Quantifying the pathogenicity of protein variants in human disease-related genes would have a profound impact on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences [1][2][3] . In principle, computational methods could support the largescale interpretation of genetic variants. However, prior methods 4-7 have relied on training machine learning models on available clinical labels. Since these labels are sparse, biased, and of variable quality, the resulting models have been considered insufficiently reliable 8 . By contrast, our approach leverages deep generative models to predict the clinical significance of protein variants without relying on labels. The natural distribution of protein sequences we observe across organisms is the result of billions of evolutionary experiments 9,10 . By modeling that distribution, we implicitly capture constraints on the protein sequences that maintain fitness. Our model EVE (Evolutionary model of Variant Effect) not only outperforms computational approaches that rely on labelled data, but also performs on par, if not better than, high-throughput assays which are increasingly used as strong evidence for variant classification [11][12][13][14][15][16][17][18][19][20][21][22][23] . After thorough validation on clinical labels, we predict the pathogenicity of 11 million variants across 1,081 disease genes, and assign high-confidence reclassification for 72k Variants of Unknown Significance 8 . Our work suggests that models of evolutionary information can provide a strong source of independent evidence for variant interpretation and that the approach will be widely useful in research and clinical settings.

A pressing problem in comparing inflationary models with observation is the accurate calculation of correlation functions. One approach is to evolve them using ordinary differential equations ("transport equations"), analogous to the Schwinger-Dyson hierarchy of in-out quantum field theory. We extend this approach to the complete set of momentum space correlation functions. A formal solution can be obtained using raytracing techniques adapted from geometrical optics. We reformulate inflationary perturbation theory in this language, and show that raytracing reproduces the familiar "δN " Taylor expansion. Our method produces ordinary differential equations which allow the Taylor coefficients to be computed efficiently. We use raytracing methods to express the gauge transformation between field fluctuations and the curvature perturbation, ζ, in geometrical terms. Using these results we give a compact expression for the nonlinear gauge-transform part of f NL in terms of the principal curvatures of uniform energy-density hypersurfaces in field space.

We present a complete framework for numerical calculation of the power spectrum and bispectrum in canonical inflation with an arbitrary number of light or heavy fields. Our method includes all relevant effects at tree-level in the loop expansion, including (i) interference between growing and decaying modes near horizon exit; (ii) correlation and coupling between species near horizon exit and on superhorizon scales; (iii) contributions from mass terms; and (iv) all contributions from coupling to gravity. We track the evolution of each correlation function from the vacuum state through horizon exit and the superhorizon regime, with no need to match quantum and classical parts of the calculation; when integrated, our approach corresponds exactly with the tree-level Schwinger or 'in-in' formulation of quantum field theory. In this paper we give the equations necessary to evolve all two-and three-point correlation functions together with suitable initial conditions. The final formalism is suitable to compute the amplitude, shape, and scale dependence of the bispectrum in models with |f NL | of order unity or less, which are a target for future galaxy surveys such as Euclid, DESI and LSST. As an illustration we apply our framework to a number of examples, obtaining quantitatively accurate predictions for their bispectra for the first time. Two accompanying reports describe publicly-available software packages that implement the method.