论文检索

Applications/Genetics, Cell Biology, etc

Pascal Notin, Aaron Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Han Spinner, Nathan Rollins, Ada Shaw, Rose Orenbuch, Ruben Weitzman 等

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins to address our most pressing challenges in climate, agriculture and healthcare. Despite an increase in machine learning-based protein modeling methods, assessing their effectiveness is problematic due to the use of distinct, often contrived, experimental datasets and variable performance across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym v1.0, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 40 high-performing models from various subfields (eg., mutation effects, inverse folding) into a unified benchmark. We open source the corresponding codebase, datasets, MSAs, structures, predictions and develop a user-friendly website that facilitates comparisons across all settings.

Applications/Climate

Mélisande Teng, Amna Elmustafa, Benjamin Akera, Yoshua Bengio, Hager Radi, Hugo Larochelle, David Rolnick

Biodiversity is declining at an unprecedented rate, impacting ecosystem services necessary to ensure food, water, and human health and well-being. Understanding the distribution of species and their habitats is crucial for conservation policy planning. However, traditional methods in ecology for species distribution models (SDMs) generally focus either on narrow sets of species or narrow geographical areas and there remain significant knowledge gaps about the distribution of species. A major reason for this is the limited availability of data traditionally used, due to the prohibitive amount of effort and expertise required for traditional field monitoring. The wide availability of remote sensing data and the growing adoption of citizen science tools to collect species observations data at low cost offer an opportunity for improving biodiversity monitoring and enabling the modelling of complex ecosystems. We introduce a novel task for mapping bird species to their habitats by predicting species encounter rates from satellite images, and present SatBird, a satellite dataset of locations in the USA with labels derived from presence-absence observation data from the citizen science database eBird, considering summer (breeding) and winter seasons. We also provide a dataset in Kenya representing low-data regimes. We additionally provide environmental data and species range maps for each location. We benchmark a set of baselines on our dataset, including SOTA models for remote sensing tasks. SatBird opens up possibilities for scalably modelling properties of ecosystems worldwide.

Applications/Climate

Andrea Nascetti, Ritu Yadav, Kirill Brodt, Qixun Qu, Hongwei Fan, Yuri Shendryk, Isha Shah, Christine Chung

Above Ground Biomass is an important variable as forests play a crucial role in mitigating climate change as they act as an efficient, natural and cost-effective carbon sink. Traditional field and airborne LiDAR measurements have been proven to provide reliable estimations of forest biomass. Nevertheless, the use of these techniques at a large scale can be challenging and expensive. Satellite data have been widely used as a valuable tool in estimating biomass on a global scale. However, the full potential of dense multi-modal satellite time series data, in combination with modern deep learning approaches, has yet to be fully explored. The aim of the "BioMassters" data challenge and benchmark dataset is to investigate the potential of multi-modal satellite data (Sentinel-1 SAR and Sentinel-2 MSI) to estimate forest biomass at a large scale using the Finnish Forest Centre's open forest and nature airborne LiDAR data as a reference. The performance of the top three baseline models shows the potential of deep learning to produce accurate and higher-resolution biomass maps. Our benchmark dataset is publically available at https://huggingface.co/datasets/nascetti-a/BioMassters (doi:10.57967/hf/1009) and the implementation of the top three winning models are available at https://github.com/drivendataorg/the-biomassters.

Miscellaneous Aspects of Machine Learning/Kernel methods

Mathieu Chalvidal, Thomas Serre, Rufin VanRullen

Research in statistical learning has polarized into two general approaches to perform regression analysis: Transductive methods construct estimates directly based on exemplar data using generic relational principles which might suffer from the curse of dimensionality. Conversely, inductive methods can potentially fit highly complex functions at the cost of compute-intensive solution searches. In this work, we leverage the theory of vector-valued Reproducing Kernel Banach Spaces (RKBS) to propose a hybrid approach: We show that transductive regression systems can be meta-learned with gradient descent to form efficient _in-context_ neural approximators of function defined over both finite and infinite-dimensional spaces (operator regression). Once trained, our _Transducer_ can almost instantaneously capture new functional relationships and produce original image estimates, given a few pairs of input and output examples. We demonstrate the benefit of our meta-learned transductive approach to model physical systems influenced by varying external factors with little data at a fraction of the usual deep learning training costs for partial differential equations and climate modeling applications.

Applications/Climate

Anthony Fuller, Koreen Millard, James Green

A vital and rapidly growing application, remote sensing offers vast yet sparsely labeled, spatially aligned multimodal data; this makes self-supervised learning algorithms invaluable. We present CROMA: a framework that combines contrastive and reconstruction self-supervised objectives to learn rich unimodal and multimodal representations. Our method separately encodes masked-out multispectral optical and synthetic aperture radar samples—aligned in space and time—and performs cross-modal contrastive learning. Another encoder fuses these sensors, producing joint multimodal encodings that are used to predict the masked patches via a lightweight decoder. We show that these objectives are complementary when leveraged on spatially aligned multimodal data. We also introduce X- and 2D-ALiBi, which spatially biases our cross- and self-attention matrices. These strategies improve representations and allow our models to effectively extrapolate to images up to $17.6\times$ larger at test-time. CROMA outperforms the current SoTA multispectral model, evaluated on: four classification benchmarks—finetuning (avg.$\uparrow$ 1.8%), linear (avg.$\uparrow$ 2.4%) and nonlinear (avg.$\uparrow$ 1.4%) probing, $k$NN classification (avg.$\uparrow$ 3.5%), and $K$-means clustering (avg.$\uparrow$ 8.4%); and three segmentation benchmarks (avg.$\uparrow$ 6.4%). CROMA’s rich, optionally multimodal representations can be widely leveraged across remote sensing applications.

Applications/Climate

Yuchen BAI, Jean-Baptiste Durand, Grégoire Vincent, Florence Forbes

Lidar (Light Detection and Ranging) has become an essential part of the remote sensing toolbox used for biosphere monitoring. In particular, Lidar provides the opportunity to map forest leaf area with unprecedented accuracy, while leaf area has remained an important source of uncertainty affecting models of gas exchanges between the vegetation and the atmosphere. Unmanned Aerial Vehicles (UAV) are easy to mobilize and therefore allow frequent revisits to track the response of vegetation to climate change. However, miniature sensors embarked on UAVs usually provide point clouds of limited density, which are further affected by a strong decrease in density from top to bottom of the canopy due to progressively stronger occlusion. In such a context, discriminating leaf points from wood points presents a significant challenge due in particular to strong class imbalance and spatially irregular sampling intensity. Here we introduce a neural network model based on the Pointnet ++ architecture which makes use of point geometry only (excluding any spectral information). To cope with local data sparsity, we propose an innovative sampling scheme which strives to preserve local important geometric information. We also propose a loss function adapted to the severe class imbalance. We show that our model outperforms state-of-the-art alternatives on UAV point clouds. We discuss future possible improvements, particularly regarding much denser point clouds acquired from below the canopy.

Applications/Climate

Zhong Yi Wan, Ricardo Baptista, Anudhyan Boral, Yi-Fan Chen, John Anderson, Fei Sha, Leonardo Zepeda-Núñez

We introduce a two-stage probabilistic framework for statistical downscaling using unpaired data. Statistical downscaling seeks a probabilistic map to transform low-resolution data from a biased coarse-grained numerical scheme to high-resolution data that is consistent with a high-fidelity scheme. Our framework tackles the problem bycomposing two transformations: (i) a debiasing step via an optimal transport map, and (ii) an upsampling step achieved by a probabilistic diffusion model with a posteriori conditional sampling. This approach characterizes a conditional distribution without needing paired data, and faithfully recovers relevant physical statistics from biased samples. We demonstrate the utility of the proposed approach on one- and two-dimensional fluid flow problems, which are representative of the core difficulties present in numerical simulations of weather and climate. Our method produces realistic high-resolution outputs from low-resolution inputs, by upsampling resolutions of $8\times$ and $16\times$. Moreover, our procedure correctly matches the statistics of physical quantities, even when the low-frequency content of the inputs and outputs do not match, a crucial but difficult-to-satisfy assumption needed by current state-of-the-art alternatives. Code for this work is available at: https://github.com/google-research/swirl-dynamics/tree/main/swirl_dynamics/projects/probabilistic_diffusion.

Deep Learning

Oussama Boussif, Ghait Boukachab, Dan Assouline, Stefano Massaroli, Tianle Yuan, Loubna Benabbou, Yoshua Bengio

Solar power harbors immense potential in mitigating climate change by substantially reducing CO$_{2}$ emissions. Nonetheless, the inherent variability of solar irradiance poses a significant challenge for seamlessly integrating solar power into the electrical grid. While the majority of prior research has centered on employing purely time series-based methodologies for solar forecasting, only a limited number of studies have taken into account factors such as cloud cover or the surrounding physical context.In this paper, we put forth a deep learning architecture designed to harness spatio-temporal context using satellite data, to attain highly accurate day-ahead time-series forecasting for any given station, with a particular emphasis on forecasting Global Horizontal Irradiance (GHI). We also suggest a methodology to extract a distribution for each time step prediction, which can serve as a very valuable measure of uncertainty attached to the forecast. When evaluating models, we propose a testing scheme in which we separate particularly difficult examples from easy ones, in order to capture the model performances in crucial situations, which in the case of this study are the days suffering from varying cloudy conditions. Furthermore, we present a new multi-modal dataset gathering satellite imagery over a large zone and time series for solar irradiance and other related physical variables from multiple geographically diverse solar stations. Our approach exhibits robust performance in solar irradiance forecasting, including zero-shot generalization tests at unobserved solar stations, and holds great promise in promoting the effective integration of solar power into the grid.

Oscar Mañas, Alexandre Lacoste, Xavier Giró-i-Nieto, David Vazquez, Pau Rodríguez

Remote sensing and automatic earth monitoring are key to solve global-scale challenges such as disaster prevention, land use monitoring, or tackling climate change. Although there exist vast amounts of remote sensing data, most of it remains unlabeled and thus inaccessible for supervised learning algorithms. Transfer learning approaches can reduce the data requirements of deep learning algorithms. However, most of these methods are pre-trained on ImageNet and their generalization to remote sensing imagery is not guaranteed due to the domain gap. In this work, we propose Seasonal Contrast (SeCo), an effective pipeline to leverage unlabeled data for in-domain pre-training of remote sensing representations. The SeCo pipeline is composed of two parts. First, a principled procedure to gather large-scale, unlabeled and uncurated remote sensing datasets containing images from multiple Earth locations at different timestamps. Second, a self-supervised algorithm that takes advantage of time and position invariance to learn transferable representations for remote sensing applications. We empirically show that models trained with SeCo achieve better performance than their ImageNet pre-trained counterparts and state-of-the-art self-supervised learning methods on multiple downstream tasks. The datasets and models in SeCo will be made public to facilitate transfer learning and enable rapid progress in remote sensing applications.

Roi Ronen, Yoav Y. Schechner, Eshkol Eytan

We derive computed tomography (CT) of a time-varying volumetric scattering object, using a small number of moving cameras. We focus on passive tomography of dynamic clouds, as clouds have a major effect on the Earth's climate. State of the art scattering CT assumes a static object. Existing 4D CT methods rely on a linear image formation model and often on significant priors. In this paper, the angular and temporal sampling rates needed for a proper recovery are discussed. Spatiotemporal CT is achieved using gradient-based optimization, which accounts for the correlation time of the dynamic object content. We demonstrate this in physics-based simulations and on experimental real-world data.

Tamar Loeub, Aviad Levis, Vadim Holodovsky, Yoav Y. Schechner

We introduce a differentiable monotonicity prior, useful to express signals of monotonic tendency. An important natural signal of this tendency is the optical extinction coefficient, as a function of altitude in a cloud. Cloud droplets become larger as vapor condenses on them in an updraft. Reconstruction of the volumetric structure of clouds is important for climate research. Data for such reconstruction is multi-view images taken simultaneously of each cloud. This acquisition mode is expected by upcoming future spaceborne imagers. We achieve three-dimensional volumetric reconstruction through stochastic scattering tomography, which is based on optimization of a cost function. Part of the cost is the monotonicity prior, which helps to improve the reconstruction quality. The stochastic tomography is based on Monte-Carlo radiative transfer. It is formulated and implemented in a coarse-to-fine form, making it scalable to large fields.