In many real-world deployments of machine learning, we use a prediction algorithm to choose what data to test next. For example, in the protein design problem, we have a regression model that predicts some real-valued property of a protein sequence, which we use to propose new sequences believed to exhibit higher property values than observed in the training data. Since validating designed sequences in the wet lab is typically costly, it is important to know how much we can trust the model's predictions. In such settings, however, there is a distinct type of distribution shift between the training and test data: one where the training and test data are statistically dependent, as the latter is chosen based on the former. Consequently, the model's error on the test data -- that is, the designed sequences -- has some non-trivial relationship with its error on the training data. Herein, we introduce a method to quantify predictive uncertainty in such settings. We do so by constructing confidence sets for predictions that account for the dependence between the training and test data. The confidence sets we construct have finite-sample guarantees that hold for any prediction algorithm, even when a trained model chooses the test-time input distribution. As a motivating use case, we demonstrate how our method quantifies uncertainty for the predicted fitness of designed protein using several real data sets.
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This paper presents a control framework on Lie groups by designing the control objective in its Lie algebra. Control on Lie groups is challenging due to its nonlinear nature and difficulties in system parameterization. Existing methods to design the control objective on a Lie group and then derive the gradient for controller design are non-trivial and can result in slow convergence in tracking control. We show that with a proper left-invariant metric, setting the gradient of the cost function as the tracking error in the Lie algebra leads to a quadratic Lyapunov function that enables globally exponential convergence. In the PD control case, we show that our controller can maintain an exponential convergence rate even when the initial error is approaching $\pi$ in SO(3). We also show the merit of this proposed framework in trajectory optimization. The proposed cost function enables the iterative Linear Quadratic Regulator (iLQR) to converge much faster than the Differential Dynamic Programming (DDP) with a well-adopted cost function when the initial trajectory is poorly initialized on SO(3).
We consider the question of adaptive data analysis within the framework of convex optimization. We ask how many samples are needed in order to compute $\epsilon$-accurate estimates of $O(1/\epsilon^2)$ gradients queried by gradient descent, and we provide two intermediate answers to this question. First, we show that for a general analyst (not necessarily gradient descent) $\Omega(1/\epsilon^3)$ samples are required. This rules out the possibility of a foolproof mechanism. Our construction builds upon a new lower bound (that may be of interest of its own right) for an analyst that may ask several non adaptive questions in a batch of fixed and known $T$ rounds of adaptivity and requires a fraction of true discoveries. We show that for such an analyst $\Omega (\sqrt{T}/\epsilon^2)$ samples are necessary. Second, we show that, under certain assumptions on the oracle, in an interaction with gradient descent $\tilde \Omega(1/\epsilon^{2.5})$ samples are necessary. Our assumptions are that the oracle has only \emph{first order access} and is \emph{post-hoc generalizing}. First order access means that it can only compute the gradients of the sampled function at points queried by the algorithm. Our assumption of \emph{post-hoc generalization} follows from existing lower bounds for statistical queries. More generally then, we provide a generic reduction from the standard setting of statistical queries to the problem of estimating gradients queried by gradient descent. These results are in contrast with classical bounds that show that with $O(1/\epsilon^2)$ samples one can optimize the population risk to accuracy of $O(\epsilon)$ but, as it turns out, with spurious gradients.
Adverse events are a serious issue in drug development and many prediction methods using machine learning have been developed. The random split cross-validation is the de facto standard for model building and evaluation in machine learning, but care should be taken in adverse event prediction because this approach tends to be overoptimistic compared with the real-world situation. The time split, which uses the time axis, is considered suitable for real-world prediction. However, the differences in model performance obtained using the time and random splits are not fully understood. To understand the differences, we compared the model performance between the time and random splits using eight types of compound information as input, eight adverse events as targets, and six machine learning algorithms. The random split showed higher area under the curve values than did the time split for six of eight targets. The chemical spaces of the training and test datasets of the time split were similar, suggesting that the concept of applicability domain is insufficient to explain the differences derived from the splitting. The area under the curve differences were smaller for the protein interaction than for the other datasets. Subsequent detailed analyses suggested the danger of confounding in the use of knowledge-based information in the time split. These findings indicate the importance of understanding the differences between the time and random splits in adverse event prediction and suggest that appropriate use of the splitting strategies and interpretation of results are necessary for the real-world prediction of adverse events.
Approximate Policy Iteration (API) algorithms alternate between (approximate) policy evaluation and (approximate) greedification. Many different approaches have been explored for approximate policy evaluation, but less is understood about approximate greedification and what choices guarantee policy improvement. In this work, we investigate approximate greedification when reducing the KL divergence between the parameterized policy and the Boltzmann distribution over action values. In particular, we investigate the difference between the forward and reverse KL divergences, with varying degrees of entropy regularization. We show that the reverse KL has stronger policy improvement guarantees, but that reducing the forward KL can result in a worse policy. We also demonstrate, however, that a large enough reduction of the forward KL can induce improvement under additional assumptions. Empirically, we show on simple continuous-action environments that the forward KL can induce more exploration, but at the cost of a more suboptimal policy. No significant differences were observed in the discrete-action setting or on a suite of benchmark problems. Throughout, we highlight that many policy gradient methods can be seen as an instance of API, with either the forward or reverse KL for the policy update, and discuss next steps for understanding and improving our policy optimization algorithms.
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules or applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When trained on the same quantum chemical small molecule dataset used to parameterize the openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-\`a-vis experiments in computing relative alchemical free energy calculations for a popular benchmark set.
Existing inferential methods for small area data involve a trade-off between maintaining area-level frequentist coverage rates and improving inferential precision via the incorporation of indirect information. In this article, we propose a method to obtain an area-level prediction region for a future observation which mitigates this trade-off. The proposed method takes a conformal prediction approach in which the conformity measure is the posterior predictive density of a working model that incorporates indirect information. The resulting prediction region has guaranteed frequentist coverage regardless of the working model, and, if the working model assumptions are accurate, the region has minimum expected volume compared to other regions with the same coverage rate. When constructed under a normal working model, we prove such a prediction region is an interval and construct an efficient algorithm to obtain the exact interval. We illustrate the performance of our method through simulation studies and an application to EPA radon survey data.
One of the most important problems in system identification and statistics is how to estimate the unknown parameters of a given model. Optimization methods and specialized procedures, such as Empirical Minimization (EM) can be used in case the likelihood function can be computed. For situations where one can only simulate from a parametric model, but the likelihood is difficult or impossible to evaluate, a technique known as the Two-Stage (TS) Approach can be applied to obtain reliable parametric estimates. Unfortunately, there is currently a lack of theoretical justification for TS. In this paper, we propose a statistical decision-theoretical derivation of TS, which leads to Bayesian and Minimax estimators. We also show how to apply the TS approach on models for independent and identically distributed samples, by computing quantiles of the data as a first step, and using a linear function as the second stage. The proposed method is illustrated via numerical simulations.
We present a novel static analysis technique to derive higher moments for program variables for a large class of probabilistic loops with potentially uncountable state spaces. Our approach is fully automatic, meaning it does not rely on externally provided invariants or templates. We employ algebraic techniques based on linear recurrences and introduce program transformations to simplify probabilistic programs while preserving their statistical properties. We develop power reduction techniques to further simplify the polynomial arithmetic of probabilistic programs and define the theory of moment-computable probabilistic loops for which higher moments can precisely be computed. Our work has applications towards recovering probability distributions of random variables and computing tail probabilities. The empirical evaluation of our results demonstrates the applicability of our work on many challenging examples.
Traditional methods for link prediction can be categorized into three main types: graph structure feature-based, latent feature-based, and explicit feature-based. Graph structure feature methods leverage some handcrafted node proximity scores, e.g., common neighbors, to estimate the likelihood of links. Latent feature methods rely on factorizing networks' matrix representations to learn an embedding for each node. Explicit feature methods train a machine learning model on two nodes' explicit attributes. Each of the three types of methods has its unique merits. In this paper, we propose SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction), a new framework for link prediction which combines the power of all the three types into a single graph neural network (GNN). GNN is a new type of neural network which directly accepts graphs as input and outputs their labels. In SEAL, the input to the GNN is a local subgraph around each target link. We prove theoretically that our local subgraphs also reserve a great deal of high-order graph structure features related to link existence. Another key feature is that our GNN can naturally incorporate latent features and explicit features. It is achieved by concatenating node embeddings (latent features) and node attributes (explicit features) in the node information matrix for each subgraph, thus combining the three types of features to enhance GNN learning. Through extensive experiments, SEAL shows unprecedentedly strong performance against a wide range of baseline methods, including various link prediction heuristics and network embedding methods.
Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.
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