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The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating configurations sampled from thermodynamic states with a prior distribution, BayesMBAR computes a posterior distribution of free energies. Using the posterior distribution, we derive free energy estimations and compute their associated uncertainties. Notably, when a uniform prior distribution is used, BayesMBAR recovers the MBAR's result but provides more accurate uncertainty estimates. Additionally, when prior knowledge about free energies is available, BayesMBAR can incorporate this information into the estimation procedure by using non-uniform prior distributions. As an example, we show that, by incorporating the prior knowledge about the smoothness of free energy surfaces, BayesMBAR provides more accurate estimates than the MBAR method. Given MBAR's widespread use in free energy calculations, we anticipate BayesMBAR to be an essential tool in various applications of free energy calculations.

Optimal transport (OT) and unbalanced optimal transport (UOT) are central in many machine learning, statistics and engineering applications. 1D OT is easily solved, with complexity O(n log n), but no efficient algorithm was known for 1D UOT. We present a new approach that leverages the successive shortest path algorithm for the corresponding network flow problem. By employing a suitable representation, we bundle together multiple steps that do not change the cost of the shortest path. We prove that our algorithm solves 1D UOT in O(n log n), closing the gap.

We present a method for producing unbiased parameter estimates and valid confidence intervals under the constraints of differential privacy, a formal framework for limiting individual information leakage from sensitive data. Prior work in this area is limited in that it is tailored to calculating confidence intervals for specific statistical procedures, such as mean estimation or simple linear regression. While other recent work can produce confidence intervals for more general sets of procedures, they either yield only approximately unbiased estimates, are designed for one-dimensional outputs, or assume significant user knowledge about the data-generating distribution. Our method induces distributions of mean and covariance estimates via the bag of little bootstraps (BLB) and uses them to privately estimate the parameters' sampling distribution via a generalized version of the CoinPress estimation algorithm. If the user can bound the parameters of the BLB-induced parameters and provide heavier-tailed families, the algorithm produces unbiased parameter estimates and valid confidence intervals which hold with arbitrarily high probability. These results hold in high dimensions and for any estimation procedure which behaves nicely under the bootstrap.

As large language models (LLMs) become more capable, fine-tuning techniques for aligning with human intent are increasingly important. A key consideration for aligning these models is how to most effectively use human resources, or model resources in the case where LLMs themselves are used as oracles. Reinforcement learning from Human or AI preferences (RLHF/RLAIF) is the most prominent example of such a technique, but is complex and often unstable. Direct Preference Optimization (DPO) has recently been proposed as a simpler and more stable alternative. In this work, we develop an active learning strategy for DPO to make better use of preference labels. We propose a practical acquisition function for prompt/completion pairs based on the predictive entropy of the language model and a measure of certainty of the implicit preference model optimized by DPO. We demonstrate how our approach improves both the rate of learning and final performance of fine-tuning on pairwise preference data.

We present a polynomial-time algorithm for online differentially private synthetic data generation. For a data stream within the hypercube $[0,1]^d$ and an infinite time horizon, we develop an online algorithm that generates a differentially private synthetic dataset at each time $t$. This algorithm achieves a near-optimal accuracy bound of $O(t^{-1/d}\log(t))$ for $d\geq 2$ and $O(t^{-1}\log^{4.5}(t))$ for $d=1$ in the 1-Wasserstein distance. This result generalizes the previous work on the continual release model for counting queries to include Lipschitz queries. Compared to the offline case, where the entire dataset is available at once, our approach requires only an extra polylog factor in the accuracy bound.

We resolve the open question regarding the sample complexity of policy learning for maximizing the long-run average reward associated with a uniformly ergodic Markov decision process (MDP), assuming a generative model. In this context, the existing literature provides a sample complexity upper bound of $\widetilde O(|S||A|t_{\text{mix}}^2 \epsilon^{-2})$ and a lower bound of $\Omega(|S||A|t_{\text{mix}} \epsilon^{-2})$. In these expressions, $|S|$ and $|A|$ denote the cardinalities of the state and action spaces respectively, $t_{\text{mix}}$ serves as a uniform upper limit for the total variation mixing times, and $\epsilon$ signifies the error tolerance. Therefore, a notable gap of $t_{\text{mix}}$ still remains to be bridged. Our primary contribution is the development of an estimator for the optimal policy of average reward MDPs with a sample complexity of $\widetilde O(|S||A|t_{\text{mix}}\epsilon^{-2})$. This marks the first algorithm and analysis to reach the literature's lower bound. Our new algorithm draws inspiration from ideas in Li et al. (2020), Jin and Sidford (2021), and Wang et al. (2023). Additionally, we conduct numerical experiments to validate our theoretical findings.

This paper presents a new approach for assembling graph neural networks based on framelet transforms. The latter provides a multi-scale representation for graph-structured data. With the framelet system, we can decompose the graph feature into low-pass and high-pass frequencies as extracted features for network training, which then defines a framelet-based graph convolution. The framelet decomposition naturally induces a graph pooling strategy by aggregating the graph feature into low-pass and high-pass spectra, which considers both the feature values and geometry of the graph data and conserves the total information. The graph neural networks with the proposed framelet convolution and pooling achieve state-of-the-art performance in many types of node and graph prediction tasks. Moreover, we propose shrinkage as a new activation for the framelet convolution, which thresholds the high-frequency information at different scales. Compared to ReLU, shrinkage in framelet convolution improves the graph neural network model in terms of denoising and signal compression: noises in both node and structure can be significantly reduced by accurately cutting off the high-pass coefficients from framelet decomposition, and the signal can be compressed to less than half its original size with the prediction performance well preserved.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

This paper is an attempt to explain all the matrix calculus you need in order to understand the training of deep neural networks. We assume no math knowledge beyond what you learned in calculus 1, and provide links to help you refresh the necessary math where needed. Note that you do not need to understand this material before you start learning to train and use deep learning in practice; rather, this material is for those who are already familiar with the basics of neural networks, and wish to deepen their understanding of the underlying math. Don't worry if you get stuck at some point along the way---just go back and reread the previous section, and try writing down and working through some examples. And if you're still stuck, we're happy to answer your questions in the Theory category at forums.fast.ai. Note: There is a reference section at the end of the paper summarizing all the key matrix calculus rules and terminology discussed here. See related articles at //explained.ai

The dominant sequence transduction models are based on complex recurrent or convolutional neural networks in an encoder-decoder configuration. The best performing models also connect the encoder and decoder through an attention mechanism. We propose a new simple network architecture, the Transformer, based solely on attention mechanisms, dispensing with recurrence and convolutions entirely. Experiments on two machine translation tasks show these models to be superior in quality while being more parallelizable and requiring significantly less time to train. Our model achieves 28.4 BLEU on the WMT 2014 English-to-German translation task, improving over the existing best results, including ensembles by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model establishes a new single-model state-of-the-art BLEU score of 41.8 after training for 3.5 days on eight GPUs, a small fraction of the training costs of the best models from the literature. We show that the Transformer generalizes well to other tasks by applying it successfully to English constituency parsing both with large and limited training data.