Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable sequences but also representing the sheer diversity of potential solutions. However, existing discriminative models, such as transformer-based auto-regressive models, struggle to encapsulate the diverse range of plausible solutions. In contrast, diffusion probabilistic models, as an emerging genre of generative approaches, offer the potential to generate a diverse set of sequence candidates for determined protein backbones. We propose a novel graph denoising diffusion model for inverse protein folding, where a given protein backbone guides the diffusion process on the corresponding amino acid residue types. The model infers the joint distribution of amino acids conditioned on the nodes' physiochemical properties and local environment. Moreover, we utilize amino acid replacement matrices for the diffusion forward process, encoding the biologically meaningful prior knowledge of amino acids from their spatial and sequential neighbors as well as themselves, which reduces the sampling space of the generative process. Our model achieves state-of-the-art performance over a set of popular baseline methods in sequence recovery and exhibits great potential in generating diverse protein sequences for a determined protein backbone structure.

Adaptive gradient methods have shown excellent performances for solving many machine learning problems. Although multiple adaptive gradient methods were recently studied, they mainly focus on either empirical or theoretical aspects and also only work for specific problems by using some specific adaptive learning rates. Thus, it is desired to design a universal framework for practical algorithms of adaptive gradients with theoretical guarantee to solve general problems. To fill this gap, we propose a faster and universal framework of adaptive gradients (i.e., SUPER-ADAM) by introducing a universal adaptive matrix that includes most existing adaptive gradient forms. Moreover, our framework can flexibly integrate the momentum and variance reduced techniques. In particular, our novel framework provides the convergence analysis support for adaptive gradient methods under the nonconvex setting. In theoretical analysis, we prove that our SUPER-ADAM algorithm can achieve the best known gradient (i.e., stochastic first-order oracle (SFO)) complexity of O( 3) for finding an -stationary point of nonconvex optimization, which matches the lower bound for stochastic smooth nonconvex optimization. In numerical experiments, we employ various deep learning tasks to validate that our algorithm consistently outperforms the existing adaptive algorithms.

The tremendous success of large models trained on extensive datasets demonstrates that scale is a key ingredient in achieving superior results. Therefore, the reflection on the rationality of designing knowledge distillation (KD) approaches for limited-capacity architectures solely based on small-scale datasets is now deemed imperative. In this paper, we identify the small data pitfall that presents in previous KD methods, which results in the underestimation of the power of vanilla KD framework on large-scale datasets such as ImageNet-1K. Specifically, we show that employing stronger data augmentation techniques and using larger datasets can directly decrease the gap between vanilla KD and other meticulously designed KD variants. This highlights the necessity of designing and evaluating KD approaches in the context of practical scenarios, casting off the limitations of small-scale datasets. Our investigation of the vanilla KD and its variants in more complex schemes, including stronger training strategies and different model capacities, demonstrates that vanilla KD is elegantly simple but astonishingly effective in large-scale scenarios. Without bells and whistles, we obtain state-of-the-art ResNet50, ViT-S, and ConvNeXtV2-T models for ImageNet, which achieve 83.1%, 84.3%, and 85.0% top-1 accuracy, respectively.

In this paper, we comparatively analyze the Bures-Wasserstein (BW) geometry with the popular Affine-Invariant (AI) geometry for Riemannian optimization on the symmetric positive definite (SPD) matrix manifold. Our study begins with an observation that the BW metric has a linear dependence on SPD matrices in contrast to the quadratic dependence of the AI metric. We build on this to show that the BW metric is a more suitable and robust choice for several Riemannian optimization problems over ill-conditioned SPD matrices. We show that the BW geometry has a non-negative curvature, which further improves convergence rates of algorithms over the non-positively curved AI geometry. Finally, we verify that several popular cost functions, which are known to be geodesic convex under the AI geometry, are also geodesic convex under the BW geometry. Extensive experiments on various applications support our findings.

Silicon-photonics-based optical neural network (ONN) is a promising hardware platform that could represent a paradigm shift in efficient AI with its CMOScompatibility, flexibility, ultra-low execution latency, and high energy efficiency. In-situ training on the online programmable photonic chips is appealing but still encounters challenging issues in on-chip implementability, scalability, and efficiency. In this work, we propose a closed-loop ONN on-chip learning framework L2ight to enable scalable ONN mapping and efficient in-situ learning. L2ightadopts a three-stage learning flow that first calibrates the complicated photonic circuit states under challenging physical constraints, then performs photonic core mapping via combined analytical solving and zeroth-order optimization. A subspace learning procedure with multi-level sparsity is integrated into L2ightto enable in-situ gradient evaluation and fast adaptation, unleashing the power of optics for real on-chip intelligence. Extensive experiments demonstrate our proposed L2ightoutperforms prior ONN training protocols with 3-order-of-magnitude higher scalability and over 30 better efficiency, when benchmarked on various models and learning tasks. This synergistic framework is the first scalable on-chip learning solution that pushes this emerging field from intractable to scalable and further to efficient for next-generation self-learnable photonic neural chips. From a co-design perspective, L2ightalso provides essential insights for hardware-restricted unitary subspace optimization and efficient sparse training.

Active Learning (AL) aims to reduce the labeling burden by interactively selecting the most informative samples from a pool of unlabeled data. While there has been extensive research on improving AL query methods in recent years, some studies have questioned the effectiveness of AL compared to emerging paradigms such as semi-supervised (Semi-SL) and self-supervised learning (Self-SL), or a simple optimization of classifier configurations. Thus, today's AL literature presents an inconsistent and contradictory landscape, leaving practitioners uncertain about whether and how to use AL in their tasks. In this work, we make the case that this inconsistency arises from a lack of systematic and realistic evaluation of AL methods. Specifically, we identify five key pitfalls in the current literature that reflect the delicate considerations required for AL evaluation. Further, we present an evaluation framework that overcomes these pitfalls and thus enables meaningful statements about the performance of AL methods. To demonstrate the relevance of our protocol, we present a large-scale empirical study and benchmark for image classification spanning various data sets, query methods, AL settings, and training paradigms. Our findings clarify the inconsistent picture in the literature and enable us to give hands-on recommendations for practitioners.

We analyze the dynamics of finite width effects in wide but finite feature learning neural networks. Starting from a dynamical mean field theory description of infinite width deep neural network kernel and prediction dynamics, we provide a characterization of the O(1/ width) fluctuations of the DMFT order parameters over random initializations of the network weights. Our results, while perturbative in width, unlike prior analyses, are non-perturbative in the strength of feature learning. In the lazy limit of network training, all kernels are random but static in time and the prediction variance has a universal form. However, in the rich, feature learning regime, the fluctuations of the kernels and predictions are dynamically coupled with a variance that can be computed self-consistently.