arXiv subjects

Charlotte Bunne

Publications and source records attributed to Charlotte Bunne.

22 records · Page 2Linked to original sources

arXiv2022

Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein

Optimal transport tools (OTT-JAX) is a Python toolbox that can solve optimal transport problems between point clouds and histograms. The toolbox builds on various JAX features, such as automatic and custom reverse mode differentiation, vectorization, just-in-time compilation and accelerators support. The toolbox covers elementary computations, such as the resolution of the regularized OT problem, and more advanced extensions, such as barycenters, Gromov-Wasserstein, low-rank solvers, estimation of convex maps, differentiable generalizations of quantiles and ranks, and approximate OT between Gaussian mixtures. The toolbox code is available at \texttt{https://github.com/ott-jax/ott}

cs.LG↗

arXiv2021

Learning Graph Models for Retrosynthesis Prediction

Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is aligning model design with strategies adopted by chemists. Building on this viewpoint, this paper introduces a graph-based approach that capitalizes on the idea that the graph topology of precursor molecules is largely unaltered during a chemical reaction. The model first predicts the set of graph edits transforming the target into incomplete molecules called synthons. Next, the model learns to expand synthons into complete molecules by attaching relevant leaving groups. This decomposition simplifies the architecture, making its predictions more interpretable, and also amenable to manual correction. Our model achieves a top-1 accuracy of $53.7\%$, outperforming previous template-free and semi-template-based methods.

cs.LG↗

arXiv2019

Learning Generative Models across Incomparable Spaces

Generative Adversarial Networks have shown remarkable success in learning a distribution that faithfully recovers a reference distribution in its entirety. However, in some cases, we may want to only learn some aspects (e.g., cluster or manifold structure), while modifying others (e.g., style, orientation or dimension). In this work, we propose an approach to learn generative models across such incomparable spaces, and demonstrate how to steer the learned distribution towards target properties. A key component of our model is the Gromov-Wasserstein distance, a notion of discrepancy that compares distributions relationally rather than absolutely. While this framework subsumes current generative models in identically reproducing distributions, its inherent flexibility allows application to tasks in manifold learning, relational learning and cross-domain learning.

cs.LG↗

arXiv2018

Studying Invariances of Trained Convolutional Neural Networks

Convolutional Neural Networks (CNNs) define an exceptionally powerful class of models for image classification, but the theoretical background and the understanding of how invariances to certain transformations are learned is limited. In a large scale screening with images modified by different affine and nonaffine transformations of varying magnitude, we analyzed the behavior of the CNN architectures AlexNet and ResNet. If the magnitude of different transformations does not exceed a class- and transformation dependent threshold, both architectures show invariant behavior. In this work we furthermore introduce a new learnable module, the Invariant Transformer Net, which enables us to learn differentiable parameters for a set of affine transformations. This allows us to extract the space of transformations to which the CNN is invariant and its class prediction robust.

cs.CV↗