In this paper, we investigate the latent geometry of generative diffusion models under the manifold hypothesis. For this purpose, we analyze the spectrum of eigenvalues (and singular values) of the Jacobian of the score function, whose discontinuities (gaps) reveal the presence and dimensionality of distinct sub-manifolds. Using a statistical physics approach, we derive the spectral distributions and formulas for the spectral gaps under several distributional assumptions, and we compare these theoretical predictions with the spectra estimated from trained networks. Our analysis reveals the existence of three distinct qualitative phases during the generative process: a trivial phase; a manifold coverage phase where the diffusion process fits the distribution internal to the manifold; a consolidation phase where the score becomes orthogonal to the manifold and all particles are projected on the support of the data. This `division of labor' between different timescales provides an elegant explanation of why generative diffusion models are not affected by the manifold overfitting phenomenon that plagues likelihood-based models, since the internal distribution and the manifold geometry are produced at different time points during generation.

We present InvMSAFold, an inverse folding method for generating protein sequences optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a pairwise probability distribution over the space of sequences, capturing the amino acid covariances observed in Multiple Sequence Alignments (MSA) of homologous proteins. This allows for the efficient generation of highly diverse protein sequences while preserving structural and functional integrity. We demonstrate that this increased diversity in sampled sequences translates into greater variability in biochemical properties, highlighting the exciting potential of our method for applications such as protein design. The orders of magnitude improvement in sampling speed compared to existing methods unlocks new possibilities for high-throughput in virtual screening.

We consider random instances of non-convex perceptron problems in the high-dimensional limit of a large number of examples $M$ and weights $N$, with finite load $\alpha = M/N$. We develop a formalism based on replica theory to predict the fundamental limits of efficiently sampling the solution space using generative diffusion algorithms, conjectured to be saturated when the score function is provided by Approximate Message Passing. For the spherical perceptron with negative margin $\kappa$, we find that the uniform distribution over solutions can be efficiently sampled in most of the Replica Symmetric region of the $\alpha$–$\kappa$ plane. In contrast, for binary weights, sampling from the uniform distribution remains intractable. A theoretical analysis of this obstruction leads us to identify a potential $U(s) = -\log(s)$, under which the corresponding tilted distribution becomes efficiently samplable via diffusion. Moreover, we show numerically that an annealing procedure over the shape of this potential yields a fast and robust Markov Chain Monte Carlo algorithm for sampling the solution space of the binary perceptron.

GraphNeuralNetworks.jl is an open-source framework for deep learning on graphs, written in the Julia programming language. It supports multiple GPU backends, generic sparse or dense graph representations, and offers convenient interfaces for manipulating standard, heterogeneous, and temporal graphs with attributes at the node, edge, and graph levels. The framework allows users to define custom graph convolutional layers using gather/scatter message-passing primitives or optimized fused operations. It also includes several popular layers, enabling efficient experimentation with complex deep architectures. The package is available on GitHub: https://github.com/JuliaGraphs/GraphNeuralNetworks.jl.

Noiseless compressive sensing is a protocol that enables undersampling and later recovery of a signal without loss of information. This compression is possible because the signal is usually sufficiently sparse in a given basis. Currently, the algorithm offering the best tradeoff between compression rate, robustness, and speed for compressive sensing is the LASSO (ℓ1-norm bias) algorithm. However, many studies have pointed out the possibility that the implementation of ℓp-norms biases, with p smaller than one, could give better performance while sacrificing convexity. In this work, we focus specifically on the extreme case of the ℓ0-based reconstruction, a task that is complicated by the discontinuity of the loss. In the first part of the paper, we describe via statistical physics methods, and in particular the replica method, how the solutions to this optimization problem are arranged in a clustered structure. We observe two distinct regimes: one at low compression rate where the signal can be recovered exactly, and one at high compression rate where the signal cannot be recovered accurately. In the second part, we present two message-passing algorithms based on our first results for the ℓ0-norm optimization problem. The proposed algorithms are able to recover the signal at compression rates higher than the ones achieved by LASSO while being computationally efficient.

Many different types of generative models for protein sequences have been proposed in literature. Their uses include the prediction of mutational effects, protein design and the prediction of structural properties. Neural network (NN) architectures have shown great performances, commonly attributed to the capacity to extract non-trivial higher-order interactions from the data. In this work, we analyze two different NN models and assess how close they are to simple pairwise distributions, which have been used in the past for similar problems. We present an approach for extracting pairwise models from more complex ones using an energy-based modeling framework. We show that for the tested models the extracted pairwise models can replicate the energies of the original models and are also close in performance in tasks like mutational effect prediction. In addition, we show that even simpler, factorized models often come close in performance to the original models.

In Generalized Linear Estimation (GLE) problems, we seek to estimate a signal that is observed through a linear transform followed by a component-wise, possibly nonlinear and noisy, channel. In the Bayesian optimal setting, Generalized Approximate Message Passing (GAMP) is known to achieve optimal performance for GLE. However, its performance can significantly deteriorate whenever there is a mismatch between the assumed and the true generative model, a situation frequently encountered in practice. In this paper, we propose a new algorithm, named Generalized Approximate Survey Propagation (GASP), for solving GLE in the presence of prior or model misspecifications. As a prototypical example, we consider the phase retrieval problem, where we show that GASP outperforms the corresponding GAMP, reducing the reconstruction threshold and, for certain choices of its parameters, approaching Bayesian optimal performance. Furthermore, we present a set of state evolution equations that can precisely characterize the performance of GASP in the high-dimensional limit.