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Linear assignment problems hold a pivotal role in combinatorial optimization, offering a broad spectrum of applications within the field of data sciences. They consist of assigning “agents” to “tasks” in a way that leads to a minimum total cost associated with the assignment. The assignment is balanced when the number of agents equals the number of tasks, with a one-to-one correspondence between agents and tasks, and it is and unbalanced otherwise. Additional options and constraints may be imposed, such as allowing agents to perform multiple tasks or allowing tasks to be performed by multiple agents. In this paper, we propose a novel framework that can solve all these assignment problems employing methodologies derived from the field of statistical physics. We describe this formalism in detail and validate all its assertions. A major part of this framework is the definition of a concave effective free energy function that encapsulates the constraints of the assignment problem within a finite temperature context. We demonstrate that this free energy monotonically decreases as a function of a parameter β representing the inverse of temperature. As β increases, the free energy converges to the optimal assignment cost. Furthermore, we demonstrate that when β values are sufficiently large, the exact solution to the assignment problem can be derived by rounding off the elements of the computed assignment matrix to the nearest integer. We describe a computer implementation of our framework and illustrate its application to multi-task assignment problems for which the Hungarian algorithm is not applicable. 

Abstract Recent progress in solving macromolecular structures and assemblies by cryogenic electron microscopy techniques enables sampling of their conformations in different states that are relevant to their biological function. Knowing the transition path between these conformations would provide new avenues for drug discovery. While the experimental study of transition paths is intrinsically difficult, in-silico methods can be used to generate an initial guess for those paths. The Elastic Network Model (ENM), along with a coarse-grained representation (CG) of the structures are among the most popular models to explore such possible paths. Here we propose an update to our software platform MinActionPath that generates non-linear transition paths based on ENM and CG models, using action minimization to solve the equations of motion. The new website enables the study of large structures such as ribosomes or entire virus envelopes. It provides direct visualization of the trajectories along with quantitative analyses of their behaviors at http://dynstr.pasteur.fr/servers/minactionpath/minactionpath2_submission. 

A new algorithm is presented to compute nonrigid, possibly partial comparisons of shapes defined by unstructured triangulations of their surfaces. The algorithm takes as input a pair of surfaces with each surface given by a distinct and unrelated triangulation. Its goal is to define a possibly partial correspondence between the vertices of the two triangulations, with a cost associated with this correspondence that can serve as a measure of the similarity of the two shapes. To find this correspondence, the vertices in each triangulation are characterized by a signature vector of features. We tested both the LD-SIFT signatures, based on the concept of spin images, and the wave kernel signatures obtained by solving the Shrödinger equation on the triangulation. A cost matrix C is constructed such that C(k,l) is the norm of the difference of the signature vectors of vertices k and l. The correspondence between the triangulations is then computed as the transport plan that solves the optimal transport or optimal partial transport problem between their sets of vertices. We use a statistical physics approach to solve these problems. The presentation of the proposed algorithm is complemented with examples that illustrate its effectiveness and manageable computing cost. 

The Gromov-Wasserstein (GW) formalism can be seen as a generalization of the optimal transport (OT) formalism for comparing two distributions associated with different metric spaces. It is a quadratic optimization problem and solving it usually has computational costs that can rise sharply if the problem size exceeds a few hundred points. Recently fast techniques based on entropy regularization have being developed to solve an approximation of the GW problem quickly. There are issues, however, with the numerical convergence of those regularized approximations to the true GW solution. To circumvent those issues, we introduce a novel strategy to solve the discrete GW problem using methods taken from statistical physics. We build a temperature-dependent free energy function that reflects the GW problem’s constraints. To account for possible differences of scales between the two metric spaces, we introduce a scaling factor s in the definition of the energy. From the extremum of the free energy, we derive a mapping between the two probability measures that are being compared, as well as a distance between those measures. This distance is equal to the GW distance when the temperature goes to zero. The optimal scaling factor itself is obtained by minimizing the free energy with respect to s. We illustrate our approach on the problem of comparing shapes defined by unstructured triangulations of their surfaces. We use several synthetic and “real life” datasets. We demonstrate the accuracy and automaticity of our approach in non-rigid registration of shapes. We provide numerical evidence that there is a strong correlation between the GW distances computed from low-resolution, surface-based representations of proteins and the analogous distances computed from atomistic models of the same proteins. 

The 3D Zernike polynomials form an orthonormal basis of the unit ball. The associated 3D Zernike moments have been successfully applied for 3D shape recognition; they are popular in structural biology for comparing protein structures and properties. Many algorithms have been proposed for computing those moments, starting from a voxel-based representation or from a surface based geometric mesh of the shape. As the order of the 3D Zernike moments increases, however, those algorithms suffer from decrease in computational efficiency and more importantly from numerical accuracy. In this paper, new algorithms are proposed to compute the 3D Zernike moments of a homogeneous shape defined by an unstructured triangulation of its surface that remove those numerical inaccuracies. These algorithms rely on the analytical integration of the moments on tetrahedra defined by the surface triangles and a central point and on a set of novel recurrent relationships between the corresponding integrals. The mathematical basis and implementation details of the algorithms are presented and their numerical stability is evaluated. 

We present a new method to sample conditioned trajectories of a system evolving under Langevin dynamics based on Brownian bridges. The trajectories are conditioned to end at a certain point (or in a certain region) in space. The bridge equations can be recast exactly in the form of a non-linear stochastic integro-differential equation. This equation can be very well approximated when the trajectories are closely bundled together in space, i.e., at low temperature, or for transition paths. The approximate equation can be solved iteratively using a fixed point method. We discuss how to choose the initial trajectories and show some examples of the performance of this method on some simple problems. This method allows us to generate conditioned trajectories with a high accuracy. 

Abstract “Paintings fade like flowers”: van Gogh’s prediction on the impact of age on paintings came true for most of his paintings. We have studied the consequences of this aging on the Sunflowers in a vase with a yellow background series, namely its original, F454, currently in London, and two replicates, F457, in Tokyo, and F458, in Amsterdam, which van Gogh painted using the original as a model. The background and flower renditions in those paintings have faded and turned brown, making them less vibrant that van Gogh had most likely intended. We have attempted to restore van Gogh’s intent using a computational approach based on data science. After identifications of regions of interest (ROI) within the three paintings F454, F457, and F458 that capture the flowers, stems of the flowers, and background, respectively, we studied the geometry of the color space (in RGB representation) occupied by those ROIs. By comparing those color spaces with those occupied by similar ROIs in photographs of real sunflowers, we identified shifts in all three color coordinates, R, G, and B, with the positive shift in the blue coordinate being the more salient. We have proposed two algorithms, PCR-1 and PCR-2, for correcting that shift in blue and generate representations of the paintings that aim to restore their original conditions. The reduction of the blue component in the yellow hues has lead to more vibrant and less brownish digital rendition of the three Sunflowers in a vase with a yellow background .