6 accepted papers
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 Multipl…
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…
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…
The properties of flat minima in the empirical risk landscape of neural networks have been debated for some time. Increasing evidence suggests they possess better generalization capabilities with respect to sharp ones. In this work we first discuss the relationship between alternative measures of fl…
The training of stochastic neural network models with binary ($\pm1$) weights and activations via continuous surrogate networks is investigated. We derive new surrogates using a novel derivation based on writing the stochastic neural network as a Markov chain. This derivation also encompasses existi…
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 p…