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. On experimental data, we show that cryoSPIN outperforms the state-of-the-art cryoAI in speed and reconstruction quality.

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. Experiments show that our method is up to 73 times faster than the plain IHT without degrading accuracy.

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. We analyze this algorithm and show that it is a novel approach incorporating momentum and adaptive rescaling based on noise levels. Our findings show that even linear transformers possess the surprising ability to discover sophisticated optimization strategies.

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. We validate our approach through simulations, successfully recovering established rules such as Oja's, as well as more intricate plasticity rules with reward-modulated terms. We assess the robustness of our technique to noise and apply it to behavioral data from \textit{Drosophila} in a probabilistic reward-learning experiment. Notably, our findings reveal an active forgetting component in reward learning in flies, improving predictive accuracy over previous models. This modeling framework offers a promising new avenue for elucidating the computational principles of synaptic plasticity and learning in the brain.

This paper studies the generalization performance of iterates obtained by Gradient Descent (GD), Stochastic Gradient Descent (SGD) and their proximal variants in high-dimensional robust regression problems. The number of features is comparable to the sample size and errors may be heavy-tailed. We introduce estimators that precisely track the generalization error of the iterates along the trajectory of the iterative algorithm. These estimators are provably consistent under suitable conditions. The results are illustrated through several examples, including Huber regression, pseudo-Huber regression, and their penalized variants with non-smooth regularizer. We provide explicit generalization error estimates for iterates generated from GD and SGD, or from proximal SGD in the presence of a non-smooth regularizer. The proposed risk estimates serve as effective proxies for the actual generalization error, allowing us to determine the optimal stopping iteration that minimizes the generalization error. Extensive simulations confirm the effectiveness of the proposed generalization error estimates.

In this work, we study the mean-field flow for learning subspace-sparse polynomials using stochastic gradient descent and two-layer neural networks, where the input distribution is standard Gaussian and the output only depends on the projection of the input onto a low-dimensional subspace. We establish a necessary condition for SGD-learnability, involving both the characteristics of the target function and the expressiveness of the activation function. In addition, we prove that the condition is almost sufficient, in the sense that a condition slightly stronger than the necessary condition can guarantee the exponential decay of the loss functional to zero.

In this work, we provide a fundamental unified convergence theorem used for deriving expected and almost sure convergence results for a series of stochastic optimization methods. Our unified theorem only requires to verify several representative conditions and is not tailored to any specific algorithm. As a direct application, we recover expected and almost sure convergence results of the stochastic gradient method (SGD) and random reshuffling (RR) under more general settings. Moreover, we establish new expected and almost sure convergence results for the stochastic proximal gradient method (prox-SGD) and stochastic model-based methods for nonsmooth nonconvex optimization problems. These applications reveal that our unified theorem provides a plugin-type convergence analysis and strong convergence guarantees for a wide class of stochastic optimization methods.

In the absence of class priors, recent deep clustering methods resort to data augmentation and pseudo-labeling strategies to generate supervision signals. Though achieved remarkable success, existing works struggle to discriminate hard samples at cluster boundaries, mining which is particularly challenging due to their unreliable cluster assignments. To break such a performance bottleneck, we propose incorporating user interaction to facilitate clustering instead of exhaustively mining semantics from the data itself. To be exact, we present Interactive Deep Clustering (IDC), a plug-and-play method designed to boost the performance of pre-trained clustering models with minimal interaction overhead. More specifically, IDC first quantitatively evaluates sample values based on hardness, representativeness, and diversity, where the representativeness avoids selecting outliers and the diversity prevents the selected samples from collapsing into a small number of clusters. IDC then queries the cluster affiliations of high-value samples in a user-friendly manner.

We study stochastic linear bandits where, in each round, the learner receives a set of actions (i.e., feature vectors), from which it chooses an element and obtains a stochastic reward. The expected reward is a fixed but unknown linear function of the chosen action. We study \emph{sparse} regret bounds, that depend on the number $S$ of non-zero coefficients in the linear reward function. Previous works focused on the case where $S$ is known, or the action sets satisfy additional assumptions. In this work, we obtain the first sparse regret bounds that hold when $S$ is unknown and the action sets are adversarially generated. Our techniques combine online to confidence set conversions with a novel randomized model selection approach over a hierarchy of nested confidence sets. When $S$ is known, our analysis recovers state-of-the-art bounds for adversarial action sets. We also show that a variant of our approach, using Exp3 to dynamically select the confidence sets, can be used to improve the empirical performance of stochastic linear bandits while enjoying a regret bound with optimal dependence on the time horizon.