayes-adaptive POMDP. In our simulated experiments, we consider an instantiation of our framework for humans who are subjectively optimistic about the AI's future behaviour. Our results show that when equipped with a model of the human, the AI can infer the human's bounds and nudge them towards better decisions. We discuss ways in which the machine can learn to improve upon its own limitations as well with the help of the human. We identify a novel trade-off for centaurs in partially observable tasks: for the AI's actions to be acceptable to the human, the machine must make sure their beliefs are sufficiently aligned, but aligning beliefs might be costly. We present a preliminary theoretical analysis of this trade-off and its dependence on task structure.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deconfounded Representation Similarity for Comparison of Neural Networks

Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population structure of data items in the input space, leading to spuriously high similarity for even completely random neural networks and inconsistent domain relations in transfer learning. We introduce a simple and generally applicable fix to adjust for the confounder with covariate adjustment regression, which retains the intuitive invariance properties of the original similarity measures. We show that deconfounding the similarity metrics increases the resolution of detecting semantically similar neural networks. Moreover, in real-world applications, deconfounding improves the consistency of representation similarities with domain similarities in transfer learning, and increases correlation with out-of-distribution accuracy.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Human-in-the-Loop Large-Scale Predictive Maintenance of Workstations

Predictive maintenance (PdM) is the task of scheduling maintenance operations based on a statistical analysis of the system's condition. We propose a human-in-the-loop PdM approach in which a machine learning system predicts future problems in sets of workstations (computers, laptops, and servers). Our system interacts with domain experts to improve predictions and elicit their knowledge. In our approach, domain experts are included in the loop not only as providers of correct labels, as in traditional active learning, but as a source of explicit decision rule feedback. The system is automated and designed to be easily extended to novel domains, such as maintaining workstations of several organizations. In addition, we develop a simulator for reproducible experiments in a controlled environment and deploy the system in a large-scale case of real-life workstations PdM with thousands of workstations for dozens of companies.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Parallel MCMC Without Embarrassing Failures

Embarrassingly parallel Markov Chain Monte Carlo (MCMC) exploits parallel computing to scale Bayesian inference to large datasets by using a two-step approach. First, MCMC is run in parallel on (sub)posteriors defined on data partitions. Then, a server combines local results. While efficient, this framework is very sensitive to the quality of subposterior sampling. Common sampling problems such as missing modes or misrepresentation of low-density regions are amplified -- instead of being corrected -- in the combination phase, leading to catastrophic failures. In this work, we propose a novel combination strategy to mitigate this issue. Our strategy, Parallel Active Inference (PAI), leverages Gaussian Process (GP) surrogate modeling and active learning. After fitting GPs to subposteriors, PAI (i) shares information between GP surrogates to cover missing modes; and (ii) uses active sampling to individually refine subposterior approximations. We validate PAI in challenging benchmarks, including heavy-tailed and multi-modal posteriors and a real-world application to computational neuroscience. Empirical results show that PAI succeeds where previous methods catastrophically fail, with a small communication overhead.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Privacy-preserving Data Sharing on Vertically Partitioned Data

In this work, we introduce a differentially private method for generating synthetic data from vertically partitioned data, \emph{i.e.}, where data of the same individuals is distributed across multiple data holders or parties. We present a differentially privacy stochastic gradient descent (DP-SGD) algorithm to train a mixture model over such partitioned data using variational inference. We modify a secure multiparty computation (MPC) framework to combine MPC with differential privacy (DP), in order to use differentially private MPC effectively to learn a probabilistic generative model under DP on such vertically partitioned data. Assuming the mixture components contain no dependencies across different parties, the objective function can be factorized into a sum of products of the contributions calculated by the parties. Finally, MPC is used to compute the aggregate between the different contributions. Moreover, we rigorously define the privacy guarantees with respect to the different players in the system. To demonstrate the accuracy of our method, we run our algorithm on the Adult dataset from the UCI machine learning repository, where we obtain comparable results to the non-partitioned case.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Tackling covariate shift with node-based Bayesian neural networks

Bayesian neural networks (BNNs) promise improved generalization under covariate shift by providing principled probabilistic representations of epistemic uncertainty. However, weight-based BNNs often struggle with high computational complexity of large-scale architectures and datasets. Node-based BNNs have recently been introduced as scalable alternatives, which induce epistemic uncertainty by multiplying each hidden node with latent random variables, while learning a point-estimate of the weights. In this paper, we interpret these latent noise variables as implicit representations of simple and domain-agnostic data perturbations during training, producing BNNs that perform well under covariate shift due to input corruptions. We observe that the diversity of the implicit corruptions depends on the entropy of the latent variables, and propose a straightforward approach to increase the entropy of these variables during training. We evaluate the method on out-of-distribution image classification benchmarks, and show improved uncertainty estimation of node-based BNNs under covariate shift due to input perturbations. As a side effect, the method also provides robustness against noisy training labels.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Variational multiple shooting for Bayesian ODEs with Gaussian processes

Recent machine learning advances have proposed black-box estimation of unknown continuous-time system dynamics directly from data. However, earlier works are based on approximative ODE solutions or point estimates. We propose a novel Bayesian nonparametric model that uses Gaussian processes to infer posteriors of unknown ODE systems directly from data. We derive sparse variational inference with decoupled functional sampling to represent vector field posteriors. We also introduce a probabilistic shooting augmentation to enable efficient inference from arbitrarily long trajectories. The method demonstrates the benefit of computing vector field posteriors, with predictive uncertainty scores outperforming alternative methods on multiple ODE learning tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

D3p -- A Python Package for Differentially-Private Probabilistic Programming

We present d3p, a software package designed to help fielding runtime efficient widely-applicable Bayesian inference under differential privacy guarantees. d3p achieves general applicability to a wide range of probabilistic modelling problems by implementing the differentially private variational inference algorithm, allowing users to fit any parametric probabilistic model with a differentiable density function. d3p adopts the probabilistic programming paradigm as a powerful way for the user to flexibly define such models. We demonstrate the use of our software on a hierarchical logistic regression example, showing the expressiveness of the modelling approach as well as the ease of running the parameter inference. We also perform an empirical evaluation of the runtime of the private inference on a complex model and find a $\sim$10 fold speed-up compared to an implementation using TensorFlow Privacy.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A High-Performance Implementation of Bayesian Matrix Factorization with Limited Communication

Matrix factorization is a very common machine learning technique in recommender systems. Bayesian Matrix Factorization (BMF) algorithms would be attractive because of their ability to quantify uncertainty in their predictions and avoid over-fitting, combined with high prediction accuracy. However, they have not been widely used on large-scale data because of their prohibitive computational cost. In recent work, efforts have been made to reduce the cost, both by improving the scalability of the BMF algorithm as well as its implementation, but so far mainly separately. In this paper we show that the state-of-the-art of both approaches to scalability can be combined. We combine the recent highly-scalable Posterior Propagation algorithm for BMF, which parallelizes computation of blocks of the matrix, with a distributed BMF implementation that users asynchronous communication within each block. We show that the combination of the two methods gives substantial improvements in the scalability of BMF on web-scale datasets, when the goal is to reduce the wall-clock time.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Correlated Feature Selection with Extended Exclusive Group Lasso

In many high dimensional classification or regression problems set in a biological context, the complete identification of the set of informative features is often as important as predictive accuracy, since this can provide mechanistic insight and conceptual understanding. Lasso and related algorithms have been widely used since their sparse solutions naturally identify a set of informative features. However, Lasso performs erratically when features are correlated. This limits the use of such algorithms in biological problems, where features such as genes often work together in pathways, leading to sets of highly correlated features. In this paper, we examine the performance of a Lasso derivative, the exclusive group Lasso, in this setting. We propose fast algorithms to solve the exclusive group Lasso, and introduce a solution to the case when the underlying group structure is unknown. The solution combines stability selection with random group allocation and introduction of artificial features. Experiments with both synthetic and real-world data highlight the advantages of this proposed methodology over Lasso in comprehensive selection of informative features.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Learning Global Pairwise Interactions with Bayesian Neural Networks

Estimating global pairwise interaction effects, i.e., the difference between the joint effect and the sum of marginal effects of two input features, with uncertainty properly quantified, is centrally important in science applications. We propose a non-parametric probabilistic method for detecting interaction effects of unknown form. First, the relationship between the features and the output is modelled using a Bayesian neural network, capable of representing complex interactions and principled uncertainty. Second, interaction effects and their uncertainty are estimated from the trained model. For the second step, we propose an intuitive global interaction measure: Bayesian Group Expected Hessian (GEH), which aggregates information of local interactions as captured by the Hessian. GEH provides a natural trade-off between type I and type II error and, moreover, comes with theoretical guarantees ensuring that the estimated interaction effects and their uncertainty can be improved by training a more accurate BNN. The method empirically outperforms available non-probabilistic alternatives on simulated and real-world data. Finally, we demonstrate its ability to detect interpretable interactions between higher-level features (at deeper layers of the neural network).

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Bayesian inference in hierarchical models by combining independent posteriors

Hierarchical models are versatile tools for joint modeling of data sets arising from different, but related, sources. Fully Bayesian inference may, however, become computationally prohibitive if the source-specific data models are complex, or if the number of sources is very large. To facilitate computation, we propose an approach, where inference is first made independently for the parameters of each data set, whereupon the obtained posterior samples are used as observed data in a substitute hierarchical model, based on a scaled likelihood function. Compared to direct inference in a full hierarchical model, the approach has the advantage of being able to speed up convergence by breaking down the initial large inference problem into smaller individual subproblems with better convergence properties. Moreover it enables parallel processing of the possibly complex inferences of the source-specific parameters, which may otherwise create a computational bottleneck if processed jointly as part of a hierarchical model. The approach is illustrated with both simulated and real data.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Bayesian multi-tensor factorization

We introduce Bayesian multi-tensor factorization, a model that is the first Bayesian formulation for joint factorization of multiple matrices and tensors. The research problem generalizes the joint matrix-tensor factorization problem to arbitrary sets of tensors of any depth, including matrices, can be interpreted as unsupervised multi-view learning from multiple data tensors, and can be generalized to relax the usual trilinear tensor factorization assumptions. The result is a factorization of the set of tensors into factors shared by any subsets of the tensors, and factors private to individual tensors. We demonstrate the performance against existing baselines in multiple tensor factorization tasks in structural toxicogenomics and functional neuroimaging.

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preprint2016arXiv

Classification of weak multi-view signals by sharing factors in a mixture of Bayesian group factor analyzers

We propose a novel classification model for weak signal data, building upon a recent model for Bayesian multi-view learning, Group Factor Analysis (GFA). Instead of assuming all data to come from a single GFA model, we allow latent clusters, each having a different GFA model and producing a different class distribution. We show that sharing information across the clusters, by sharing factors, increases the classification accuracy considerably; the shared factors essentially form a flexible noise model that explains away the part of data not related to classification. Motivation for the setting comes from single-trial functional brain imaging data, having a very low signal-to-noise ratio and a natural multi-view setting, with the different sensors, measurement modalities (EEG, MEG, fMRI) and possible auxiliary information as views. We demonstrate our model on a MEG dataset.

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preprint2016arXiv

Convex Factorization Machine for Regression

We propose the convex factorization machine (CFM), which is a convex variant of the widely used Factorization Machines (FMs). Specifically, we employ a linear+quadratic model and regularize the linear term with the $\ell_2$-regularizer and the quadratic term with the trace norm regularizer. Then, we formulate the CFM optimization as a semidefinite programming problem and propose an efficient optimization procedure with Hazan's algorithm. A key advantage of CFM over existing FMs is that it can find a globally optimal solution, while FMs may get a poor locally optimal solution since the objective function of FMs is non-convex. In addition, the proposed algorithm is simple yet effective and can be implemented easily. Finally, CFM is a general factorization method and can also be used for other factorization problems including including multi-view matrix factorization and tensor completion problems. Through synthetic and movielens datasets, we first show that the proposed CFM achieves results competitive to FMs. Furthermore, in a toxicogenomics prediction task, we show that CFM outperforms a state-of-the-art tensor factorization method.

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preprint2016arXiv

Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorization

A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially valuable in oncology, where molecular and genetic heterogeneity of the cells has a major impact on the response. However, the prediction task is extremely challenging, raising the need for methods that can effectively model and predict drug responses. In this study, we propose a novel formulation of multi-task matrix factorization that allows selective data integration for predicting drug responses. To solve the modeling task, we extend the state-of-the-art kernelized Bayesian matrix factorization (KBMF) method with component-wise multiple kernel learning. In addition, our approach exploits the known pathway information in a novel and biologically meaningful fashion to learn the drug response associations. Our method quantitatively outperforms the state of the art on predicting drug responses in two publicly available cancer data sets as well as on a synthetic data set. In addition, we validated our model predictions with lab experiments using an in-house cancer cell line panel. We finally show the practical applicability of the proposed method by utilizing prior knowledge to infer pathway-drug response associations, opening up the opportunity for elucidating drug action mechanisms. We demonstrate that pathway-response associations can be learned by the proposed model for the well known EGFR and MEK inhibitors.

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preprint2016arXiv

GFA: Exploratory Analysis of Multiple Data Sources with Group Factor Analysis

The R package GFA provides a full pipeline for factor analysis of multiple data sources that are represented as matrices with co-occurring samples. It allows learning dependencies between subsets of the data sources, decomposed into latent factors. The package also implements sparse priors for the factorization, providing interpretable biclusters of the multi-source data

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Interactive Modeling of Concept Drift and Errors in Relevance Feedback

Users giving relevance feedback in exploratory search are often uncertain about the correctness of their feedback, which may result in noisy or even erroneous feedback. Additionally, the search intent of the user may be volatile as the user is constantly learning and reformulating her search hypotheses during the search. This may lead to a noticeable concept drift in the feedback. We formulate a Bayesian regression model for predicting the accuracy of each individual user feedback and thus find outliers in the feedback data set. Additionally, we introduce a timeline interface that visualizes the feedback history to the user and gives her suggestions on which past feedback is likely in need of adjustment. This interface also allows the user to adjust the feedback accuracy inferences made by the model. Simulation experiments demonstrate that the performance of the new user model outperforms a simpler baseline and that the performance approaches that of an oracle, given a small amount of additional user interaction. A user study shows that the proposed modelling technique, combined with the timeline interface, makes it easier for the users to notice and correct mistakes in their feedback, and to discover new items.

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preprint2016arXiv

Localized Lasso for High-Dimensional Regression

We introduce the localized Lasso, which is suited for learning models that are both interpretable and have a high predictive power in problems with high dimensionality $d$ and small sample size $n$. More specifically, we consider a function defined by local sparse models, one at each data point. We introduce sample-wise network regularization to borrow strength across the models, and sample-wise exclusive group sparsity (a.k.a., $\ell_{1,2}$ norm) to introduce diversity into the choice of feature sets in the local models. The local models are interpretable in terms of similarity of their sparsity patterns. The cost function is convex, and thus has a globally optimal solution. Moreover, we propose a simple yet efficient iterative least-squares based optimization procedure for the localized Lasso, which does not need a tuning parameter, and is guaranteed to converge to a globally optimal solution. The solution is empirically shown to outperform alternatives for both simulated and genomic personalized medicine data.

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preprint2016arXiv

Modelling-based experiment retrieval: A case study with gene expression clustering

Motivation: Public and private repositories of experimental data are growing to sizes that require dedicated methods for finding relevant data. To improve on the state of the art of keyword searches from annotations, methods for content-based retrieval have been proposed. In the context of gene expression experiments, most methods retrieve gene expression profiles, requiring each experiment to be expressed as a single profile, typically of case vs. control. A more general, recently suggested alternative is to retrieve experiments whose models are good for modelling the query dataset. However, for very noisy and high-dimensional query data, this retrieval criterion turns out to be very noisy as well. Results: We propose doing retrieval using a denoised model of the query dataset, instead of the original noisy dataset itself. To this end, we introduce a general probabilistic framework, where each experiment is modelled separately and the retrieval is done by finding related models. For retrieval of gene expression experiments, we use a probabilistic model called product partition model, which induces a clustering of genes that show similar expression patterns across a number of samples. The suggested metric for retrieval using clusterings is the normalized information distance. Empirical results finally suggest that inference for the full probabilistic model can be approximated with good performance using computationally faster heuristic clustering approaches (e.g. $k$-means). The method is highly scalable and straightforward to apply to construct a general-purpose gene expression experiment retrieval method. Availability: The method can be implemented using standard clustering algorithms and normalized information distance, available in many statistical software packages.

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preprint2016arXiv

Multi-view Kernel Completion

In this paper, we introduce the first method that (1) can complete kernel matrices with completely missing rows and columns as opposed to individual missing kernel values, (2) does not require any of the kernels to be complete a priori, and (3) can tackle non-linear kernels. These aspects are necessary in practical applications such as integrating legacy data sets, learning under sensor failures and learning when measurements are costly for some of the views. The proposed approach predicts missing rows by modelling both within-view and between-view relationships among kernel values. We show, both on simulated data and real world data, that the proposed method outperforms existing techniques in the restricted settings where they are available, and extends applicability to new settings.

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preprint2016arXiv

Multiple Output Regression with Latent Noise

In high-dimensional data, structured noise caused by observed and unobserved factors affecting multiple target variables simultaneously, imposes a serious challenge for modeling, by masking the often weak signal. Therefore, (1) explaining away the structured noise in multiple-output regression is of paramount importance. Additionally, (2) assumptions about the correlation structure of the regression weights are needed. We note that both can be formulated in a natural way in a latent variable model, in which both the interesting signal and the noise are mediated through the same latent factors. Under this assumption, the signal model then borrows strength from the noise model by encouraging similar effects on correlated targets. We introduce a hyperparameter for the \emph{latent signal-to-noise ratio} which turns out to be important for modelling weak signals, and an ordered infinite-dimensional shrinkage prior that resolves the rotational unidentifiability in reduced-rank regression models. Simulations and prediction experiments with metabolite, gene expression, FMRI measurement, and macroeconomic time series data show that our model equals or exceeds the state-of-the-art performance and, in particular, outperforms the standard approach of assuming independent noise and signal models.

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preprint2016arXiv

Sparse group factor analysis for biclustering of multiple data sources

Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments. These biclustering techniques have focused on one data source, often gene expression data. We present a Bayesian approach for joint biclustering of multiple data sources, extending a recent method Group Factor Analysis (GFA) to have a biclustering interpretation with additional sparsity assumptions. The resulting method enables data-driven detection of linear structure present in parts of the data sources. Results: Our simulation studies show that the proposed method reliably infers bi-clusters from heterogeneous data sources. We tested the method on data from the NCI-DREAM drug sensitivity prediction challenge, resulting in an excellent prediction accuracy. Moreover, the predictions are based on several biclusters which provide insight into the data sources, in this case on gene expression, DNA methylation, protein abundance, exome sequence, functional connectivity fingerprints and drug sensitivity.

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preprint2016arXiv

Visualizations Relevant to The User By Multi-View Latent Variable Factorization

A main goal of data visualization is to find, from among all the available alternatives, mappings to the 2D/3D display which are relevant to the user. Assuming user interaction data, or other auxiliary data about the items or their relationships, the goal is to identify which aspects in the primary data support the userś input and, equally importantly, which aspects of the userś potentially noisy input have support in the primary data. For solving the problem, we introduce a multi-view embedding in which a latent factorization identifies which aspects in the two data views (primary data and user data) are related and which are specific to only one of them. The factorization is a generative model in which the display is parameterized as a part of the factorization and the other factors explain away the aspects not expressible in a two-dimensional display. Functioning of the model is demonstrated on several data sets.

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preprint2015arXiv

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

We present a novel approach for fully non-stationary Gaussian process regression (GPR), where all three key parameters -- noise variance, signal variance and lengthscale -- can be simultaneously input-dependent. We develop gradient-based inference methods to learn the unknown function and the non-stationary model parameters, without requiring any model approximations. We propose to infer full parameter posterior with Hamiltonian Monte Carlo (HMC), which conveniently extends the analytical gradient-based GPR learning by guiding the sampling with model gradients. We also learn the MAP solution from the posterior by gradient ascent. In experiments on several synthetic datasets and in modelling of temporal gene expression, the nonstationary GPR is shown to be necessary for modeling realistic input-dependent dynamics, while it performs comparably to conventional stationary or previous non-stationary GPR models otherwise.

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preprint2014arXiv

Exploration and retrieval of whole-metagenome sequencing samples

Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation. In this paper, we develop a content-based exploration and retrieval method for whole metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence $k$-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome data sets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and very high accuracy in discriminating between different body sites even though the method is unsupervised. A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework

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preprint2014arXiv

Group Factor Analysis

Factor analysis provides linear factors that describe relationships between individual variables of a data set. We extend this classical formulation into linear factors that describe relationships between groups of variables, where each group represents either a set of related variables or a data set. The model also naturally extends canonical correlation analysis to more than two sets, in a way that is more flexible than previous extensions. Our solution is formulated as variational inference of a latent variable model with structural sparsity, and it consists of two hierarchical levels: The higher level models the relationships between the groups, whereas the lower models the observed variables given the higher level. We show that the resulting solution solves the group factor analysis problem accurately, outperforming alternative factor analysis based solutions as well as more straightforward implementations of group factor analysis. The method is demonstrated on two life science data sets, one on brain activation and the other on systems biology, illustrating its applicability to the analysis of different types of high-dimensional data sources.

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preprint2014arXiv

Identification of structural features in chemicals associated with cancer drug response: A systematic data-driven analysis

Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corresponding genome-wide responses of multiple cell models. Results: In this paper, we present the first comprehensive multi-set analysis on how the chemical structure of drugs impacts on ge-nome-wide gene expression across several cancer cell lines (CMap database). The task is formulated as searching for drug response components across multiple cancers to reveal shared effects of drugs and the chemical features that may be responsible. The com-ponents can be computed with an extension of a very recent ap-proach called Group Factor Analysis (GFA). We identify 11 compo-nents that link the structural descriptors of drugs with specific gene expression responses observed in the three cell lines, and identify structural groups that may be responsible for the responses. Our method quantitatively outperforms the limited earlier studies on CMap and identifies both the previously reported associations and several interesting novel findings, by taking into account multiple cell lines and advanced 3D structural descriptors. The novel observations include: previously unknown similarities in the effects induced by 15-delta prostaglandin J2 and HSP90 inhibitors, which are linked to the 3D descriptors of the drugs; and the induction by simvastatin of leukemia-specific anti-inflammatory response, resem-bling the effects of corticosteroids.

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preprint2014arXiv

PinView: Implicit Feedback in Content-Based Image Retrieval

This paper describes PinView, a content-based image retrieval system that exploits implicit relevance feedback collected during a search session. PinView contains several novel methods to infer the intent of the user. From relevance feedback, such as eye movements or pointer clicks, and visual features of images, PinView learns a similarity metric between images which depends on the current interests of the user. It then retrieves images with a specialized online learning algorithm that balances the tradeoff between exploring new images and exploiting the already inferred interests of the user. We have integrated PinView to the content-based image retrieval system PicSOM, which enables applying PinView to real-world image databases. With the new algorithms PinView outperforms the original PicSOM, and in online experiments with real users the combination of implicit and explicit feedback gives the best results.

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preprint2014arXiv

Retrieval of Experiments by Efficient Estimation of Marginal Likelihood

We study the task of retrieving relevant experiments given a query experiment. By experiment, we mean a collection of measurements from a set of `covariates' and the associated `outcomes'. While similar experiments can be retrieved by comparing available `annotations', this approach ignores the valuable information available in the measurements themselves. To incorporate this information in the retrieval task, we suggest employing a retrieval metric that utilizes probabilistic models learned from the measurements. We argue that such a metric is a sensible measure of similarity between two experiments since it permits inclusion of experiment-specific prior knowledge. However, accurate models are often not analytical, and one must resort to storing posterior samples which demands considerable resources. Therefore, we study strategies to select informative posterior samples to reduce the computational load while maintaining the retrieval performance. We demonstrate the efficacy of our approach on simulated data with simple linear regression as the models, and real world datasets.

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preprint2014arXiv

Retrieval of Experiments with Sequential Dirichlet Process Mixtures in Model Space

We address the problem of retrieving relevant experiments given a query experiment, motivated by the public databases of datasets in molecular biology and other experimental sciences, and the need of scientists to relate to earlier work on the level of actual measurement data. Since experiments are inherently noisy and databases ever accumulating, we argue that a retrieval engine should possess two particular characteristics. First, it should compare models learnt from the experiments rather than the raw measurements themselves: this allows incorporating experiment-specific prior knowledge to suppress noise effects and focus on what is important. Second, it should be updated sequentially from newly published experiments, without explicitly storing either the measurements or the models, which is critical for saving storage space and protecting data privacy: this promotes life long learning. We formulate the retrieval as a ``supermodelling'' problem, of sequentially learning a model of the set of posterior distributions, represented as sets of MCMC samples, and suggest the use of Particle-Learning-based sequential Dirichlet process mixture (DPM) for this purpose. The relevance measure for retrieval is derived from the supermodel through the mixture representation. We demonstrate the performance of the proposed retrieval method on simulated data and molecular biological experiments.

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preprint2014arXiv

Stronger findings from mass spectral data through multi-peak modeling

Mass spectrometry-based metabolomic analysis depends upon the identification of spectral peaks by their mass and retention time. Statistical analysis that follows the identification currently relies on one main peak of each compound. However, a compound present in the sample typically produces several spectral peaks due to its isotopic properties and the ionization process of the mass spectrometer device. In this work, we investigate the extent to which these additional peaks can be used to increase the statistical strength of differential analysis. We present a Bayesian approach for integrating data of multiple detected peaks that come from one compound. We demonstrate the approach through a simulated experiment and validate it on ultra performance liquid chromatography-mass spectrometry (UPLC-MS) experiments for metabolomics and lipidomics. Peaks that are likely to be associated with one compound can be clustered by the similarity of their chromatographic shape. Changes of concentration between sample groups can be inferred more accurately when multiple peaks are available. When the sample-size is limited, the proposed multi-peak approach improves the accuracy at inferring covariate effects. An R implementation, data and the supplementary material are available at http://research.ics.aalto.fi/mi/software/peakANOVA/ .

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preprint2014arXiv

Toward computational cumulative biology by combining models of biological datasets

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to both include biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer and the model-based search was more accurate than keyword search; it moreover recovered biologically meaningful relationships that are not straightforwardly visible from annotations, for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

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preprint2013arXiv

Bayesian Information Sharing Between Noise And Regression Models Improves Prediction of Weak Effects

We consider the prediction of weak effects in a multiple-output regression setup, when covariates are expected to explain a small amount, less than $\approx 1%$, of the variance of the target variables. To facilitate the prediction of the weak effects, we constrain our model structure by introducing a novel Bayesian approach of sharing information between the regression model and the noise model. Further reduction of the effective number of parameters is achieved by introducing an infinite shrinkage prior and group sparsity in the context of the Bayesian reduced rank regression, and using the Bayesian infinite factor model as a flexible low-rank noise model. In our experiments the model incorporating the novelties outperformed alternatives in genomic prediction of rich phenotype data. In particular, the information sharing between the noise and regression models led to significant improvement in prediction accuracy.

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preprint2013arXiv

Genome-wide association studies with high-dimensional phenotypes

High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been proposed for testing jointly all traits in a high-dimensional vector of phenotypes, with prospect of increased power to detect small effects that would be missed if tested individually. However, the methods have rarely been compared to the extent of enabling assessment of their relative merits and setting up guidelines on which method to use, and how to use it. We compare the methods on simulated data and with a real metabolomics data set comprising 137 highly correlated variables and approximately 550,000 SNPs. Applying the methods to genome-wide data with hundreds of thousands of markers inevitably requires division of the problem into manageable parts facilitating parallel processing, parts corresponding to individual genetic variants, pathways, or genes, for example. Here we utilize a straightforward formulation according to which the genome is divided into blocks of nearby correlated genetic markers, tested jointly for association with the phenotypes. This formulation is computationally feasible, reduces the number of tests, and lets the methods take advantage of combining information over several correlated variables not only on the phenotype side, but also on the genotype side. Our experiments show that canonical correlation analysis has higher power than alternative methods, while remaining computationally tractable for routine use in the GWAS setting, provided the number of samples is sufficient compared to the numbers of phenotype and genotype variables tested. Sparse canonical correlation analysis and regression models with latent confounding factors show promising performance when the number of samples is small.

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preprint2013arXiv

Kernelized Bayesian Matrix Factorization

We extend kernelized matrix factorization with a fully Bayesian treatment and with an ability to work with multiple side information sources expressed as different kernels. Kernel functions have been introduced to matrix factorization to integrate side information about the rows and columns (e.g., objects and users in recommender systems), which is necessary for making out-of-matrix (i.e., cold start) predictions. We discuss specifically bipartite graph inference, where the output matrix is binary, but extensions to more general matrices are straightforward. We extend the state of the art in two key aspects: (i) A fully conjugate probabilistic formulation of the kernelized matrix factorization problem enables an efficient variational approximation, whereas fully Bayesian treatments are not computationally feasible in the earlier approaches. (ii) Multiple side information sources are included, treated as different kernels in multiple kernel learning that additionally reveals which side information sources are informative. Our method outperforms alternatives in predicting drug-protein interactions on two data sets. We then show that our framework can also be used for solving multilabel learning problems by considering samples and labels as the two domains where matrix factorization operates on. Our algorithm obtains the lowest Hamming loss values on 10 out of 14 multilabel classification data sets compared to five state-of-the-art multilabel learning algorithms.

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preprint2013arXiv

RPA: Probabilistic analysis of probe performance and robust summarization

Probe-level models have led to improved performance in microarray studies but the various sources of probe-level contamination are still poorly understood. Data-driven analysis of probe performance can be used to quantify the uncertainty in individual probes and to highlight the relative contribution of different noise sources. Improved understanding of the probe-level effects can lead to improved preprocessing techniques and microarray design. We have implemented probabilistic tools for probe performance analysis and summarization on short oligonucleotide arrays. In contrast to standard preprocessing approaches, the methods provide quantitative estimates of probe-specific noise and affinity terms and tools to investigate these parameters. Tools to incorporate prior information of the probes in the analysis are provided as well. Comparisons to known probe-level error sources and spike-in data sets validate the approach. Implementation is freely available in R/BioConductor: http://www.bioconductor.org/packages/release/bioc/html/RPA.html

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preprint2012arXiv

Bayesian exponential family projections for coupled data sources

Exponential family extensions of principal component analysis (EPCA) have received a considerable amount of attention in recent years, demonstrating the growing need for basic modeling tools that do not assume the squared loss or Gaussian distribution. We extend the EPCA model toolbox by presenting the first exponential family multi-view learning methods of the partial least squares and canonical correlation analysis, based on a unified representation of EPCA as matrix factorization of the natural parameters of exponential family. The models are based on a new family of priors that are generally usable for all such factorizations. We also introduce new inference strategies, and demonstrate how the methods outperform earlier ones when the Gaussianity assumption does not hold.

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preprint2012arXiv

Global modeling of transcriptional responses in interaction networks

Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between physiological conditions, and potentially as yet unknown processes. We introduce a novel approach for organism-wide discovery and analysis of transcriptional responses in interaction networks. The method searches for local, connected regions in a network that exhibit coordinated transcriptional response in a subset of conditions. Known interactions between genes are used to limit the search space and to guide the analysis. Validation on a human pathway network reveals physiologically coherent responses, functional relatedness between physiological conditions, and coordinated, context-specific regulation of the genes. Availability: Implementation is freely available in R and Matlab at http://netpro.r-forge.r-project.org

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preprint2012arXiv

Two-Way Latent Grouping Model for User Preference Prediction

We introduce a novel latent grouping model for predicting the relevance of a new document to a user. The model assumes a latent group structure for both users and documents. We compared the model against a state-of-the-art method, the User Rating Profile model, where only users have a latent group structure. We estimate both models by Gibbs sampling. The new method predicts relevance more accurately for new documents that have few known ratings. The reason is that generalization over documents then becomes necessary and hence the twoway grouping is profitable.

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preprint2011arXiv

Bayesian Group Factor Analysis

We introduce a factor analysis model that summarizes the dependencies between observed variable groups, instead of dependencies between individual variables as standard factor analysis does. A group may correspond to one view of the same set of objects, one of many data sets tied by co-occurrence, or a set of alternative variables collected from statistics tables to measure one property of interest. We show that by assuming group-wise sparse factors, active in a subset of the sets, the variation can be decomposed into factors explaining relationships between the sets and factors explaining away set-specific variation. We formulate the assumptions in a Bayesian model which provides the factors, and apply the model to two data analysis tasks, in neuroimaging and chemical systems biology.

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preprint2011arXiv

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditional methods for analyzing structure-function relationships are not comprehensive enough. Therefore more advanced integrative models are needed for predicting biological effects elicited by specific chemical features. As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical space) of 1159 drugs with the gene expression responses (biological space) they elicited in three cancer cell lines. The analysis covering 11350 genes was based on data from the Connectivity Map. We decomposed these biological response profiles into components, each linked to a characteristic chemical descriptor profile. The integrated quantitative analysis of the chemical and biological spaces was more informative about protein-target based drug similarity than either dataset separately. We identified ten major components that link distinct VolSurf features across multiple compounds to specific biological activity types. For example, component 2 (hydrophobic properties) strongly links to DNA damage response, while component 3 (hydrogen bonding) connects to metabolic stress. Individual structural and biological features were often linked to one cell line only, such as leukemia cells (HL-60) specifically responding to cardiac glycosides. In summary, our approach identified specific chemical structures shared across multiple drugs causing distinct biological responses. The decoding of such systematic chemical-biological relationships is necessary to build better models of drug effects, including unidentified types of molecular properties with strong biological effects.

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preprint2011arXiv

Dependency detection with similarity constraints

Unsupervised two-view learning, or detection of dependencies between two paired data sets, is typically done by some variant of canonical correlation analysis (CCA). CCA searches for a linear projection for each view, such that the correlations between the projections are maximized. The solution is invariant to any linear transformation of either or both of the views; for tasks with small sample size such flexibility implies overfitting, which is even worse for more flexible nonparametric or kernel-based dependency discovery methods. We develop variants which reduce the degrees of freedom by assuming constraints on similarity of the projections in the two views. A particular example is provided by a cancer gene discovery application where chromosomal distance affects the dependencies between gene copy number and activity levels. Similarity constraints are shown to improve detection performance of known cancer genes.

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preprint2010arXiv

Translating biomarkers between multi-way time-series experiments

Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes or metabolites) between the species. However, many experiments have a complicated multi-way experimental design often involving irregularly-sampled time-series measurements, and for instance metabolites do not always have known matchings between organisms. We introduce a Bayesian modelling framework for translating between multiple species the results from 'omics' experiments having a complex multi-way, time-series experimental design. The underlying assumption is that the unknown matching can be inferred from the response of the variables to multiple covariates including time.

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