As scientific instruments and the literature generate ever larger volumes of data, machine learning (ML) has become essential for organizing, analyzing and interpreting complex information. This Perspective examines how ML accelerates discovery across disciplines, with examples such as brain mapping and exoplanet detection. It also considers situations with different levels of prior knowledge about the underlying phenomenon, outlining strategies to address limitations and exploit ML effectively. Although growing reliance on ML raises challenges for research practice and validation, it is reshaping scientific methods and expanding what can be studied. We also highlight foundation models as a promising route to faster, broader scientific discovery.

Idempotent Generative Networks (IGNs) are deep generative models that also function as local data manifold projectors, mapping arbitrary inputs back onto the manifold. They are trained to act as identity operators on the data and as idempotent operators off the data manifold. However, IGNs suffer from mode collapse, mode dropping, and training instability due to their objectives, which contain adversarial components and can cause the model to cover the data manifold only partially – an issue shared with generative adversarial networks. We introduce Non-Adversarial Idempotent Generative Networks (NAIGNs) to address these issues. Our loss function combines reconstruction with the non-adversarial generative objective of Implicit Maximum Likelihood Estimation (IMLE). This improves on IGN’s ability to restore corrupted data and generate new samples that closely match the data distribution. We moreover demonstrate that NAIGNs implicitly learn the distance field to the data manifold, as well as an energy-based model.

Urbanization advances at unprecedented rates, leading to negative environmental and societal impacts. Remote sensing can help mitigate these effects by supporting sustainable development strategies with accurate information on urban growth. Deep learning-based methods have achieved promising urban change detection results from optical satellite image pairs using convolutional neural networks (ConvNets), transformers, and a multi-task learning setup. However, bi-temporal methods are limited for continuous urban change detection, i.e., the detection of changes in consecutive image pairs of satellite image time series (SITS), as they fail to fully exploit multi-temporal data (> 2 images). Existing multi-temporal change detection methods, on the other hand, collapse the temporal dimension, restricting their ability to capture continuous urban changes. Additionally, multi-task learning methods lack integration approaches that combine change and segmentation outputs. To address these challenges, we propose a continuous urban change detection framework incorporating two key modules. The temporal feature refinement (TFR) module employs self-attention to improve ConvNet-based multi-temporal building representations. The temporal dimension is preserved in the TFR module, enabling the detection of continuous changes. The multi-task integration (MTI) module utilizes Markov networks to find an optimal building map time series based on segmentation and dense change outputs. The proposed framework effectively identifies urban changes based on high-resolution SITS acquired by the PlanetScope constellation (F1 score 0.551), Gaofen-2 (F1 score 0.440), and WorldView-2 (F1 score 0.543). Moreover, our experiments on three challenging datasets demonstrate the effectiveness of the proposed framework compared to bi-temporal and multi-temporal urban change detection and segmentation methods.

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules’ constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent advances in generative modeling, such as diffusion models and flow matching, have made great progress on these tasks by modeling molecular conformations as a distribution. In this work, we focus on flow matching and adopt an energybased perspective to improve training and inference of structure generation models. Our view results in a mapping function, represented by a deep network, that is directly learned to iteratively map random configurations, i.e. samples from the source distribution, to target structures, i.e. points in the data manifold. This yields a conceptually simple and empirically effective flow matching setup that is theoretically justified and has interesting connections to fundamental properties such as idempotency and stability, as well as the empirically useful techniques such as structure refinement in AlphaFold. Experiments on protein docking as well as protein backbone generation consistently demonstrate the method’s effectiveness, where it outperforms recent baselines of task-associated flow matching and diffusion models, using a similar computational budget.

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent advances in generative modeling, such as diffusion models and flow matching, have made great progress on these tasks by modeling molecular conformations as a distribution. In this work, we focus on flow matching and adopt an energy-based perspective to improve training and inference of structure generation models. Our view results in a mapping function, represented by a deep network, that is directly learned to iteratively map random configurations, i.e. samples from the source distribution, to target structures, i.e. points in the data manifold. This yields a conceptually simple and empirically effective flow matching setup that is theoretically justified and has interesting connections to fundamental properties such as idempotency and stability, as well as the empirically useful techniques such as structure refinement in AlphaFold. Experiments on protein docking as well as protein backbone generation consistently demonstrate the method's effectiveness, where it outperforms recent baselines of task-associated flow matching and diffusion models, using a similar computational budget.

Fully-convolutional neural networks (FCN) were proven to be effective for predicting the instantaneous state of a fully-developed turbulent flow at different wall-normal locations using quantities measured at the wall. In Guastoni et al. (J Fluid Mech 928:A27, 2021. https://doi.org/10.1017/jfm.2021.812), we focused on wall-shear-stress distributions as input, which are difficult to measure in experiments. In order to overcome this limitation, we introduce a model that can take as input the heat-flux field at the wall from a passive scalar. Four different Prandtl numbers Pr=ν/α=(1,2,4,6) are considered (where ν is the kinematic viscosity and α is the thermal diffusivity of the scalar quantity). A turbulent boundary layer is simulated since accurate heat-flux measurements can be performed in experimental settings: first we train the network on aptly-modified DNS data and then we fine-tune it on the experimental data. Finally, we test our network on experimental data sampled in a water tunnel. These predictions represent the first application of transfer learning on experimental data of neural networks trained on simulations. This paves the way for the implementation of a non-intrusive sensing approach for the flow in practical applications.

Inverse problems have many applications in science and engineering. In Computer vision, several image restoration tasks such as inpainting, deblurring, and super-resolution can be formally modeled as inverse problems. Recently, methods have been developed for solving inverse problems that only leverage a pre-trained unconditional diffusion model and do not require additional task-specific training. In such methods, however, the inherent intractability of determining the conditional score function during the reverse diffusion process poses a real challenge, leaving the methods to settle with an approximation instead, which affects their performance in practice. Here, we propose a MAP estimation framework to model the reverse conditional generation process of a continuous time diffusion model as an optimization process of the underlying MAP objective, whose gradient term is tractable. In theory, the proposed framework can be applied to solve general inverse problems using gradient-based optimization methods. However, given the highly non-convex nature of the loss objective, finding a perfect gradient-based optimization algorithm can be quite challenging, nevertheless, our framework offers several potential research directions. We use our proposed formulation to develop empirically effective algorithms for image restoration. We validate our proposed algorithms with extensive experiments over multiple datasets across several restoration tasks.

Climate change is leading to an increase in extreme weather events, causing significant environmental damage and loss of life. Early detection of such events is essential for improving disaster response. In this work, we propose SITS-Extreme, a novel framework that leverages satellite image time series to detect extreme events by incorporating multiple pre-disaster observations. This approach effectively filters out irrelevant changes while isolating disaster-relevant signals, enabling more accurate detection. Extensive experiments on both real-world and synthetic datasets validate the effectiveness of SITS-Extreme, demonstrating substantial improvements over widely used strong bi-temporal baselines. Additionally, we examine the impact of incorporating more timesteps, analyze the contribution of key components in our framework, and evaluate its performance across different disaster types, offering valuable insights into its scalability and applicability for large-scale disaster monitoring.

The field of medical image segmentation is hindered by the scarcity of large, publicly available annotated datasets. Not all datasets are made public for privacy reasons, and creating annotations for a large dataset is time-consuming and expensive, as it requires specialized expertise to accurately identify regions of interest (ROIs) within the images. To address these challenges, we evaluate the performance of the Segment Anything Model (SAM) as an annotation tool for medical data by using it to produce so-called "pseudo labels" on the Medical Segmentation Decathlon (MSD) computed tomography (CT) tasks. The pseudo labels are then used in place of ground truth labels to train a UNet model in a weakly-supervised manner. We experiment with different prompt types on SAM and find that the bounding box prompt is a simple yet effective method for generating pseudo labels. This method allows us to develop a weakly-supervised model that performs comparably to a fully supervised model.

Understanding the behavior of deep networks is crucial to increase our confidence in their results. Despite an extensive body of work for explaining their predictions, researchers have faced reliability issues, which can be attributed to insufficient formalism. In our research, we adopt novel probabilistic and spectral perspectives to formally analyze explanation methods. Our study reveals a pervasive spectral bias stemming from the use of gradient, and sheds light on some common design choices that have been discovered experimentally, in particular, the use of squared gradient and input perturbation. We further characterize how the choice of perturbation hyperparameters in explanation methods, such as SmoothGrad, can lead to inconsistent explanations and introduce two remedies based on our proposed formalism: (i) a mechanism to determine a standard perturbation scale, and (ii) an aggregation method which we call SpectralLens. Finally, we substantiate our theoretical results through quantitative evaluations.