ClimODE: Climate and Weather Forecasting with Physics-informed Neural ODEs

Climate and weather prediction traditionally relies on complex numerical simulations of atmospheric physics. Deep learning approaches, such as transformers, have recently challenged the simulation paradigm with complex network forecasts. However, they often act as data-driven black-box models that neglect the underlying physics and lack uncertainty quantification. We address these limitations with ClimODE, a spatiotemporal continuous-time process that implements a key principle of advection from statistical mechanics, namely, weather changes due to a spatial movement of quantities over time. ClimODE models precise weather evolution with value-conserving dynamics, learning global weather transport as a neural flow, which also enables estimating the uncertainty in predictions. Our approach outperforms existing data-driven methods in global and regional forecasting with an order of magnitude smaller parameterization, establishing a new state of the art.

Field-based Molecule Generation

This work introduces FMG, a field-based model for drug-like molecule generation. We show how the flexibility of this method provides crucial advantages over the prevalent, point-cloud based methods, and achieves competitive molecular stability generation. We tackle optical isomerism (enantiomers), a previously omitted molecular property that is crucial for drug safety and effectiveness, and thus account for all molecular geometry aspects. We demonstrate how previous methods are invariant to a group of transformations that includes enantiomer pairs, leading them invariant to the molecular R and S configurations, while our field-based generative model captures this property.

Understanding deep neural networks through the lens of their non-linearity

The remarkable success of deep neural networks (DNN) is often attributed to their high expressive power and their ability to approximate functions of arbitrary complexity. Indeed, DNNs are highly non-linear models, and activation functions introduced into them are largely responsible for this. While many works studied the expressive power of DNNs through the lens of their approximation capabilities, quantifying the non-linearity of DNNs or of individual activation functions remains an open problem. In this paper, we propose the first theoretically sound solution to track non-linearity propagation in deep neural networks with a specific focus on computer vision applications. Our proposed affinity score allows us to gain insights into the inner workings of a wide range of different architectures and learning paradigms. We provide extensive experimental results that highlight the practical utility of the proposed affinity score and its potential for long-reaching applications.

Learning Space-Time Continuous Neural PDEs from Partially Observed States

We introduce a novel grid-independent model for learning partial differential equations (PDEs) from noisy and partial observations on irregular spatiotemporal grids. We propose a space-time continuous latent neural PDE model with an efficient probabilistic framework and a novel encoder design for improved data efficiency and grid independence. The latent state dynamics are governed by a PDE model that combines the collocation method and the method of lines. We employ amortized variational inference for approximate posterior estimation and utilize a multiple shooting technique for enhanced training speed and stability. Our model demonstrates state-of-the-art performance on complex synthetic and real-world datasets, overcoming limitations of previous approaches and effectively handling partially-observed data. The proposed model outperforms recent methods, showing its potential to advance data-driven PDE modeling and enabling robust, grid-independent modeling of complex partially-observed dynamic processes.

Input gradient diversity for neural network ensembles

Deep Ensembles (DEs) demonstrate improved accuracy, calibration and robustness to perturbations over single neural networks partly due to their functional diversity. Particle-based variational inference (ParVI) methods enhance diversity by formalizing a repulsion term based on a network similarity kernel. However, weight-space repulsion is inefficient due to over-parameterization, while direct function-space repulsion has been found to produce little improvement over DEs. To sidestep these difficulties, we propose First-order Repulsive Deep Ensemble (FoRDE), an ensemble learning method based on ParVI, which performs repulsion in the space of first-order input gradients. As input gradients uniquely characterize a function up to translation and are much smaller in dimension than the weights, this method guarantees that ensemble members are functionally different. Intuitively, diversifying the input gradients encourages each network to learn different features, which is expected to improve the robustness of an ensemble. Experiments on image classification datasets show that FoRDE significantly outperforms the gold-standard DEs and other ensemble methods in accuracy and calibration under covariate shift due to input perturbations.

AbODE: Ab Initio Antibody Design using Conjoined ODEs

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Beyond invariant representation learning: linearly alignable latent spaces for efficient closed-form domain adaptation

Optimal transport (OT) is a powerful geometric tool used to compare and align probability measures following the least effort principle. Among many successful applications of OT in machine learning (ML), domain adaptation (DA) -- a field of study where the goal is to transfer a classifier from one labelled domain to another similar, yet different unlabelled or scarcely labelled domain -- has been historically among the most investigated ones. This success is due to the ability of OT to provide both a meaningful discrepancy measure to assess the similarity of two domains' distributions and a mapping that can project source domain data onto the target one. In this paper, we propose a principally new OT-based approach applied to DA that uses the closed-form solution of the OT problem given by an affine mapping and learns an embedding space for which this solution is optimal and computationally less complex. We show that our approach works in both homogeneous and heterogeneous DA settings and outperforms or is on par with other famous baselines based on both traditional OT and OT in incomparable spaces. Furthermore, we show that our proposed method vastly reduces computational complexity.

Uncertainty-Aware Natural Language Inference with Stochastic Weight Averaging

This paper introduces Bayesian uncertainty modeling using Stochastic Weight Averaging-Gaussian (SWAG) in Natural Language Understanding (NLU) tasks. We apply the approach to standard tasks in natural language inference (NLI) and demonstrate the effectiveness of the method in terms of prediction accuracy and correlation with human annotation disagreements. We argue that the uncertainty representations in SWAG better reflect subjective interpretation and the natural variation that is also present in human language understanding. The results reveal the importance of uncertainty modeling, an often neglected aspect of neural language modeling, in NLU tasks.

Learning Energy Conserving Dynamics Efficiently with Hamiltonian Gaussian Processes

Hamiltonian mechanics is one of the cornerstones of natural sciences. Recently there has been significant interest in learning Hamiltonian systems in a free-form way directly from trajectory data. Previous methods have tackled the problem of learning from many short, low-noise trajectories, but learning from a small number of long, noisy trajectories, whilst accounting for model uncertainty has not been addressed. In this work, we present a Gaussian process model for Hamiltonian systems with efficient decoupled parameterisation, and introduce an energy-conserving shooting method that allows robust inference from both short and long trajectories. We demonstrate the method's success in learning Hamiltonian systems in various data settings.

Continuous-Time Functional Diffusion Processes

We introduce functional diffusion processes (FDPs), which generalize traditional score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of the Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on synthetic and real data illustrate the advantages of FDPs in simplifying the design requirements of diffusion models.