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Publications
EarthView: A Large Scale Remote Sensing Dataset for Self-Supervision
This paper presents EarthView, a comprehensive dataset specifically designed for self-supervision on remote sensing data, intended to enhanc… (see more)e deep learning applications on Earth monitoring tasks. The dataset spans 15 tera pixels of global remote-sensing data, combining imagery from a diverse range of sources, including NEON, Sentinel, and a novel release of 1m spatial resolution data from Satellogic. Our dataset provides a wide spectrum of image data with varying resolutions, harnessed from different sensors and organized coherently into an accessible HuggingFace dataset in parquet format. This data spans five years, from 2017 to 2022. Accompanying the dataset, we introduce EarthMAE, a tailored Masked Autoencoder, developed to tackle the distinct challenges of remote sensing data. Trained in a self-supervised fashion, EarthMAE effectively processes different data modalities such as hyperspectral, multispectral, topographical data, segmentation maps, and temporal structure. This model helps us show that pre-training on Satellogic data improves performance on downstream tasks. While there is still a gap to fill in MAE for heterogeneous data, we regard this innovative combination of an expansive, diverse dataset and a versatile model adapted for self-supervised learning as a stride forward in deep learning for Earth monitoring.
Biotic interactions play a fundamental role in shaping multitrophic species communities, yet incorporating these interactions into species d… (see more)istribution models (SDMs) remains challenging. With the growing availability of species interaction networks, it is now feasible to integrate these interactions into SDMs for more comprehensive predictions. Here, we propose a novel framework that combines trophic interaction networks with Bayesian structural equation models, enabling each species to be modeled based on its interactions with predators or prey alongside environmental factors. This framework addresses issues of multicollinearity and error propagation, making it possible to predict species distributions in unobserved locations or under future environmental conditions, even when prey or predator distributions are unknown. We tested and validated our framework on realistic simulated communities spanning different theoretical models and ecological setups. scenarios. Our approach significantly improved the estimation of both potential and realized niches compared to single SDMs, with mean performance gains of 8% and 6%, respectively. These improvements were especially notable for species strongly regulated by biotic factors, thereby enhancing model predictive accuracy. Our framework supports integration with various SDM extensions, such as occupancy and integrated models, offering flexibility and adaptability for future developments. While not a universal solution that consistently outperforms single SDMs, our approach provides a valuable new tool for modeling multitrophic community distributions when biotic interactions are known or assumed.
Generative modeling of symmetric densities has a range of applications in AI for science, from drug discovery to physics simulations. The ex… (see more)isting generative modeling paradigm for invariant densities combines an invariant prior with an equivariant generative process. However, we observe that this technique is not necessary and has several drawbacks resulting from the limitations of equivariant networks. Instead, we propose to model a learned slice of the density so that only one representative element per orbit is learned. To accomplish this, we learn a group-equivariant canonicalization network that maps training samples to a canonical pose and train a non-equivariant generative model over these canonicalized samples. We implement this idea in the context of diffusion models. Our preliminary experimental results on molecular modeling are promising, demonstrating improved sample quality and faster inference time.
Classical psychedelics induce complex visual hallucinations in humans, generating percepts that are co-herent at a low level, but which have… (see more) surreal, dream-like qualities at a high level. While there are many hypotheses as to how classical psychedelics could induce these effects, there are no concrete mechanistic models that capture the variety of observed effects in humans, while remaining consistent with the known pharmacological effects of classical psychedelics on neural circuits. In this work, we propose the “oneirogen hypothesis”, which posits that the perceptual effects of classical psychedelics are a result of their pharmacological actions inducing neural activity states that truly are more similar to dream-like states. We simulate classical psychedelics’ effects via manipulating neural network models trained on perceptual tasks with the Wake-Sleep algorithm. This established machine learning algorithm leverages two activity phases, a perceptual phase (wake) where sensory inputs are encoded, and a generative phase (dream) where the network internally generates activity consistent with stimulus-evoked responses. We simulate the action of psychedelics by partially shifting the model to the ‘Sleep’ state, which entails a greater influence of top-down connections, in line with the impact of psychedelics on apical dendrites. The effects resulting from this manipulation capture a number of experimentally observed phenomena including the emergence of hallucinations, increases in stimulus-conditioned variability, and large increases in synaptic plasticity. We further provide a number of testable predictions which could be used to validate or invalidate our oneirogen hypothesis.
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (see more)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (see more)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (see more)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (see more)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (see more)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (see more)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
