Publications

We introduce OpenRAND, a C++17 library aimed at facilitating reproducible scientific research by generating statistically robust yet replicable random numbers in as little as two lines of code, overcoming some of the unnecessary complexities of existing RNG libraries. OpenRAND accommodates single and multi-threaded applications on CPUs and GPUs and offers a simplified, user-friendly API that complies with the C++ standard’s random number engine interface. It is lightweight; provided as a portable, header-only library. It is statistically robust: a suite of built-in tests ensures no pattern exists within single or multiple streams. Despite its simplicity and portability, it remains performant—matching and sometimes outperforming native libraries. Our tests, including a Brownian walk simulation, affirm its reproducibility and ease-of-use while highlight its computational efficiency, outperforming CUDA’s cuRAND by up to 1.8 times.

The motion of rigid particles in complex fluids is ubiquitous in natural and industrial processes. The most popular toy model for understanding the physics of such systems is the settling of a solid sphere in a viscoelastic fluid. There is general agreement that an elastic wake develops downstream of the sphere, causing the breakage of fore-and-aft symmetry, while the flow remains axisymmetric, independent of fluid viscoelasticity and flow conditions. Using a continuum mechanics model, we reveal that axisymmetry holds only for weak viscoelastic flows. Beyond a critical value of the settling velocity, steady, non-axisymmetric disturbances develop peripherally of the rear pole of the sphere, giving rise to a four-lobed fingering instability. The transition from axisymmetric to non-axisymmetric flow fields is characterized by a regular bifurcation and depends solely on the interplay between shear and extensional properties of the viscoelastic fluid under different flow regimes. At higher settling velocities, each lobe tip is split into two new lobes, resembling fractal fingering in interfacial flows. For the first time, we capture an elastic fingering instability under steady-state conditions, and provide the missing information for understanding and predicting such instabilities in the response of viscoelastic fluids and soft media.

We present a deterministic algorithm for the efficient evaluation of imaginary time diagrams based on the recently introduced discrete Lehmann representation (DLR) of imaginary time Green's functions. In addition to the efficient discretization of diagrammatic integrals afforded by its approximation properties, the DLR basis is separable in imaginary time, allowing us to decompose diagrams into linear combinations of nested sequences of one-dimensional products and convolutions. Focusing on the strong coupling bold-line expansion of generalized Anderson impurity models, we show that our strategy reduces the computational complexity of evaluating an $M$th-order diagram at inverse temperature $\beta$ and spectral width $\omega_{\max}$ from $\mathcal{O}((\beta \omega_{\max})^{2M-1})$ for a direct quadrature to $\mathcal{O}(M (\log (\beta \omega_{\max}))^{M+1})$, with controllable high-order accuracy. We benchmark our algorithm using third-order expansions for multi-band impurity problems with off-diagonal hybridization and spin-orbit coupling, presenting comparisons with exact diagonalization and quantum Monte Carlo approaches. In particular, we perform a self-consistent dynamical mean-field theory calculation for a three-band Hubbard model with strong spin-orbit coupling representing a minimal model of Ca$_2$RuO$_4$, demonstrating the promise of the method for modeling realistic strongly correlated multi-band materials. For both strong and weak coupling expansions of low and intermediate order, in which diagrams can be enumerated, our method provides an efficient, straightforward, and robust black-box evaluation procedure. In this sense, it fills a gap between diagrammatic approximations of the lowest order, which are simple and inexpensive but inaccurate, and those based on Monte Carlo sampling of high-order diagrams.

We present a comprehensive investigation combining numerical simulations with experimental validation, focusing on the creeping flow behavior of a shear-banding, viscoelastic wormlike micellar (WLM) solution over concavities with various depths (D) and lengths (L). The fluid is modeled using the diffusive Giesekus model, with model parameters set to quantitatively describe the shear rheology of a 100 : 60 mM cetylpyridinium chloride:sodium salicylate aqueous WLM solution used for the experimental validation. We observe a transition from “cavity flow” to “expansion–contraction flow” as the length L exceeds the sum of depth D and channel width W. This transition is manifested by a change of vortical structures within the concavity. For L ≤ D + W, “cavity flow” is characterized by large scale recirculations spanning the concavity length. For L > D + W, the recirculations observed in “expansion–contraction flow” are confined to the salient corners downstream of the expansion plane and upstream of the contraction plane. Using the numerical dataset, we construct phase diagrams in L–D at various fixed Weissenberg numbers Wi, characterizing the transitions and describing the evolution of vortical structures influenced by viscoelastic effects.

The standard ΛCDM cosmological model predicts the presence of cold dark matter, with the current accelerated expansion of the Universe driven by dark energy. This model has recently come under scrutiny because of tensions in measurements of the expansion and growth histories of the Universe, parameterized using H0 and S8. The three-dimensional clustering of galaxies encodes key cosmological information that addresses these tensions. Here we present a set of cosmological constraints using simulation-based inference that exploits additional non-Gaussian information on nonlinear scales from galaxy clustering, inaccessible with current analyses. We analyse a subset of the Baryon Oscillation Spectroscopic Survey (BOSS) galaxy survey using SimBIG, a new framework for cosmological inference that leverages high-fidelity simulations and deep generative models. We use two clustering statistics beyond the standard power spectrum: the bispectrum and a summary of the galaxy field based on a convolutional neural network. We constrain H0 and S8 1.5 and 1.9 times more tightly than power spectrum analyses. With this increased precision, our constraints are competitive with those of other cosmological probes, even with only 10% of the full BOSS volume. Future work extending SimBIG to upcoming spectroscopic galaxy surveys (DESI, PFS, Euclid) will produce improved cosmological constraints that will develop understanding of cosmic tensions.

Unraveling the phenotypic and genetic complexity of autism is extremely challenging yet critical for understanding the biology, inheritance, trajectory, and clinical manifestations of the many forms of the condition. Here, we leveraged broad phenotypic data from a large cohort with matched genetics to characterize classes of autism and their patterns of core, associated, and co-occurring traits, ultimately demonstrating that phenotypic patterns are associated with distinct genetic and molecular programs. We used a generative mixture modeling approach to identify robust, clinically-relevant classes of autism which we validate and replicate in a large independent cohort. We link the phenotypic findings to distinct patterns of de novo and inherited variation which emerge from the deconvolution of these genetic signals, and demonstrate that class-specific common variant scores strongly align with clinical outcomes. We further provide insights into the distinct biological pathways and processes disrupted by the sets of mutations in each class. Remarkably, we discover class-specific differences in the developmental timing of genes that are dysregulated, and these temporal patterns correspond to clinical milestone and outcome differences between the classes. These analyses embrace the phenotypic complexity of children with autism, unraveling genetic and molecular programs underlying their heterogeneity and suggesting specific biological dysregulation patterns and mechanistic hypotheses.

Adapting the step size locally in the no-U-turn sampler (NUTS) is challenging because the step-size and path-length tuning parameters are interdependent. The determination of an optimal path length requires a predefined step size, while the ideal step size must account for errors along the selected path. Ensuring reversibility further complicates this tuning problem. In this paper, we present a method for locally adapting the step size in NUTS that is an instance of the Gibbs self-tuning (GIST) framework. Our approach guarantees reversibility with an acceptance probability that depends exclusively on the conditional distribution of the step size. We validate our step-size-adaptive NUTS method on Neal's funnel density and a high-dimensional normal distribution, demonstrating its effectiveness in challenging scenarios.

We study the problem of learning multi-index models in high-dimensions using a two-layer neural network trained with the mean-field Langevin algorithm. Under mild distributional assumptions on the data, we characterize the effective dimension $d_{\mathrm{eff}}$ that controls both sample and computational complexity by utilizing the adaptivity of neural networks to latent low-dimensional structures. When the data exhibit such a structure, $d_{\mathrm{eff}}$ can be significantly smaller than the ambient dimension. We prove that the sample complexity grows almost linearly with $d_{\mathrm{eff}}$, bypassing the limitations of the information and generative exponents that appeared in recent analyses of gradient-based feature learning. On the other hand, the computational complexity may inevitably grow exponentially with $d_{\mathrm{eff}}$ in the worst-case scenario. Motivated by improving computational complexity, we take the first steps towards polynomial time convergence of the mean-field Langevin algorithm by investigating a setting where the weights are constrained to be on a compact manifold with positive Ricci curvature, such as the hypersphere. There, we study assumptions under which polynomial time convergence is achievable, whereas similar assumptions in the Euclidean setting lead to exponential time complexity.

The canonical polyadic (CP) tensor decomposition decomposes a multidimensional data array into a sum of outer products of finite-dimensional vectors. Instead, we can replace some or all of the vectors with continuous functions (infinite-dimensional vectors) from a reproducing kernel Hilbert space (RKHS). We refer to tensors with some infinite-dimensional modes as quasitensors, and the approach of decomposing a tensor with some continuous RKHS modes is referred to as CP-HiFi (hybrid infinite and finite dimensional) tensor decomposition. An advantage of CP-HiFi is that it can enforce smoothness in the infinite dimensional modes. Further, CP-HiFi does not require the observed data to lie on a regular and finite rectangular grid and naturally incorporates misaligned data. We detail the methodology and illustrate it on a synthetic example.

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. As this technique can capture dynamic biomolecular complexes, 3D reconstruction methods are increasingly being developed to resolve this intrinsic structural heterogeneity. However, the absence of standardized benchmarks with ground truth structures and validation metrics limits the advancement of the field. Here, we propose CryoBench, a suite of datasets, metrics, and performance benchmarks for heterogeneous reconstruction in cryo-EM. We propose five datasets representing different sources of heterogeneity and degrees of difficulty. These include conformational heterogeneity generated from simple motions and random configurations of antibody complexes and from tens of thousands of structures sampled from a molecular dynamics simulation. We also design datasets containing compositional heterogeneity from mixtures of ribosome assembly states and 100 common complexes present in cells. We then perform a comprehensive analysis of state-of-the-art heterogeneous reconstruction tools including neural and non-neural methods and their sensitivity to noise, and propose new metrics for quantitative comparison of methods. We hope that this benchmark will be a foundational resource for analyzing existing methods and new algorithmic development in both the cryo-EM and machine learning communities.