We study a data-driven approach to the bee identification problem for DNA strands. The bee-identification problem, introduced by Tandon et al. (2019), requires one to identify $M$ bees, each tagged by a unique barcode, via a set of $M$ noisy measurements. Later, Chrisnata et al. (2022) extended the model to case where one observes $N$ noisy measurements of each bee, and applied the model to address the unordered nature of DNA storage systems. In such systems, a unique address is typically prepended to each DNA data block to form a DNA strand, but the address may possibly be corrupted. While clustering is usually used to identify the address of a DNA strand, this requires $\mathcal{M}^2$ data comparisons (when $\mathcal{M}$ is the number of reads). In contrast, the approach of Chrisnata et al. (2022) avoids data comparisons completely. In this work, we study an intermediate, data-driven approach to this identification task. For the binary erasure channel, we first show that we can almost surely correctly identify all DNA strands under certain mild assumptions. Then we propose a data-driven pruning procedure and demonstrate that on average the procedure uses only a fraction of $\mathcal{M}^2$ data comparisons. Specifically, for $\mathcal{M}= 2^n$ and erasure probability $p$, the expected number of data comparisons performed by the procedure is $\kappa\mathcal{M}^2$, where $\left(\frac{1+2p-p^2}{2}\right)^n \leq \kappa \leq \left(\frac{1+p}{2}\right)^n $.
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Natural agents can effectively learn from multiple data sources that differ in size, quality, and types of measurements. We study this heterogeneity in the context of offline reinforcement learning (RL) by introducing a new, practically motivated semi-supervised setting. Here, an agent has access to two sets of trajectories: labelled trajectories containing state, action and reward triplets at every timestep, along with unlabelled trajectories that contain only state and reward information. For this setting, we develop and study a simple meta-algorithmic pipeline that learns an inverse dynamics model on the labelled data to obtain proxy-labels for the unlabelled data, followed by the use of any offline RL algorithm on the true and proxy-labelled trajectories. Empirically, we find this simple pipeline to be highly successful -- on several D4RL benchmarks~\cite{fu2020d4rl}, certain offline RL algorithms can match the performance of variants trained on a fully labelled dataset even when we label only 10\% of trajectories which are highly suboptimal. To strengthen our understanding, we perform a large-scale controlled empirical study investigating the interplay of data-centric properties of the labelled and unlabelled datasets, with algorithmic design choices (e.g., choice of inverse dynamics, offline RL algorithm) to identify general trends and best practices for training RL agents on semi-supervised offline datasets.
Recent years have seen many successful applications of machine learning (ML) to facilitate fluid dynamic computations. As simulations grow, generating new training datasets for traditional offline learning creates I/O and storage bottlenecks. Additionally, performing inference at runtime requires non-trivial coupling of ML framework libraries with simulation codes. This work offers a solution to both limitations by simplifying this coupling and enabling in situ training and inference workflows on heterogeneous clusters. Leveraging SmartSim, the presented framework deploys a database to store data and ML models in memory, thus circumventing the file system. On the Polaris supercomputer, we demonstrate perfect scaling efficiency to the full machine size of the data transfer and inference costs thanks to a novel co-located deployment of the database. Moreover, we train an autoencoder in situ from a turbulent flow simulation, showing that the framework overhead is negligible relative to a solver time step and training epoch.
Value at Risk (VaR) and Conditional Value at Risk (CVaR) have become the most popular measures of market risk in Financial and Insurance fields. However, the estimation of both risk measures is challenging, because it requires the knowledge of the tail of the distribution. Therefore, tools from Extreme Value Theory are usually employed, considering that the tail data follow a Generalized Pareto distribution (GPD). Using the existing relations from the parameters of the baseline distribution and the limit GPD's parameters, we define highly informative priors that incorporate all the information available for the whole set of observations. We show how to perform Metropolis-Hastings (MH) algorithm to estimate VaR and CVaR employing the highly informative priors, in the case of exponential, stable and Gamma distributions. Afterwards, we perform a thorough simulation study to compare the accuracy and precision provided by three different methods. Finally, data from a real example is analyzed to show the practical application of the methods.
We study statistical/computational tradeoffs for the following density estimation problem: given $k$ distributions $v_1, \ldots, v_k$ over a discrete domain of size $n$, and sampling access to a distribution $p$, identify $v_i$ that is "close" to $p$. Our main result is the first data structure that, given a sublinear (in $n$) number of samples from $p$, identifies $v_i$ in time sublinear in $k$. We also give an improved version of the algorithm of Acharya et al. (2018) that reports $v_i$ in time linear in $k$. The experimental evaluation of the latter algorithm shows that it achieves a significant reduction in the number of operations needed to achieve a given accuracy compared to prior work.
We examine the problem of variance components testing in general mixed effects models using the likelihood ratio test. We account for the presence of nuisance parameters, i.e. the fact that some untested variances might also be equal to zero. Two main issues arise in this context leading to a non regular setting. First, under the null hypothesis the true parameter value lies on the boundary of the parameter space. Moreover, due to the presence of nuisance parameters the exact location of these boundary points is not known, which prevents from using classical asymptotic theory of maximum likelihood estimation. Then, in the specific context of nonlinear mixed-effects models, the Fisher information matrix is singular at the true parameter value. We address these two points by proposing a shrinked parametric bootstrap procedure, which is straightforward to apply even for nonlinear models. We show that the procedure is consistent, solving both the boundary and the singularity issues, and we provide a verifiable criterion for the applicability of our theoretical results. We show through a simulation study that, compared to the asymptotic approach, our procedure has a better small sample performance and is more robust to the presence of nuisance parameters. A real data application is also provided.
This paper considers a single-trajectory system identification problem for linear systems under general nonlinear and/or time-varying policies with i.i.d. random excitation noises. The problem is motivated by safe learning-based control for constrained linear systems, where the safe policies during the learning process are usually nonlinear and time-varying for satisfying the state and input constraints. In this paper, we provide a non-asymptotic error bound for least square estimation when the data trajectory is generated by any nonlinear and/or time-varying policies as long as the generated state and action trajectories are bounded. This significantly generalizes the existing non-asymptotic guarantees for linear system identification, which usually consider i.i.d. random inputs or linear policies. Interestingly, our error bound is consistent with that for linear policies with respect to the dependence on the trajectory length, system dimensions, and excitation levels. Lastly, we demonstrate the applications of our results by safe learning with robust model predictive control and provide numerical analysis.
Synthetic data is seen as the most promising solution to share individual-level data while preserving privacy. Shadow modeling-based membership inference attacks (MIAs) have become the standard approach to evaluate the privacy risk of synthetic data. While very effective, they require a large number of datasets to be created and models trained to evaluate the risk posed by a single record. The privacy risk of a dataset is thus currently evaluated by running MIAs on a handful of records selected using ad-hoc methods. We here propose what is, to the best of our knowledge, the first principled vulnerable record identification technique for synthetic data publishing, leveraging the distance to a record's closest neighbors. We show our method to strongly outperform previous ad-hoc methods across datasets and generators. We also show evidence of our method to be robust to the choice of MIA and to specific choice of parameters. Finally, we show it to accurately identify vulnerable records when synthetic data generators are made differentially private. The choice of vulnerable records is as important as more accurate MIAs when evaluating the privacy of synthetic data releases, including from a legal perspective. We here propose a simple yet highly effective method to do so. We hope our method will enable practitioners to better estimate the risk posed by synthetic data publishing and researchers to fairly compare ever improving MIAs on synthetic data.
Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.
In 1954, Alston S. Householder published Principles of Numerical Analysis, one of the first modern treatments on matrix decomposition that favored a (block) LU decomposition-the factorization of a matrix into the product of lower and upper triangular matrices. And now, matrix decomposition has become a core technology in machine learning, largely due to the development of the back propagation algorithm in fitting a neural network. The sole aim of this survey is to give a self-contained introduction to concepts and mathematical tools in numerical linear algebra and matrix analysis in order to seamlessly introduce matrix decomposition techniques and their applications in subsequent sections. However, we clearly realize our inability to cover all the useful and interesting results concerning matrix decomposition and given the paucity of scope to present this discussion, e.g., the separated analysis of the Euclidean space, Hermitian space, Hilbert space, and things in the complex domain. We refer the reader to literature in the field of linear algebra for a more detailed introduction to the related fields.
Recent advances in sensor and mobile devices have enabled an unprecedented increase in the availability and collection of urban trajectory data, thus increasing the demand for more efficient ways to manage and analyze the data being produced. In this survey, we comprehensively review recent research trends in trajectory data management, ranging from trajectory pre-processing, storage, common trajectory analytic tools, such as querying spatial-only and spatial-textual trajectory data, and trajectory clustering. We also explore four closely related analytical tasks commonly used with trajectory data in interactive or real-time processing. Deep trajectory learning is also reviewed for the first time. Finally, we outline the essential qualities that a trajectory management system should possess in order to maximize flexibility.
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