Daily Papers

Deep ensemble methods often improve predictive performance, yet they suffer from three practical limitations: redundancy among base models that inflates computational cost and degrades conditioning, unstable weighting under multicollinearity, and overfitting in meta-learning pipelines. We propose a regularized meta-learning framework that addresses these challenges through a four-stage pipeline combining redundancy-aware projection, statistical meta-feature augmentation, and cross-validated regularized meta-models (Ridge, Lasso, and ElasticNet). Our multi-metric de-duplication strategy removes near-collinear predictors using correlation and MSE thresholds (τ_{corr}=0.95), reducing the effective condition number of the meta-design matrix while preserving predictive diversity. Engineered ensemble statistics and interaction terms recover higher-order structure unavailable to raw prediction columns. A final inverse-RMSE blending stage mitigates regularizer-selection variance. On the Playground Series S6E1 benchmark (100K samples, 72 base models), the proposed framework achieves an out-of-fold RMSE of 8.582, improving over simple averaging (8.894) and conventional Ridge stacking (8.627), while matching greedy hill climbing (8.603) with substantially lower runtime (4 times faster). Conditioning analysis shows a 53.7\% reduction in effective matrix condition number after redundancy projection. Comprehensive ablations demonstrate consistent contributions from de-duplication, statistical meta-features, and meta-ensemble blending. These results position regularized meta-learning as a stable and deployment-efficient stacking strategy for high-dimensional ensemble systems.

Memory-efficient matrix optimizers such as Sinkhorn gradient descent remove most AdamW optimizer state for dense Transformer matrices, but direct application to Mixture-of-Experts (MoE) training is unreliable. We study this failure in a controlled 110M-parameter nanowhale DeepSeek-style MoE pretraining setting. A SAGE/Sinkhorn hybrid reduces optimizer state from 0.883GB to 0.331GB but degrades evaluation loss to 3.8265, far above the AdamW baselines observed in the same setup (3.58--3.64 across the seeds we study). We show that routed MoE expert matrices are the dominant failure point: their gradients are conditional, temporally varying, and poorly served by stateless Sinkhorn normalization. We propose MESH, a hidden-momentum Sinkhorn update for MoE experts. MESH restores a temporal first-moment signal through the gradient-buffer lifecycle, without storing the expert first moment as optimizer state. MESH is an optional block-preconditioned variant that adds a coarse neuron/block inverse-RMS multiplier. Across ablations, temporal smoothing before matrix normalization is the primary causal ingredient; block/neuron preconditioning can improve the memory-quality frontier, but is not established as universally necessary. In two additional seeds, MESH and MESH-B reduce optimizer-state memory by 62.5\% and peak PyTorch CUDA allocation by about 12.6\% relative to AdamW, with a modest evaluation-loss gap. Full-state diagnostic variants recover AdamW-like performance in ablations, supporting the conclusion that MoE experts need temporal smoothing, but not necessarily full coordinate-wise AdamW state.

Stacking heterogeneous vision backbones (CNNs, ViTs, and hybrids) is the de facto recipe for accuracy, calibration, and robustness, yet two coupled pathologies limit its returns. Prediction-space multicollinearity ill-conditions the meta-learner's Gram matrix, inflating weight variance and producing brittle solutions on a thin manifold. Calibration collapse compounds constituent miscalibration through naive linear stacking, so adding more models can hurt expected calibration error (ECE). Existing remedies, ridge regularization, greedy selection, model soups, and SWAG address at most one of these issues, and none jointly target conditioning and calibration in heterogeneous prediction pools. We introduce CORE-STACK+, a preconditioning pipeline with four components: (i) a kernelized redundancy filter that removes non-linear inter-model dependencies invisible to Pearson correlation, using Centered Kernel Alignment (CKA) [23]; (ii) a <15K-parameter differentiable meta-feature gate that learns per-sample attention over ensemble statistics; (iii) a spectrum-adaptive Ridge penalty lambda^{star}=lmax(Chat)/SNR(Chat) derived from a Marchenko-Pastur signal-noise decomposition, eliminating nested cross-validation; and (iv) a Laplace-approximate Bayesian blender replacing inverse-RMSE heuristics. We prove a PAC-Bayes excess-risk bound that, for the first time, jointly accounts for prediction-space redundancy and meta-learner capacity. Across six benchmarks, CORE-STACK+ delivers +1.8% top-1 on ImageNet-1K, -4.2 mCE on ImageNet-C, +0.9 mIoU on ADE20K, and +1.3 AP on COCO, while reducing retained models by 35-57% and inference FLOPs by up to 41%. ECE improves 2.1times over deep ensembles without post hoc temperature scaling.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

We propose a neural network for both forward and inverse continuous nonlinear Fourier transforms, NFT and INFT respectively. We demonstrate the network's capability to perform NFT and INFT for a random mix of NFDM-QAM signals. The network transformations (NFT and INFT) exhibit true characteristics of these transformations; they are significantly different for low and high-power input pulses. The network shows adequate accuracy with an RMSE of 5e-3 for forward and 3e-2 for inverse transforms. We further show that the trained network can be used to perform general nonlinear Fourier transforms on arbitrary pulses beyond the training pulse types.

This work presents the network architecture EVP (Enhanced Visual Perception). EVP builds on the previous work VPD which paved the way to use the Stable Diffusion network for computer vision tasks. We propose two major enhancements. First, we develop the Inverse Multi-Attentive Feature Refinement (IMAFR) module which enhances feature learning capabilities by aggregating spatial information from higher pyramid levels. Second, we propose a novel image-text alignment module for improved feature extraction of the Stable Diffusion backbone. The resulting architecture is suitable for a wide variety of tasks and we demonstrate its performance in the context of single-image depth estimation with a specialized decoder using classification-based bins and referring segmentation with an off-the-shelf decoder. Comprehensive experiments conducted on established datasets show that EVP achieves state-of-the-art results in single-image depth estimation for indoor (NYU Depth v2, 11.8% RMSE improvement over VPD) and outdoor (KITTI) environments, as well as referring segmentation (RefCOCO, 2.53 IoU improvement over ReLA). The code and pre-trained models are publicly available at https://github.com/Lavreniuk/EVP.

In several recently proposed stochastic optimization methods (e.g. RMSProp, Adam, Adadelta), parameter updates are scaled by the inverse square roots of exponential moving averages of squared past gradients. Maintaining these per-parameter second-moment estimators requires memory equal to the number of parameters. For the case of neural network weight matrices, we propose maintaining only the per-row and per-column sums of these moving averages, and estimating the per-parameter second moments based on these sums. We demonstrate empirically that this method produces similar results to the baseline. Secondly, we show that adaptive methods can produce larger-than-desired updates when the decay rate of the second moment accumulator is too slow. We propose update clipping and a gradually increasing decay rate scheme as remedies. Combining these methods and dropping momentum, we achieve comparable results to the published Adam regime in training the Transformer model on the WMT 2014 English-German machine translation task, while using very little auxiliary storage in the optimizer. Finally, we propose scaling the parameter updates based on the scale of the parameters themselves.

Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to drastic changes in the protein structure. In this paper, we demonstrate that RoseTTAFold does not exhibit such a robustness despite its high accuracy, and biologically small perturbations for some input sequences result in radically different predicted protein structures. This raises the challenge of detecting when these predicted protein structures cannot be trusted. We define the robustness measure for the predicted structure of a protein sequence to be the inverse of the root-mean-square distance (RMSD) in the predicted structure and the structure of its adversarially perturbed sequence. We use adversarial attack methods to create adversarial protein sequences, and show that the RMSD in the predicted protein structure ranges from 0.119A to 34.162A when the adversarial perturbations are bounded by 20 units in the BLOSUM62 distance. This demonstrates very high variance in the robustness measure of the predicted structures. We show that the magnitude of the correlation (0.917) between our robustness measure and the RMSD between the predicted structure and the ground truth is high, that is, the predictions with low robustness measure cannot be trusted. This is the first paper demonstrating the susceptibility of RoseTTAFold to adversarial attacks.