Inverse protein folding generates valid amino acid sequences that can fold into a desired protein structure, with recent deep-learning advances showing significant potential and competitive performance. However, challenges remain in predicting highly uncertain regions, such as those with loops and disorders. To tackle such low-confidence residue prediction, we propose a \textbf{Ma}sk \textbf{p}rior-guided denoising \textbf{Diff}usion (\textbf{MapDiff}) framework that accurately captures both structural and residue interactions for inverse protein folding. MapDiff is a discrete diffusion probabilistic model that iteratively generates amino acid sequences with reduced noise, conditioned on a given protein backbone. To incorporate structural and residue interactions, we develop a graph-based denoising network with a mask prior pre-training strategy. Moreover, in the generative process, we combine the denoising diffusion implicit model with Monte-Carlo dropout to improve uncertainty estimation. Evaluation on four challenging sequence design benchmarks shows that MapDiff significantly outperforms state-of-the-art methods. Furthermore, the in-silico sequences generated by MapDiff closely resemble the physico-chemical and structural characteristics of native proteins across different protein families and architectures.

We propose to quantify dependence between two systems $X$ and $Y$ in a dataset $D$ based on the Bayesian comparison of two models: one, $H_0$, of statistical independence and another one, $H_1$, of dependence. In this framework, dependence between $X$ and $Y$ in $D$, denoted $B(X,Y|D)$, is quantified as $P(H_1|D)$, the posterior probability for the model of dependence given $D$, or any strictly increasing function thereof. It is therefore a measure of the evidence for dependence between $X$ and $Y$ as modeled by $H_1$ and observed in $D$. We review several statistical models and reconsider standard results in the light of $B(X,Y|D)$ as a measure of dependence. Using simulations, we focus on two specific issues: the effect of noise and the behavior of $B(X,Y|D)$ when $H_1$ has a parameter coding for the intensity of dependence. We then derive some general properties of $B(X,Y|D)$, showing that it quantifies the information contained in $D$ in favor of $H_1$ versus $H_0$. While some of these properties are typical of what is expected from a valid measure of dependence, others are novel and naturally appear as desired features for specific measures of dependence, which we call inferential. We finally put these results in perspective; in particular, we discuss the consequences of using the Bayesian framework as well as the similarities and differences between $B(X,Y|D)$ and mutual information.

--Fuzz testing is a fundamental technique employed to identify vulnerabilities within software systems. However, the process can be protracted and resource-intensive, especially when confronted with extensive codebases. In this work, I present FuzzDistill, an approach that harnesses compile-time data and machine learning to refine fuzzing targets. By analyzing compile-time information, such as function call graphs' features, loop information, and memory operations, FuzzDistill identifies high-priority areas of the codebase that are more probable to contain vulnerabilities. I demonstrate the efficacy of my approach through experiments conducted on real-world software, demonstrating substantial reductions in testing time. Fuzz testing is a critical technique for identifying vulnerabilities in software by subjecting programs to random or semi-random inputs. As a result, large portions of the code are left unexplored, and significant vulnerabilities can go undetected.

Autonomous robot navigation in off-road environments presents a number of challenges due to its lack of structure, making it difficult to handcraft robust heuristics for diverse scenarios. While learned methods using hand labels or self-supervised data improve generalizability, they often require a tremendous amount of data and can be vulnerable to domain shifts. To improve generalization in novel environments, recent works have incorporated adaptation and self-supervision to develop autonomous systems that can learn from their own experiences online. However, current works often rely on significant prior data, for example minutes of human teleoperation data for each terrain type, which is difficult to scale with more environments and robots. To address these limitations, we propose SALON, a perception-action framework for fast adaptation of traversability estimates with minimal human input. SALON rapidly learns online from experience while avoiding out of distribution terrains to produce adaptive and risk-aware cost and speed maps. Within seconds of collected experience, our results demonstrate comparable navigation performance over kilometer-scale courses in diverse off-road terrain as methods trained on 100-1000x more data. We additionally show promising results on significantly different robots in different environments. Our code is available at https://theairlab.org/SALON.

Machine learning models have exhibited exceptional results in various domains. The most prevalent approach for learning is the empirical risk minimizer (ERM), which adapts the model's weights to reduce the loss on a training set and subsequently leverages these weights to predict the label for new test data. Nonetheless, ERM makes the assumption that the test distribution is similar to the training distribution, which may not always hold in real-world situations. In contrast, the predictive normalized maximum likelihood (pNML) was proposed as a min-max solution for the individual setting where no assumptions are made on the distribution of the tested input. This study investigates pNML's learnability for linear regression and neural networks, and demonstrates that pNML can improve the performance and robustness of these models on various tasks. Moreover, the pNML provides an accurate confidence measure for its output, showcasing state-of-the-art results for out-of-distribution detection, resistance to adversarial attacks, and active learning.

Data scarcity and data imbalance have attracted a lot of attention in many fields. Data augmentation, explored as an effective approach to tackle them, can improve the robustness and efficiency of classification models by generating new samples. This paper presents REPRINT, a simple and effective hidden-space data augmentation method for imbalanced data classification. Given hidden-space representations of samples in each class, REPRINT extrapolates, in a randomized fashion, augmented examples for target class by using subspaces spanned by principal components to summarize distribution structure of both source and target class. Consequently, the examples generated would diversify the target while maintaining the original geometry of target distribution. Besides, this method involves a label refinement component which allows to synthesize new soft labels for augmented examples. Compared with different NLP data augmentation approaches under a range of data imbalanced scenarios on four text classification benchmark, REPRINT shows prominent improvements. Moreover, through comprehensive ablation studies, we show that label refinement is better than label-preserving for augmented examples, and that our method suggests stable and consistent improvements in terms of suitable choices of principal components. Moreover, REPRINT is appealing for its easy-to-use since it contains only one hyperparameter determining the dimension of subspace and requires low computational resource.

There has been extensive research on community detection in directed and bipartite networks. However, these studies often fail to consider the popularity of nodes in different communities, which is a common phenomenon in real-world networks. To address this issue, we propose a new probabilistic framework called the Two-Way Node Popularity Model (TNPM). The TNPM also accommodates edges from different distributions within a general sub-Gaussian family. We introduce the Delete-One-Method (DOM) for model fitting and community structure identification, and provide a comprehensive theoretical analysis with novel technical skills dealing with sub-Gaussian generalization. Additionally, we propose the Two-Stage Divided Cosine Algorithm (TSDC) to handle large-scale networks more efficiently. Our proposed methods offer multi-folded advantages in terms of estimation accuracy and computational efficiency, as demonstrated through extensive numerical studies. We apply our methods to two real-world applications, uncovering interesting findings.

Classical optimization theory requires a small step-size for gradient-based methods to converge. Nevertheless, recent findings challenge the traditional idea by empirically demonstrating Gradient Descent (GD) converges even when the step-size $\eta$ exceeds the threshold of $2/L$, where $L$ is the global smooth constant. This is usually known as the Edge of Stability (EoS) phenomenon. A widely held belief suggests that an objective function with subquadratic growth plays an important role in incurring EoS. In this paper, we provide a more comprehensive answer by considering the task of finding linear interpolator $\beta \in R^{d}$ for regression with loss function $l(\cdot)$, where $\beta$ admits parameterization as $\beta = w^2_{+} - w^2_{-}$. Contrary to the previous work that suggests a subquadratic $l$ is necessary for EoS, our novel finding reveals that EoS occurs even when $l$ is quadratic under proper conditions. This argument is made rigorous by both empirical and theoretical evidence, demonstrating the GD trajectory converges to a linear interpolator in a non-asymptotic way. Moreover, the model under quadratic $l$, also known as a depth-$2$ diagonal linear network, remains largely unexplored under the EoS regime. Our analysis then sheds some new light on the implicit bias of diagonal linear networks when a larger step-size is employed, enriching the understanding of EoS on more practical models.

Despite the widespread use of the data augmentation (DA) algorithm, the theoretical understanding of its convergence behavior remains incomplete. We prove the first non-asymptotic polynomial upper bounds on mixing times of three important DA algorithms: DA algorithm for Bayesian Probit regression (Albert and Chib, 1993, ProbitDA), Bayesian Logit regression (Polson, Scott, and Windle, 2013, LogitDA), and Bayesian Lasso regression (Park and Casella, 2008, Rajaratnam et al., 2015, LassoDA). Concretely, we demonstrate that with $\eta$-warm start, parameter dimension $d$, and sample size $n$, the ProbitDA and LogitDA require $\mathcal{O}\left(nd\log \left(\frac{\log \eta}{\epsilon}\right)\right)$ steps to obtain samples with at most $\epsilon$ TV error, whereas the LassoDA requires $\mathcal{O}\left(d^2(d\log d +n \log n)^2 \log \left(\frac{\eta}{\epsilon}\right)\right)$ steps. The results are generally applicable to settings with large $n$ and large $d$, including settings with highly imbalanced response data in the Probit and Logit regression. The proofs are based on the Markov chain conductance and isoperimetric inequalities. Assuming that data are independently generated from either a bounded, sub-Gaussian, or log-concave distribution, we improve the guarantees for ProbitDA and LogitDA to $\tilde{\mathcal{O}}(n+d)$ with high probability, and compare it with the best known guarantees of Langevin Monte Carlo and Metropolis Adjusted Langevin Algorithm. We also discuss the mixing times of the three algorithms under feasible initialization.

Spectral networks derived from multivariate time series data arise in many domains, from brain science to Earth science. Often, it is of interest to study how these networks change under different conditions. For instance, to better understand epilepsy, it would be interesting to capture the changes in the brain connectivity network as a patient experiences a seizure, using electroencephalography data. A common approach relies on estimating the networks in each condition and calculating their difference. Such estimates may behave poorly in high dimensions as the networks themselves may not be sparse in structure while their difference may be. We build upon this observation to develop an estimator of the difference in inverse spectral densities across two conditions. Using an L1 penalty on the difference, consistency is established by only requiring the difference to be sparse. We illustrate the method on synthetic data experiments, on experiments with electroencephalography data, and on experiments with optogentic stimulation and micro-electrocorticography data.