The phenomenon of hysteresis is commonly observed in many UV thermal experiments involving unmodified or modified nucleic acids. In presence of hysteresis, the thermal curves are irreversible and demand a significant effort to produce the reaction-specific kinetic and thermodynamic parameters. In this article, we describe a unified statistical procedure to analyze such thermal curves. Our method applies to experiments with intramolecular as well as intermolecular reactions. More specifically, the proposed method allows one to handle the thermal curves for the formation of duplexes, triplexes, and various quadruplexes in exactly the same way. The proposed method uses a local polynomial regression for finding the smoothed thermal curves and calculating their slopes. This method is more flexible and easy to implement than the least squares polynomial smoothing which is currently almost universally used for such purposes. Full analyses of the curves including computation of kinetic and thermodynamic parameters can be done using freely available statistical software. In the end, we illustrate our method by analyzing irreversible curves encountered in the formations of a G-quadruplex and an LNA-modified parallel duplex.
Summarization systems make numerous "decisions" about summary properties during inference, e.g. degree of copying, specificity and length of outputs, etc. However, these are implicitly encoded within model parameters and specific styles cannot be enforced. To address this, we introduce HydraSum, a new summarization architecture that extends the single decoder framework of current models to a mixture-of-experts version with multiple decoders. We show that HydraSum's multiple decoders automatically learn contrasting summary styles when trained under the standard training objective without any extra supervision. Through experiments on three summarization datasets (CNN, Newsroom and XSum), we show that HydraSum provides a simple mechanism to obtain stylistically-diverse summaries by sampling from either individual decoders or their mixtures, outperforming baseline models. Finally, we demonstrate that a small modification to the gating strategy during training can enforce an even stricter style partitioning, e.g. high- vs low-abstractiveness or high- vs low-specificity, allowing users to sample from a larger area in the generation space and vary summary styles along multiple dimensions.
Discovering new intents is of great significance to establishing Bootstrapped Task-Oriented Dialogue System. Most existing methods either lack the ability to transfer prior knowledge in the known intent data or fall into the dilemma of forgetting prior knowledge in the follow-up. More importantly, these methods do not deeply explore the intrinsic structure of unlabeled data, so they can not seek out the characteristics that make an intent in general. In this paper, starting from the intuition that discovering intents could be beneficial to the identification of the known intents, we propose a probabilistic framework for discovering intents where intent assignments are treated as latent variables. We adopt Expectation Maximization framework for optimization. Specifically, In E-step, we conduct discovering intents and explore the intrinsic structure of unlabeled data by the posterior of intent assignments. In M-step, we alleviate the forgetting of prior knowledge transferred from known intents by optimizing the discrimination of labeled data. Extensive experiments conducted in three challenging real-world datasets demonstrate our method can achieve substantial improvements.
Two-stage randomized experiments are becoming an increasingly popular experimental design for causal inference when the outcome of one unit may be affected by the treatment assignments of other units in the same cluster. In this paper, we provide a methodological framework for general tools of statistical inference and power analysis for two-stage randomized experiments. Under the randomization-based framework, we consider the estimation of a new direct effect of interest as well as the average direct and spillover effects studied in the literature. We provide unbiased estimators of these causal quantities and their conservative variance estimators in a general setting. Using these results, we then develop hypothesis testing procedures and derive sample size formulas. We theoretically compare the two-stage randomized design with the completely randomized and cluster randomized designs, which represent two limiting designs. Finally, we conduct simulation studies to evaluate the empirical performance of our sample size formulas. For empirical illustration, the proposed methodology is applied to the randomized evaluation of the Indian national health insurance program. An open-source software package is available for implementing the proposed methodology.
Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.
Simulation of stochastic partial differential equations (SPDE) on a general domain requires a discretization of the noise. In this paper, the noise is discretized by a piecewise linear interpolation. The error caused by this is analyzed in the context of a fully discrete finite element approximation of a semilinear stochastic reaction-advection-diffusion equation on a convex polygon. The noise is Gaussian, white in time and correlated in space. It is modeled as a standard cylindrical Wiener process on the reproducing kernel Hilbert space associated to the covariance kernel. The noise is assumed to extend to a larger polygon than the SPDE domain to allow for sampling by the circulant embedding method. The interpolation error is analyzed under mild assumptions on the kernel. The main tools used are Hilbert--Schmidt bounds of multiplication operators onto negative order Sobolev spaces and an error bound for the finite element interpolant in fractional Sobolev norms. Examples with covariance kernels encountered in applications are illustrated in numerical simulations using the FEniCS finite element software. Conclusions from the analysis include that interpolation of noise with Mat\'ern kernels does not cause an additional error, that there exist kernels where the interpolation error dominates and that generation of noise on a coarser mesh than that of the SPDE discretization does not always result in a loss of accuracy.
Variational Bayes methods are a scalable estimation approach for many complex state space models. However, existing methods exhibit a trade-off between accurate estimation and computational efficiency. This paper proposes a variational approximation that mitigates this trade-off. This approximation is based on importance densities that have been proposed in the context of efficient importance sampling. By directly conditioning on the observed data, the proposed method produces an accurate approximation to the exact posterior distribution. Because the steps required for its calibration are computationally efficient, the approach is faster than existing variational Bayes methods. The proposed method can be applied to any state space model that has a closed-form measurement density function and a state transition distribution that belongs to the exponential family of distributions. We illustrate the method in numerical experiments with stochastic volatility models and a macroeconomic empirical application using a high-dimensional state space model.
Learning policies via preference-based reward learning is an increasingly popular method for customizing agent behavior, but has been shown anecdotally to be prone to spurious correlations and reward hacking behaviors. While much prior work focuses on causal confusion in reinforcement learning and behavioral cloning, we aim to study it in the context of reward learning. To study causal confusion, we perform a series of sensitivity and ablation analyses on three benchmark domains where rewards learned from preferences achieve minimal test error but fail to generalize to out-of-distribution states -- resulting in poor policy performance when optimized. We find that the presence of non-causal distractor features, noise in the stated preferences, partial state observability, and larger model capacity can all exacerbate causal confusion. We also identify a set of methods with which to interpret causally confused learned rewards: we observe that optimizing causally confused rewards drives the policy off the reward's training distribution, resulting in high predicted (learned) rewards but low true rewards. These findings illuminate the susceptibility of reward learning to causal confusion, especially in high-dimensional environments -- failure to consider even one of many factors (data coverage, state definition, etc.) can quickly result in unexpected, undesirable behavior.
We develop an algorithmic framework for solving convex optimization problems using no-regret game dynamics. By converting the problem of minimizing a convex function into an auxiliary problem of solving a min-max game in a sequential fashion, we can consider a range of strategies for each of the two-players who must select their actions one after the other. A common choice for these strategies are so-called no-regret learning algorithms, and we describe a number of such and prove bounds on their regret. We then show that many classical first-order methods for convex optimization -- including average-iterate gradient descent, the Frank-Wolfe algorithm, the Heavy Ball algorithm, and Nesterov's acceleration methods -- can be interpreted as special cases of our framework as long as each player makes the correct choice of no-regret strategy. Proving convergence rates in this framework becomes very straightforward, as they follow from plugging in the appropriate known regret bounds. Our framework also gives rise to a number of new first-order methods for special cases of convex optimization that were not previously known.
We derive normal approximation results for a class of stabilizing functionals of binomial or Poisson point process, that are not necessarily expressible as sums of certain score functions. Our approach is based on a flexible notion of the add-one cost operator, which helps one to deal with the second-order cost operator via suitably appropriate first-order operators. We combine this flexible notion with the theory of strong stabilization to establish our results. We illustrate the applicability of our results by establishing normal approximation results for certain geometric and topological statistics arising frequently in practice. Several existing results also emerge as special cases of our approach.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.