Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D density of the particle, along with 3D pose of the particle in each 2D image, for which the posterior pose distribution is highly multi-modal. Recent developments in cryo-EM have focused on deep learning for which amortized inference has been used to predict pose. Here, we address key problems with this approach, and propose a new semi-amortized method, cryoSPIN, in which reconstruction begins with amortized inference and then switches to a form of auto-decoding to refine poses locally using stochastic gradient descent. Through evaluation on synthetic datasets, we demonstrate that cryoSPIN is able to handle multi-modal pose distributions during the amortized inference stage, while the later, more flexible stage of direct pose optimization yields faster and more accurate convergence of poses compared to baselines.

This paper aims at developing novel shuffling gradient-based methods for tackling two classes of minimax problems: nonconvex-linear and nonconvex-strongly concave settings. The first algorithm addresses the nonconvex-linear minimax model and achieves the state-of-the-art oracle complexity typically observed in nonconvex optimization. It also employs a new shuffling estimator for the hyper-gradient'', departing from standard shuffling techniques in optimization. The second method consists of two variants: semi-shuffling and full-shuffling schemes. These variants tackle the nonconvex-strongly concave minimax setting.

Clustering is a ubiquitous task in data science. Compared to the commonly used k-means clustering, k-medoids clustering requires the cluster centers to be actual data points and supports arbitrary distance metrics, which permits greater interpretability and the clustering of structured objects. Current state-of-the-art k-medoids clustering algorithms, such as Partitioning Around Medoids (PAM), are iterative and are quadratic in the dataset size n for each iteration, being prohibitively expensive for large datasets. We propose BanditPAM, a randomized algorithm inspired by techniques from multi-armed bandits, that reduces the complexity of each PAM iteration from O(n 2) to O(nlogn) and returns the same results with high probability, under assumptions on the data that often hold in practice. As such, BanditPAM matches state-of-the-art clustering loss while reaching solutions much faster.

We accelerate the iterative hard thresholding (IHT) method, which finds (k) important elements from a parameter vector in a linear regression model. Although the plain IHT repeatedly updates the parameter vector during the optimization, computing gradients is the main bottleneck. Our method safely prunes unnecessary gradient computations to reduce the processing time.The main idea is to efficiently construct a candidate set, which contains (k) important elements in the parameter vector, for each iteration. Specifically, before computing the gradients, we prune unnecessary elements in the parameter vector for the candidate set by utilizing upper bounds on absolute values of the parameters. Our method guarantees the same optimization results as the plain IHT because our pruning is safe.

Imperceptible adversarial attacks aim to fool DNNs by adding imperceptible perturbation to the input data. Previous methods typically improve the imperceptibility of attacks by integrating common attack paradigms with specifically designed perception-based losses or the capabilities of generative models. In this paper, we propose Adversarial Attacks in Diffusion (AdvAD), a novel modeling framework distinct from existing attack paradigms. At each step, much subtler yet effective adversarial guidance is crafted using only the attacked model without any additional network, which gradually leads the end of diffusion process from the original image to a desired imperceptible adversarial example. Grounded in a solid theoretical foundation of the proposed non-parametric diffusion process, AdvAD achieves high attack efficacy and imperceptibility with intrinsically lower overall perturbation strength.

The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons ( N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization requirement.

While training models and labeling data are resource-intensive, a wealth of pre-trained models and unlabeled data exists. To effectively utilize these resources, we present an approach to actively select pre-trained models while minimizing labeling costs. We frame this as an online contextual active model selection problem: At each round, the learner receives an unlabeled data point as a context. The objective is to adaptively select the best model to make a prediction while limiting label requests. To tackle this problem, we propose CAMS, a contextual active model selection algorithm that relies on two novel components: (1) a contextual model selection mechanism, which leverages context information to make informed decisions about which model is likely to perform best for a given context, and (2)an active query component, which strategically chooses when to request labels for data points, minimizing the overall labeling cost.

Recent research has demonstrated that transformers, particularly linear attention models, implicitly execute gradient-descent-like algorithms on data provided in-context during their forward inference step. However, their capability in handling more complex problems remains unexplored. In this paper, we prove that each layer of a linear transformer maintains a weight vector for an implicit linear regression problem and can be interpreted as performing a variant of preconditioned gradient descent. We also investigate the use of linear transformers in a challenging scenario where the training data is corrupted with different levels of noise. Remarkably, we demonstrate that for this problem linear transformers discover an intricate and highly effective optimization algorithm, surpassing or matching in performance many reasonable baselines.

Average-link is widely recognized as one of the most popular and effective methods for building hierarchical agglomerative clustering. The available theoretical analyses show that this method has a much better approximation than other popular heuristics, as single-linkage and complete-linkage, regarding variants of Dasgupta's cost function [STOC 2016]. However, these analyses do not separate average-link from a random hierarchy and they are not appealing for metric spaces since every hierarchical clustering has a 1/2 approximation with regard to the variant of Dasgupta's functionthat is employed for dissimilarity measures [Moseley and Yang 2020]. In this paper, we present a comprehensive study of the performance of \avglink \, in metric spaces, regarding several natural criteria that capture separability and cohesion, and are more interpretable than Dasgupta's cost function and its variants. We also present experimental results with real datasets that, together with our theoretical analyses, suggest that average-link is a better choice than other related methods when both cohesion and separability are important goals.

Inferring the synaptic plasticity rules that govern learning in the brain is a key challenge in neuroscience. We present a novel computational method to infer these rules from experimental data, applicable to both neural and behavioral data. Our approach approximates plasticity rules using a parameterized function, employing either truncated Taylor series for theoretical interpretability or multilayer perceptrons. These plasticity parameters are optimized via gradient descent over entire trajectories to align closely with observed neural activity or behavioral learning dynamics. This method can uncover complex rules that induce long nonlinear time dependencies, particularly involving factors like postsynaptic activity and current synaptic weights.