Data-driven optimization aims to translate a machine learning model into decision-making by optimizing decisions on estimated costs. Such a pipeline can be conducted by fitting a distributional model which is then plugged into the target optimization problem. While this fitting can utilize traditional methods such as maximum likelihood, a more recent approach uses estimation-optimization integration that minimizes decision error instead of estimation error. Although intuitive, the statistical benefit of the latter approach is not well understood yet is important to guide the prescriptive usage of machine learning. In this paper, we dissect the performance comparisons between these approaches in terms of the amount of model misspecification. In particular, we show how the integrated approach offers a “universal double benefit” on the top two dominating terms of regret when the underlying model is misspecified, while the traditional approach can be advantageous when the model is nearly well-specified. Our comparison is powered by finite-sample tail regret bounds that are derived via new higher-order expansions of regrets and the leveraging of a recent Berry-Esseen theorem.

Direct Preference Optimization (DPO) has recently emerged as a popular approach to improve reinforcement learning from human feedback (RLHF), leading to better techniques to fine-tune large language models (LLM). A weakness of DPO, however, lies in its lack of capability to characterize the diversity of human preferences. Inspired by Mallows' theory of preference ranking, we develop in this paper a new approach, the *MallowsPO*. A distinct feature of this approach is a *dispersion index*, which reflects the dispersion of human preference to prompts. We show that existing DPO models can be reduced to special cases of this dispersion index, thus unified with MallowsPO. More importantly, we demonstrate empirically how to use this dispersion index to enhance the performance of DPO in a broad array of benchmark tasks, from synthetic bandit selection to controllable generation and dialogues, while maintaining great generalization capabilities. MallowsPO is also compatible with other SOTA offline preference optimization methods, boosting nearly 2\% extra LC win rate when used as a plugin for fine-tuning Llama3-Instruct.

Data-driven stochastic optimization is ubiquitous in machine learning and operational decision-making problems. Sample average approximation (SAA) and model-based approaches such as estimate-then-optimize (ETO) or integrated estimation-optimization (IEO) are all popular, with model-based approaches being able to circumvent some of the issues with SAA in complex context-dependent problems. Yet the relative performance of these methods is poorly understood, with most results confined to the dichotomous cases of the model-based approach being either well-specified or misspecified. We develop the first results that allow for a more granular analysis of the relative performance of these methods under a local misspecification setting, which models the scenario where the model-based approach is nearly well-specified. By leveraging tools from contiguity theory in statistics, we show that there is a bias-variance tradeoff between SAA, IEO, and ETO under local misspecification, and that the relative importance of the bias and the variance depends on the degree of local misspecification. Moreover, we derive explicit expressions for the decision bias, which allows us to characterize (un)impactful misspecification directions, and provide further geometric understanding of the variance.

Ensemble learning is a popular technique to improve the accuracy of machine learning models. It traditionally hinges on the rationale that aggregating multiple weak models can lead to better models with lower variance and hence higher stability, especially for discontinuous base learners. In this paper, we provide a new perspective on ensembling. By selecting the most frequently generated model from the base learner when repeatedly applied to subsamples, we can attain exponentially decaying tails for the excess risk, even if the base learner suffers from slow (i.e., polynomial) decay rates. This tail enhancement power of ensembling applies to base learners that have reasonable predictive power to begin with and is stronger than variance reduction in the sense of exhibiting rate improvement. We demonstrate how our ensemble methods can substantially improve out-of-sample performances in a range of numerical examples involving heavy-tailed data or intrinsically slow rates.

Offline reinforcement learning (RL) offers a promising direction for learning policies from pre-collected datasets without requiring further interactions with the environment. However, existing methods struggle to handle out-of-distribution (OOD) extrapolation errors, especially in sparse reward or scarce data settings. In this paper, we propose a novel training algorithm called Conservative Density Estimation (CDE), which addresses this challenge by explicitly imposing constraints on the state-action occupancy stationary distribution. CDE overcomes the limitations of existing approaches, such as the stationary distribution correction method, by addressing the support mismatch issue in marginal importance sampling. Our method achieves state-of-the-art performance on the D4RL benchmark. Notably, CDE consistently outperforms baselines in challenging tasks with sparse rewards or insufficient data, demonstrating the advantages of our approach in addressing the extrapolation error problem in offline RL.

Cross-Validation (CV) is the default choice for estimate the out-of-sample performance of machine learning models. Despite its wide usage, their statistical benefits have remained half-understood, especially in challenging nonparametric regimes. In this paper we fill in this gap and show that, in terms of estimating the out-of-sample performances, for a wide spectrum of models, CV does not statistically outperform the simple ``plug-in'' approach where one reuses training data for testing evaluation. Specifically, in terms of both the asymptotic bias and coverage accuracy of the associated interval for out-of-sample evaluation, $K$-fold CV provably cannot outperform plug-in regardless of the rate at which the parametric or nonparametric models converge. Leave-one-out CV can have a smaller bias as compared to plug-in; however, this bias improvement is negligible compared to the variability of the evaluation, and in some important cases leave-one-out again does not outperform plug-in once this variability is taken into account. We obtain our theoretical comparisons via a novel higher-order Taylor analysis that dissects the limit theorems of testing evaluations, which applies to model classes that are not amenable to previously known sufficient conditions. Our numerical results demonstrate that plug-in performs indeed no worse than CV in estimating model performance across a wide range of examples.

Discrete-event simulation models generate random variates from input distributions and compute outputs according to the simulation logic. The input distributions are typically fitted to finite real-world data and thus are subject to estimation errors that can propagate to the simulation outputs: an issue commonly known as input uncertainty (IU). This paper investigates quantifying IU using the output confidence intervals (CIs) computed from bootstrap quantile estimators. The standard direct bootstrap method has overcoverage due to convolution of the simulation error and IU; however, the brute-force way of washing away the former is computationally demanding. We present two new bootstrap methods to enhance direct resampling in both statistical and computational efficiencies using shrinkage strategies to down-scale the variabilities encapsulated in the CIs. Our asymptotic analysis shows how both approaches produce tight CIs accounting for IU under limited input data and simulation effort along with the simulation sample-size requirements relative to the input data size. We demonstrate performances of the shrinkage strategies with several numerical experiments and investigate the conditions under which each method performs well. We also show advantages of nonparametric approaches over parametric bootstrap when the distribution family is misspecified and over metamodel approaches when the dimension of the distribution parameters is high. History: Accepted by Bruno Tuffin, Area Editor for Simulation. Funding: This work was supported by the National Science Foundation [CAREER CMMI-1834710, CAREER CMMI-2045400, DMS-1854659, and IIS-1849280]. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2022.0044 ) as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2022.0044 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .

Empirical risk minimization (ERM) and distributionally robust optimization (DRO) are popular approaches for solving stochastic optimization problems that appear in operations management and machine learning. Existing generalization error bounds for these methods depend on either the complexity of the cost function or dimension of the uncertain parameters; consequently, the performance of these methods is poor for high-dimensional problems with objective functions under high complexity. We propose a simple approach in which the distribution of uncertain parameters is approximated using a parametric family of distributions. This mitigates both sources of complexity; however, it introduces a model misspecification error. We show that this new source of error can be controlled by suitable DRO formulations. Our proposed parametric DRO approach has significantly improved generalization bounds over existing ERM / DRO methods and parametric ERM for a wide variety of settings. Our method is particularly effective under distribution shifts. We also illustrate the superior performance of our approach on both synthetic and real-data portfolio optimization and regression tasks.

One key challenge for multi-task Reinforcement learning (RL) in practice is the absence of task specifications. Robust RL has been applied to deal with task ambiguity but may result in over-conservative policies. To balance the worst-case (robustness) and average performance, we propose Group Distributionally Robust Markov Decision Process (GDR-MDP), a flexible hierarchical MDP formulation that encodes task groups via a latent mixture model. GDR-MDP identifies the optimal policy that maximizes the expected return under the worst-possible qualified belief over task groups within an ambiguity set. We rigorously show that GDR-MDP’s hierarchical structure improves distributional robustness by adding regularization to the worst possible outcomes. We then develop deep RL algorithms for GDR-MDP for both value-based and policy-based RL methods. Extensive experiments on Box2D control tasks, MuJoCo benchmarks, and Google football platforms show that our algorithms outperform classic robust training algorithms across diverse environments in terms of robustness under belief uncertainties. Demos are available on our project page (https://sites.google.com/view/gdr-rl/home).

The bootstrap is a popular data-driven method to quantify statistical uncertainty, but for modern high-dimensional problems, it could suffer from huge computational costs due to the need to repeatedly generate resamples and refit models. We study the use of bootstraps in high-dimensional environments with a small number of resamples. In particular, we show that with a recent "cheap" bootstrap perspective, using a number of resamples as small as one could attain valid coverage even when the dimension grows closely with the sample size, thus strongly supporting the implementability of the bootstrap for large-scale problems. We validate our theoretical results and compare the performance of our approach with other benchmarks via a range of experiments.

Bayesian bandit algorithms with approximate Bayesian inference have been widely used in real-world applications. However, there is a large discrepancy between the superior practical performance of these approaches and their theoretical justification. Previous research only indicates a negative theoretical result: Thompson sampling could have a worst-case linear regret $\Omega(T)$ with a constant threshold on the inference error measured by one $\alpha$-divergence. To bridge this gap, we propose an Enhanced Bayesian Upper Confidence Bound (EBUCB) framework that can efficiently accommodate bandit problems in the presence of approximate inference. Our theoretical analysis demonstrates that for Bernoulli multi-armed bandits, EBUCB can achieve the optimal regret order $O(\log T)$ if the inference error measured by two different $\alpha$-divergences is less than a constant, regardless of how large this constant is. To our best knowledge, our study provides the first theoretical regret bound that is better than $o(T)$ in the setting of constant approximate inference error. Furthermore, in concordance with the negative results in previous studies, we show that only one bounded $\alpha$-divergence is insufficient to guarantee a sub-linear regret.

Uncertainty quantification (UQ) is important for reliability assessment and enhancement of machine learning models. In deep learning, uncertainties arise not only from data, but also from the training procedure that often injects substantial noises and biases. These hinder the attainment of statistical guarantees and, moreover, impose computational challenges on UQ due to the need for repeated network retraining. Building upon the recent neural tangent kernel theory, we create statistically guaranteed schemes to principally \emph{characterize}, and \emph{remove}, the uncertainty of over-parameterized neural networks with very low computation effort. In particular, our approach, based on what we call a procedural-noise-correcting (PNC) predictor, removes the procedural uncertainty by using only \emph{one} auxiliary network that is trained on a suitably labeled dataset, instead of many retrained networks employed in deep ensembles. Moreover, by combining our PNC predictor with suitable light-computation resampling methods, we build several approaches to construct asymptotically exact-coverage confidence intervals using as low as four trained networks without additional overheads.

Many kinds of simultaneously-observed event sequences exhibit mutually exciting or inhibiting patterns. Reliable detection of such temporal dependencies is crucial for scientific investigation. A common model is the Multivariate Hawkes Process (MHP), whose impact function naturally encodes a causal structure in Granger causality. However, the vast majority of existing methods use a transformed standard MHP intensity with a constant baseline, which may be inconsistent with real-world data. On the other hand, modeling irregular and unknown background dynamics directly is a challenge, as one struggles to distinguish the effect of mutual interaction from that of fluctuations in background dynamics. In this paper, we address the short-term temporal dependency detection issue. We show that maximum likelihood estimation (MLE) for cross-impact from MHP has an error that can not be eliminated, but may be reduced by an order of magnitude using a heterogeneous intensity not for the target HP but for the interacting HP. Then we propose a robust and computationally-efficient modification of MLE that does not rely on the prior estimation of the heterogeneous intensity and is thus applicable in a data-limited regime (e.g., few-shot, unrepeated observations). Extensive experiments on various datasets show that our method outperforms existing ones by notable margins, with highlighted novel applications in neuroscience.

Standard Monte Carlo computation is widely known to exhibit a canonical square-root convergence speed in terms of sample size. Two recent techniques, one based on control variate and one on importance sampling, both derived from an integration of reproducing kernels and Stein's identity, have been proposed to reduce the error in Monte Carlo computation to supercanonical convergence. This paper presents a more general framework to encompass both techniques that is especially beneficial when the sample generator is biased and noise-corrupted. We show our general estimator, which we call the doubly robust Stein-kernelized estimator, outperforms both existing methods in terms of mean squared error rates across different scenarios. We also demonstrate the superior performance of our method via numerical examples.

Evaluating rare but high-stakes events is one of the main challenges in obtaining reliable reinforcement learning policies, especially in large or infinite state/action spaces where limited scalability dictates a prohibitively large number of testing iterations. On the other hand, a biased or inaccurate policy evaluation in a safety-critical system could potentially cause unexpected catastrophic failures during deployment. This paper proposes the Accelerated Policy Evaluation (APE) method, which simultaneously uncovers rare events and estimates the rare event probability in Markov decision processes. The APE method treats the environment nature as an adversarial agent and learns towards, through adaptive importance sampling, the zero-variance sampling distribution for the policy evaluation. Moreover, APE is scalable to large discrete or continuous spaces by incorporating function approximators. We investigate the convergence property of APE in the tabular setting. Our empirical studies show that APE can estimate the rare event probability with a smaller bias while only using orders of magnitude fewer samples than baselines in multi-agent and single-agent environments.

Established approaches to obtain generalization bounds in data-driven optimization and machine learning mostly build on solutions from empirical risk minimization (ERM), which depend crucially on the functional complexity of the hypothesis class. In this paper, we present an alternate route to obtain these bounds on the solution from distributionally robust optimization (DRO), a recent data-driven optimization framework based on worst-case analysis and the notion of ambiguity set to capture statistical uncertainty. In contrast to the hypothesis class complexity in ERM, our DRO bounds depend on the ambiguity set geometry and its compatibility with the true loss function. Notably, when using statistical distances such as maximum mean discrepancy, Wasserstein distance, or $\phi$-divergence in the DRO, our analysis implies generalization bounds whose dependence on the hypothesis class appears the minimal possible: The bound depends solely on the true loss function, independent of any other candidates in the hypothesis class. To our best knowledge, it is the first generalization bound of this type in the literature, and we hope our findings can open the door for a better understanding of DRO, especially its benefits on loss minimization and other machine learning applications.

We investigate a new approach to compute the gradients of artificial neural networks (ANNs), based on the so-called push-out likelihood ratio method. Unlike the widely used backpropagation (BP) method that requires continuity of the loss function and the activation function, our approach bypasses this requirement by injecting artificial noises into the signals passed along the neurons. We show how this approach has a similar computational complexity as BP, and moreover is more advantageous in terms of removing the backward recursion and eliciting transparent formulas. We also formalize the connection between BP, a pivotal technique for training ANNs, and infinitesimal perturbation analysis, a classic path-wise derivative estimation approach, so that both our new proposed methods and BP can be better understood in the context of stochastic gradient estimation. Our approach allows efficient training for ANNs with more flexibility on the loss and activation functions, and shows empirical improvements on the robustness of ANNs under adversarial attacks and corruptions of natural noises. Summary of Contribution: Stochastic gradient estimation has been studied actively in simulation for decades and becomes more important in the era of machine learning and artificial intelligence. The stochastic gradient descent is a standard technique for training the artificial neural networks (ANNs), a pivotal problem in deep learning. The most popular stochastic gradient estimation technique is the backpropagation method. We find that the backpropagation method lies in the family of infinitesimal perturbation analysis, a path-wise gradient estimation technique in simulation. Moreover, we develop a new likelihood ratio-based method, another popular family of gradient estimation technique in simulation, for training more general ANNs, and demonstrate that the new training method can improve the robustness of the ANN.

Evaluating the reliability of intelligent physical systems against rare safety-critical events poses a huge testing burden for real-world applications. Simulation provides a useful platform to evaluate the extremal risks of these systems before their deployments. Importance Sampling (IS), while proven to be powerful for rare-event simulation, faces challenges in handling these learning-based systems due to their black-box nature that fundamentally undermines its efficiency guarantee, which can lead to under-estimation without diagnostically detected. We propose a framework called Deep Probabilistic Accelerated Evaluation (Deep-PrAE) to design statistically guaranteed IS, by converting black-box samplers that are versatile but could lack guarantees, into one with what we call a relaxed efficiency certificate that allows accurate estimation of bounds on the safety-critical event probability. We present the theory of Deep-PrAE that combines the dominating point concept with rare-event set learning via deep neural network classifiers, and demonstrate its effectiveness in numerical examples including the safety-testing of an intelligent driving algorithm.

We study the generation of prediction intervals in regression for uncertainty quantification. This task can be formalized as an empirical constrained optimization problem that minimizes the average interval width while maintaining the coverage accuracy across data. We strengthen the existing literature by studying two aspects of this empirical optimization. First is a general learning theory to characterize the optimality-feasibility tradeoff that encompasses Lipschitz continuity and VC-subgraph classes, which are exemplified in regression trees and neural networks. Second is a calibration machinery and the corresponding statistical theory to optimally select the regularization parameter that manages this tradeoff, which bypasses the overfitting issues in previous approaches in coverage attainment. We empirically demonstrate the strengths of our interval generation and calibration algorithms in terms of testing performances compared to existing benchmarks.

We develop a model-free reinforcement learning approach to solve constrained Markov decision processes, where the objective and budget constraints are in the form of infinite-horizon discounted expectations, and the rewards and costs are learned sequentially from data. We propose a two-stage procedure where we first search over deterministic policies, followed by an aggregation with a mixture parameter search, that generates policies with simultaneous guarantees on near-optimality and feasibility. We also numerically illustrate our approach by applying it to an online advertising problem.

In many learning problems, the training and testing data follow different distributions and a particularly common situation is the \textit{covariate shift}. To correct for sampling biases, most approaches, including the popular kernel mean matching (KMM), focus on estimating the importance weights between the two distributions. Reweighting-based methods, however, are exposed to high variance when the distributional discrepancy is large. On the other hand, the alternate approach of using nonparametric regression (NR) incurs high bias when the training size is limited. In this paper, we propose and analyze a new estimator that systematically integrates the residuals of NR with KMM reweighting, based on a control-variate perspective. The proposed estimator can be shown to either strictly outperform or match the best-known existing rates for both KMM and NR, and thus is a robust combination of both estimators. The experiments shows the estimator works well in practice.

The process to certify highly automated vehicles has not yet been defined by any country in the world. Currently, companies test automated vehicles on public roads, which is time-consuming and inefficient. We proposed the accelerated evaluation concept, which uses a modified statistics of the surrounding vehicles and the importance sampling theory to reduce the evaluation time by several orders of magnitude, while ensuring the evaluation results are statistically accurate. In this paper, we further improve the accelerated evaluation concept by using piecewise mixture distribution models, instead of single parametric distribution models. We developed and applied this idea to forward collision control system reacting to vehicles making cutin lane changes. The behavior of the cutin vehicles was modeled based on more than 403,581 lane changes collected by the University of Michigan Safety Pilot Model Deployment Program. Simulation results confirm that the accuracy and efficiency of the piecewise mixture distribution method outperformed single parametric distribution methods in accuracy and efficiency, and accelerated the evaluation process by almost four orders of magnitude.

The safety of automated vehicles (AVs) must be assured before their release and deployment. The current approach to evaluation relies primarily on 1) testing AVs on public roads or 2) track testing with scenarios defined in a test matrix. These two methods have completely opposing drawbacks: the former, while offering realistic scenarios, takes too much time to execute and the latter, though it can be completed in a short amount of time, has no clear correlation to safety benefits in the real world. To avoid the aforementioned problems, we propose accelerated evaluation, focusing on the car-following scenario. The stochastic human-controlled vehicle (HV) motions are modeled based on 1.3 million miles of naturalistic driving data collected by the University of Michigan Safety Pilot Model Deployment Program. The statistics of the HV behaviors are then modified to generate more intense interactions between HVs and AVs to accelerate the evaluation procedure. The importance sampling theory was used to ensure that the safety benefits of AVs are accurately assessed under accelerated tests. Crash, injury and conflict rates for a simulated AV are simulated to demonstrate the proposed approach. Results show that test duration is reduced by a factor of 300 to 100 000 compared with the non-accelerated (naturalistic) evaluation. In other words, the proposed techniques have great potential for accelerating the AV evaluation process.

Evaluation and testing are critical for the development of Automated Vehicles (AVs). Currently, companies test AVs on public roads, which is very time-consuming and inefficient. We proposed the Accelerated Evaluation concept which uses a modified statistics of the surrounding vehicles and the Importance Sampling theory to reduce the evaluation time by several orders of magnitude, while ensuring the final evaluation results are accurate. In this paper, we further extend this idea by using Piecewise Mixture Distribution models instead of Single Distribution models. We demonstrate this idea to evaluate vehicle safety in lane change scenarios. The behavior of the cut-in vehicles was modeled based on more than 400,000 naturalistic driving lane changes collected by the University of Michigan Safety Pilot Model Deployment Program. Simulation results confirm that the accuracy and efficiency of the Piecewise Mixture Distribution method are better than the single distribution.

Automated vehicles (AVs) must be thoroughly evaluated before their release and deployment. A widely used evaluation approach is the Naturalistic-Field Operational Test (N-FOT), which tests prototype vehicles directly on the public roads. Due to the low exposure to safety-critical scenarios, N-FOTs are time consuming and expensive to conduct. In this paper, we propose an accelerated evaluation approach for AVs. The results can be used to generate motions of the other primary vehicles to accelerate the verification of AVs in simulations and controlled experiments. Frontal collision due to unsafe cut-ins is the target crash type of this paper. Human-controlled vehicles making unsafe lane changes are modeled as the primary disturbance to AVs based on data collected by the University of Michigan Safety Pilot Model Deployment Program. The cut-in scenarios are generated based on skewed statistics of collected human driver behaviors, which generate risky testing scenarios while preserving the statistical information so that the safety benefits of AVs in nonaccelerated cases can be accurately estimated. The cross-entropy method is used to recursively search for the optimal skewing parameters. The frequencies of the occurrences of conflicts, crashes, and injuries are estimated for a modeled AV, and the achieved accelerated rate is around 2000 to 20 000. In other words, in the accelerated simulations, driving for 1000 miles will expose the AV with challenging scenarios that will take about 2 to 20 million miles of real-world driving to encounter. This technique thus has the potential to greatly reduce the development and validation time for AVs.

We propose a Bayesian framework for recursively estimating the classifier weights in online learning of a classifier ensemble. In contrast with past methods, such as stochastic gradient descent or online boosting, our framework estimates the weights in terms of evolving posterior distributions. For a specified class of loss functions, we show that it is possible to formulate a suitably defined likelihood function and hence use the posterior distribution as an approximation to the global empirical loss minimizer. If the stream of training data is sampled from a stationary process, we can also show that our framework admits a superior rate of convergence to the expected loss minimizer than is possible with standard stochastic gradient descent. In experiments with real-world datasets, our formulation often performs better than online boosting algorithms.

We consider the problem of reconstructing a specific connected community S ⊂V in a graph G = (V, E), where each node v is associated with a signal whose strength grows with the likelihood that v belongs to S. This problem appears in social or protein interaction network, the latter also referred to as the signaling pathway reconstruction problem. We study this community reconstruction problem under several natural generative models, and make the following two contributions. First, in the context of social networks, where the signals are modeled as bounded-supported random variables, we design an efficient algorithm for recovering most members in S with well-controlled false positive overhead, by utilizing the network structure for a large family of “homogeneous” generative models. This positive result is complemented by an information theoretic lower bound for the case where the network structure is unknown or the network is heterogeneous. Second, we consider the case in which the graph represents the protein interaction network, in which it is customary to consider signals that have unbounded support, we generalize our first contribution to give the first theoretical justification of why existing Steiner-tree type heuristics work well in practice.

UNLABELLED: Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a 'map' of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting inevitable RT shifts. Similar, but not identical, LC instruments and settings can cause peptides to elute at very different times and sometimes in a different order, violating the assumptions of many state-of-the-art alignment tools. To meet this challenge, we developed LWBMatch, a new algorithm based on weighted bipartite matching. Unlike existing tools, which search for accurate warping functions to correct RT shifts, we directly seek a peak-to-peak mapping by maximizing a global similarity function between two LC-MS maps. For alignment tasks with large RT shifts (>500 s), an approximate warping function is determined by locally weighted scatterplot smoothing of potential matched features, detected using a novel voting scheme based on co-elution. For validation, we defined the ground truth for alignment success based on tandem mass spectrometry identifications from sequence searching. We showed that our method outperforms several existing tools in terms of precision and recall, and is capable of aligning maps from different instruments and settings. AVAILABILITY: Available at https://sourceforge.net/projects/rt-alignment/.

We study a natural information dissemination problem for multiple mobile agents in a bounded Euclidean space.Agents are placed uniformly at random in the d-dimensional space {-n, ..., n} d at time zero, and one of the agents holds a piece of information to be disseminated.All the agents then perform independent random walks over the space, and the information is transmitted from one agent to another if the two agents are sufficiently close.We wish to bound the total time before all agents receive the information (with high probability).Our work extends Pettarin et al's work [10], which solved the problem for d ≤ 2. We present tight bounds up to polylogarithmic factors for the case d = 3. (While our results extend to higher dimensions, for space and readability considerations we provide only the case d = 3 here.)Our results show the behavior when d ≥ 3 is qualitatively different from the case d ≤ 2. In particular, as the ratio between the volume of the space and the number of agents varies, we show an interesting phase transition for three dimensions that does not occur in one or two dimensions.

We prove the first Chernoff-Hoeffding bounds for general nonreversible finite-state Markov chains based on the standard L_1 (variation distance) mixing-time of the chain. Specifically, consider an ergodic Markov chain M and a weight function f: [n] -> [0,1] on the state space [n] of M with mean mu = E_{v = delta mu t ], is at most exp(-Omega(delta^2 mu t / T)) for 0 <= delta <= 1, and exp(-Omega(delta mu t / T)) for delta > 1. In fact, the bounds hold even if the weight functions f_i's for i in [t] are distinct, provided that all of them have the same mean mu. We also obtain a simplified proof for the Chernoff-Hoeffding bounds based on the spectral expansion lambda of M, which is the square root of the second largest eigenvalue (in absolute value) of M tilde{M}, where tilde{M} is the time-reversal Markov chain of M. We show that the probability Pr [ |X - mu t| >= delta mu t ] is at most exp(-Omega(delta^2 (1-lambda) mu t)) for 0 <= delta <= 1, and exp(-Omega(delta (1-lambda) mu t)) for delta > 1. Both of our results extend to continuous-time Markov chains, and to the case where the walk starts from an arbitrary distribution x, at a price of a multiplicative factor depending on the distribution x in the concentration bounds.