Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from largescale datasets through self-supervised pre-training methods. However, these models often overlook the severe corruption in cryogenic electron microscopy (cryo-EM) images by high-level noises. We introduce DRACO, a Denoising-Reconstruction Autoencoder for CryO-EM, inspired by the Noise2Noise (N2N) approach. By processing cryo-EM movies into odd and even images and treating them as independent noisy observations, we apply a denoising-reconstruction hybrid training scheme. We mask both images to create denoising and reconstruction tasks. For DRACO's pre-training, the quality of the dataset is essential, we hence build a high-quality, diverse dataset from an uncurated public database, including over 270,000 movies or micrographs. After pre-training, DRACO naturally serves as a generalizable cryo-EM image denoiser and a foundation model for various cryo-EM downstream tasks. DRACO demonstrates the best performance in denoising, micrograph curation, and particle picking tasks compared to state-of-the-art baselines.

Study of the nonlinear evolution deep neural network (DNN) parameters undergo during training has uncovered regimes of distinct dynamical behavior. While a detailed understanding of these phenomena has the potential to advance improvements in training efficiency and robustness, the lack of methods for identifying when DNN models have equivalent dynamics limits the insight that can be gained from prior work. Topological conjugacy, a notion from dynamical systems theory, provides a precise definition of dynamical equivalence, offering a possible route to address this need. However, topological conjugacies have historically been challenging to compute. By leveraging advances in Koopman operator theory, we develop a framework for identifying conjugate and non-conjugate training dynamics. To validate our approach, we demonstrate that comparing Koopman eigenvalues can correctly identify a known equivalence between online mirror descent and online gradient descent. We then utilize our approach to: (a) identify non-conjugate training dynamics between shallow and wide fully connected neural networks; (b) characterize the early phase of training dynamics in convolutional neural networks; (c) uncover non-conjugate training dynamics in Transformers that do and do not undergo grokking. Our results, across a range of DNN architectures, illustrate the flexibility of our framework and highlight its potential for shedding new light on training dynamics.

Dense Associative Memories are high storage capacity variants of the Hopfield networks that are capable of storing a large number of memory patterns in the weights of the network of a given size. Their common formulations typically require storing each pattern in a separate set of synaptic weights, which leads to the increase of the number of synaptic weights when new patterns are introduced. In this work we propose an alternative formulation of this class of models using random features, commonly used in kernel methods. In this formulation the number of network's parameters remains fixed. At the same time, new memories can be added to the network by modifying existing weights. We show that this novel network closely approximates the energy function and dynamics of conventional Dense Associative Memories and shares their desirable computational properties.

Diffusion models (DMs) have become the dominant paradigm of generative modeling in a variety of domains by learning stochastic processes from noise to data. Recently, diffusion denoising bridge models (DDBMs), a new formulation of generative modeling that builds stochastic processes between fixed data endpoints based on a reference diffusion process, have achieved empirical success across tasks with coupled data distribution, such as image-to-image translation. However, DDBM's sampling process typically requires hundreds of network evaluations to achieve decent performance, which may impede their practical deployment due to high computational demands. In this work, inspired by the recent advance of consistency models in DMs, we tackle this problem by learning the consistency function of the probability-flow ordinary differential equation (PF-ODE) of DDBMs, which directly predicts the solution at a starting step given any point on the ODE trajectory. Based on a dedicated general-form ODE solver, we propose two paradigms: consistency bridge distillation and consistency bridge training, which is flexible to apply on DDBMs with broad design choices. Experimental results show that our proposed method could sample 4 to 50 faster than the base DDBM and produce better visual quality given the same step in various tasks with pixel resolution ranging from 64 64 to 256 256, as well as supporting downstream tasks such as semantic interpolation in the data space.

A critical question about Large Language Models (LLMs) is whether their apparent deficiency in mathematical reasoning is inherent, or merely a result of insufficient exposure to high-quality mathematical data. To explore this, we developed an automated method for generating high-quality, supervised mathematical datasets. The method carefully mutates existing math problems, ensuring both diversity and validity of the newly generated problems. This is achieved by a neuro-symbolic data generation framework combining the intuitive informalization strengths of LLMs, and the precise symbolic reasoning of math solvers along with projected Markov chain Monte Carlo sampling in the highly-irregular symbolic space. Empirical experiments demonstrate the high quality of data generated by the proposed method, and that the LLMs, specifically LLaMA-2 and Mistral, when realigned with the generated data, surpass their state-of-the-art counterparts.

Most large multimodal models (LMMs) are implemented by feeding visual tokens as a sequence into the first layer of a large language model (LLM). The resulting architecture is simple but significantly increases computation and memory costs, as it has to handle a large number of additional tokens in its input layer. This paper presents a new architecture DeepStack for LMMs. Considering N layers in the language and vision transformer of LMMs, we stack the visual tokens into N groups and feed each group to its aligned transformer layer from bottom to top, as illustrated in Figure 1. Surprisingly, this simple method greatly enhances the power of LMMs to model interactions among visual tokens across layers but with minimal additional cost. We apply DeepStack to both language and vision transformer in LMMs, and validate the effectiveness of DeepStack LMMs with extensive empirical results. Using the same context length, our DeepStack 7B and 13B parameters surpass their counterparts by 2.7 and 2.9 on average across 9 benchmarks, respectively.

We present a novel diffusion-based approach for coherent 3D scene reconstruction from a single RGB image. Our method utilizes an image-conditioned 3D scene diffusion model to simultaneously denoise the 3D poses and geometries of all objects within the scene. Motivated by the ill-posed nature of the task and to obtain consistent scene reconstruction results, we learn a generative scene prior by conditioning on all scene objects simultaneously to capture the scene context and by allowing the model to learn inter-object relationships throughout the diffusion process. We further propose an efficient surface alignment loss to facilitate training even in the absence of full ground-truth annotation, which is common in publicly available datasets. This loss leverages an expressive shape representation, which enables direct point sampling from intermediate shape predictions.

Self-play via online learning is one of the premier ways to solve large-scale twoplayer zero-sum games, both in theory and practice. Particularly popular algorithms include optimistic multiplicative weights update (OMWU) and optimistic gradient-descent-ascent (OGDA). While both algorithms enjoy O(1/T) ergodic convergence to Nash equilibrium in two-player zero-sum games, OMWU offers several advantages including logarithmic dependence on the size of the payoff matrix and Õ(1/T) convergence to coarse correlated equilibria even in generalsum games. However, in terms of last-iterate convergence in two-player zero-sum games, an increasingly popular topic in this area, OGDA guarantees that the duality gap shrinks at a rate of (1/ T), while the best existing last-iterate convergence for OMWU depends on some game-dependent constant that could be arbitrarily large. This begs the question: is this potentially slow last-iterate convergence an inherent disadvantage of OMWU, or is the current analysis too loose? Somewhat surprisingly, we show that the former is true. More generally, we prove that a broad class of algorithms that do not forget the past quickly all suffer the same issue: for any arbitrarily small δ > 0, there exists a 2 2 matrix game such that the algorithm admits a constant duality gap even after 1/δ rounds. This class of algorithms includes OMWU and other standard optimistic follow-the-regularized-leader algorithms.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in crossmodality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field.