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Daphne Koller

Publications and source records attributed to Daphne Koller.

At least 19 recordsLinked to original sources
arXiv2019

Inferring Multidimensional Rates of Aging from Cross-Sectional Data

Modeling how individuals evolve over time is a fundamental problem in the natural and social sciences. However, existing datasets are often cross-sectional with each individual observed only once, making it impossible to apply traditional time-series methods. Motivated by the study of human aging, we present an interpretable latent-variable model that learns temporal dynamics from cross-sectional data. Our model represents each individual's features over time as a nonlinear function of a low-dimensional, linearly-evolving latent state. We prove that when this nonlinear function is constrained to be order-isomorphic, the model family is identifiable solely from cross-sectional data provided the distribution of time-independent variation is known. On the UK Biobank human health dataset, our model reconstructs the observed data while learning interpretable rates of aging associated with diseases, mortality, and aging risk factors.

cs.LG↗
arXiv2018

Peptide-Spectra Matching from Weak Supervision

As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to obtain. Instead, we have access to imperfect hand-coded models crafted by domain experts. In this paper, we apply deep neural networks to an important step of the protein identification problem, the pairing of mass spectra with short sequences of amino acids called peptides. We train our model to differentiate between top scoring results from a state-of-the art classical system and hard-negative second and third place results. Our resulting model is much better at identifying peptides with spectra than the model used to generate its training data. In particular, we achieve a 43% improvement over standard matching methods and a 10% improvement over a combination of the matching method and an industry standard cross-spectra reranking tool. Importantly, in a more difficult experimental regime that reflects current challenges facing biologists, our advantage over the previous state-of-the-art grows to 15% even after reranking. We believe this approach will generalize to other challenging scientific problems.

q-bio.QM↗
arXiv2013

Tuned Models of Peer Assessment in MOOCs

In massive open online courses (MOOCs), peer grading serves as a critical tool for scaling the grading of complex, open-ended assignments to courses with tens or hundreds of thousands of students. But despite promising initial trials, it does not always deliver accurate results compared to human experts. In this paper, we develop algorithms for estimating and correcting for grader biases and reliabilities, showing significant improvement in peer grading accuracy on real data with 63,199 peer grades from Coursera's HCI course offerings --- the largest peer grading networks analysed to date. We relate grader biases and reliabilities to other student factors such as student engagement, performance as well as commenting style. We also show that our model can lead to more intelligent assignment of graders to gradees.

cs.LG↗
arXiv2013

Probability Estimation in Face of Irrelevant Information

In this paper, we consider one aspect of the problem of applying decision theory to the design of agents that learn how to make decisions under uncertainty. This aspect concerns how an agent can estimate probabilities for the possible states of the world, given that it only makes limited observations before committing to a decision. We show that the naive application of statistical tools can be improved upon if the agent can determine which of his observations are truly relevant to the estimation problem at hand. We give a framework in which such determinations can be made, and define an estimation procedure to use them. Our framework also suggests several extensions, which show how additional knowledge can be used to improve tile estimation procedure still further.

cs.AI↗
arXiv2013

Generating New Beliefs From Old

In previous work [BGHK92, BGHK93], we have studied the random-worlds approach -- a particular (and quite powerful) method for generating degrees of belief (i.e., subjective probabilities) from a knowledge base consisting of objective (first-order, statistical, and default) information. But allowing a knowledge base to contain only objective information is sometimes limiting. We occasionally wish to include information about degrees of belief in the knowledge base as well, because there are contexts in which old beliefs represent important information that should influence new beliefs. In this paper, we describe three quite general techniques for extending a method that generates degrees of belief from objective information to one that can make use of degrees of belief as well. All of our techniques are bloused on well-known approaches, such as cross-entropy. We discuss general connections between the techniques and in particular show that, although conceptually and technically quite different, all of the techniques give the same answer when applied to the random-worlds method.

cs.AI↗
arXiv2013

Stochastic Simulation Algorithms for Dynamic Probabilistic Networks

Stochastic simulation algorithms such as likelihood weighting often give fast, accurate approximations to posterior probabilities in probabilistic networks, and are the methods of choice for very large networks. Unfortunately, the special characteristics of dynamic probabilistic networks (DPNs), which are used to represent stochastic temporal processes, mean that standard simulation algorithms perform very poorly. In essence, the simulation trials diverge further and further from reality as the process is observed over time. In this paper, we present simulation algorithms that use the evidence observed at each time step to push the set of trials back towards reality. The first algorithm, "evidence reversal" (ER) restructures each time slice of the DPN so that the evidence nodes for the slice become ancestors of the state variables. The second algorithm, called "survival of the fittest" sampling (SOF), "repopulates" the set of trials at each time step using a stochastic reproduction rate weighted by the likelihood of the evidence according to each trial. We compare the performance of each algorithm with likelihood weighting on the original network, and also investigate the benefits of combining the ER and SOF methods. The ER/SOF combination appears to maintain bounded error independent of the number of time steps in the simulation.

cs.AI↗
arXiv2013

Context-Specific Independence in Bayesian Networks

Bayesian networks provide a language for qualitatively representing the conditional independence properties of a distribution. This allows a natural and compact representation of the distribution, eases knowledge acquisition, and supports effective inference algorithms. It is well-known, however, that there are certain independencies that we cannot capture qualitatively within the Bayesian network structure: independencies that hold only in certain contexts, i.e., given a specific assignment of values to certain variables. In this paper, we propose a formal notion of context-specific independence (CSI), based on regularities in the conditional probability tables (CPTs) at a node. We present a technique, analogous to (and based on) d-separation, for determining when such independence holds in a given network. We then focus on a particular qualitative representation scheme - tree-structured CPTs - for capturing CSI. We suggest ways in which this representation can be used to support effective inference algorithms. In particular, we present a structural decomposition of the resulting network which can improve the performance of clustering algorithms, and an alternative algorithm based on cutset conditioning.

cs.AI↗
arXiv2013

Update Rules for Parameter Estimation in Bayesian Networks

This paper re-examines the problem of parameter estimation in Bayesian networks with missing values and hidden variables from the perspective of recent work in on-line learning [Kivinen & Warmuth, 1994]. We provide a unified framework for parameter estimation that encompasses both on-line learning, where the model is continuously adapted to new data cases as they arrive, and the more traditional batch learning, where a pre-accumulated set of samples is used in a one-time model selection process. In the batch case, our framework encompasses both the gradient projection algorithm and the EM algorithm for Bayesian networks. The framework also leads to new on-line and batch parameter update schemes, including a parameterized version of EM. We provide both empirical and theoretical results indicating that parameterized EM allows faster convergence to the maximum likelihood parameters than does standard EM.

cs.LG↗
arXiv2013

Object-Oriented Bayesian Networks

Bayesian networks provide a modeling language and associated inference algorithm for stochastic domains. They have been successfully applied in a variety of medium-scale applications. However, when faced with a large complex domain, the task of modeling using Bayesian networks begins to resemble the task of programming using logical circuits. In this paper, we describe an object-oriented Bayesian network (OOBN) language, which allows complex domains to be described in terms of inter-related objects. We use a Bayesian network fragment to describe the probabilistic relations between the attributes of an object. These attributes can themselves be objects, providing a natural framework for encoding part-of hierarchies. Classes are used to provide a reusable probabilistic model which can be applied to multiple similar objects. Classes also support inheritance of model fragments from a class to a subclass, allowing the common aspects of related classes to be defined only once. Our language has clear declarative semantics: an OOBN can be interpreted as a stochastic functional program, so that it uniquely specifies a probabilistic model. We provide an inference algorithm for OOBNs, and show that much of the structural information encoded by an OOBN--particularly the encapsulation of variables within an object and the reuse of model fragments in different contexts--can also be used to speed up the inference process.

cs.AI↗
arXiv2013

Nonuniform Dynamic Discretization in Hybrid Networks

We consider probabilistic inference in general hybrid networks, which include continuous and discrete variables in an arbitrary topology. We reexamine the question of variable discretization in a hybrid network aiming at minimizing the information loss induced by the discretization. We show that a nonuniform partition across all variables as opposed to uniform partition of each variable separately reduces the size of the data structures needed to represent a continuous function. We also provide a simple but efficient procedure for nonuniform partition. To represent a nonuniform discretization in the computer memory, we introduce a new data structure, which we call a Binary Split Partition (BSP) tree. We show that BSP trees can be an exponential factor smaller than the data structures in the standard uniform discretization in multiple dimensions and show how the BSP trees can be used in the standard join tree algorithm. We show that the accuracy of the inference process can be significantly improved by adjusting discretization with evidence. We construct an iterative anytime algorithm that gradually improves the quality of the discretization and the accuracy of the answer on a query. We provide empirical evidence that the algorithm converges.

cs.AI↗
arXiv2013

Tractable Inference for Complex Stochastic Processes

The monitoring and control of any dynamic system depends crucially on the ability to reason about its current status and its future trajectory. In the case of a stochastic system, these tasks typically involve the use of a belief state- a probability distribution over the state of the process at a given point in time. Unfortunately, the state spaces of complex processes are very large, making an explicit representation of a belief state intractable. Even in dynamic Bayesian networks (DBNs), where the process itself can be represented compactly, the representation of the belief state is intractable. We investigate the idea of maintaining a compact approximation to the true belief state, and analyze the conditions under which the errors due to the approximations taken over the lifetime of the process do not accumulate to make our answers completely irrelevant. We show that the error in a belief state contracts exponentially as the process evolves. Thus, even with multiple approximations, the error in our process remains bounded indefinitely. We show how the additional structure of a DBN can be used to design our approximation scheme, improving its performance significantly. We demonstrate the applicability of our ideas in the context of a monitoring task, showing that orders of magnitude faster inference can be achieved with only a small degradation in accuracy.

cs.AI↗
arXiv2013

Discovering the Hidden Structure of Complex Dynamic Systems

Dynamic Bayesian networks provide a compact and natural representation for complex dynamic systems. However, in many cases, there is no expert available from whom a model can be elicited. Learning provides an alternative approach for constructing models of dynamic systems. In this paper, we address some of the crucial computational aspects of learning the structure of dynamic systems, particularly those where some relevant variables are partially observed or even entirely unknown. Our approach is based on the Structural Expectation Maximization (SEM) algorithm. The main computational cost of the SEM algorithm is the gathering of expected sufficient statistics. We propose a novel approximation scheme that allows these sufficient statistics to be computed efficiently. We also investigate the fundamental problem of discovering the existence of hidden variables without exhaustive and expensive search. Our approach is based on the observation that, in dynamic systems, ignoring a hidden variable typically results in a violation of the Markov property. Thus, our algorithm searches for such violations in the data, and introduces hidden variables to explain them. We provide empirical results showing that the algorithm is able to learn the dynamics of complex systems in a computationally tractable way.

cs.AI↗
arXiv2013

A General Algorithm for Approximate Inference and its Application to Hybrid Bayes Nets

The clique tree algorithm is the standard method for doing inference in Bayesian networks. It works by manipulating clique potentials - distributions over the variables in a clique. While this approach works well for many networks, it is limited by the need to maintain an exact representation of the clique potentials. This paper presents a new unified approach that combines approximate inference and the clique tree algorithm, thereby circumventing this limitation. Many known approximate inference algorithms can be viewed as instances of this approach. The algorithm essentially does clique tree propagation, using approximate inference to estimate the densities in each clique. In many settings, the computation of the approximate clique potential can be done easily using statistical importance sampling. Iterations are used to gradually improve the quality of the estimation.

cs.AI↗
arXiv2013

SPOOK: A System for Probabilistic Object-Oriented Knowledge Representation

In previous work, we pointed out the limitations of standard Bayesian networks as a modeling framework for large, complex domains. We proposed a new, richly structured modeling language, {em Object-oriented Bayesian Netorks}, that we argued would be able to deal with such domains. However, it turns out that OOBNs are not expressive enough to model many interesting aspects of complex domains: the existence of specific named objects, arbitrary relations between objects, and uncertainty over domain structure. These aspects are crucial in real-world domains such as battlefield awareness. In this paper, we present SPOOK, an implemented system that addresses these limitations. SPOOK implements a more expressive language that allows it to represent the battlespace domain naturally and compactly. We present a new inference algorithm that utilizes the model structure in a fundamental way, and show empirically that it achieves orders of magnitude speedup over existing approaches.

cs.AI↗
arXiv2013

Utilities as Random Variables: Density Estimation and Structure Discovery

Decision theory does not traditionally include uncertainty over utility functions. We argue that the a person's utility value for a given outcome can be treated as we treat other domain attributes: as a random variable with a density function over its possible values. We show that we can apply statistical density estimation techniques to learn such a density function from a database of partially elicited utility functions. In particular, we define a Bayesian learning framework for this problem, assuming the distribution over utilities is a mixture of Gaussians, where the mixture components represent statistically coherent subpopulations. We can also extend our techniques to the problem of discovering generalized additivity structure in the utility functions in the population. We define a Bayesian model selection criterion for utility function structure and a search procedure over structures. The factorization of the utilities in the learned model, and the generalization obtained from density estimation, allows us to provide robust estimates of utilities using a significantly smaller number of utility elicitation questions. We experiment with our technique on synthetic utility data and on a real database of utility functions in the domain of prenatal diagnosis.

cs.AI↗
arXiv2013

Being Bayesian about Network Structure

In many domains, we are interested in analyzing the structure of the underlying distribution, e.g., whether one variable is a direct parent of the other. Bayesian model-selection attempts to find the MAP model and use its structure to answer these questions. However, when the amount of available data is modest, there might be many models that have non-negligible posterior. Thus, we want compute the Bayesian posterior of a feature, i.e., the total posterior probability of all models that contain it. In this paper, we propose a new approach for this task. We first show how to efficiently compute a sum over the exponential number of networks that are consistent with a fixed ordering over network variables. This allows us to compute, for a given ordering, both the marginal probability of the data and the posterior of a feature. We then use this result as the basis for an algorithm that approximates the Bayesian posterior of a feature. Our approach uses a Markov Chain Monte Carlo (MCMC) method, but over orderings rather than over network structures. The space of orderings is much smaller and more regular than the space of structures, and has a smoother posterior `landscape'. We present empirical results on synthetic and real-life datasets that compare our approach to full model averaging (when possible), to MCMC over network structures, and to a non-Bayesian bootstrap approach.

cs.LG↗
arXiv2013

Policy Iteration for Factored MDPs

Many large MDPs can be represented compactly using a dynamic Bayesian network. Although the structure of the value function does not retain the structure of the process, recent work has shown that value functions in factored MDPs can often be approximated well using a decomposed value function: a linear combination of restricted basis functions, each of which refers only to a small subset of variables. An approximate value function for a particular policy can be computed using approximate dynamic programming, but this approach (and others) can only produce an approximation relative to a distance metric which is weighted by the stationary distribution of the current policy. This type of weighted projection is ill-suited to policy improvement. We present a new approach to value determination, that uses a simple closed-form computation to directly compute a least-squares decomposed approximation to the value function for any weights . We then use this value determination algorithm as a subroutine in a policy iteration process. We show that, under reasonable restrictions, the policies induced by a factored value function are compactly represented, and can be manipulated efficiently in a policy iteration process. We also present a method for computing error bounds for decomposed value functions using a variable-elimination algorithm for function optimization. The complexity of all of our algorithms depends on the factorization of system dynamics and of the approximate value function.

cs.AI↗