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Aug 24

A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning

In this work we introduce Sen4AgriNet, a Sentinel-2 based time series multi country benchmark dataset, tailored for agricultural monitoring applications with Machine and Deep Learning. Sen4AgriNet dataset is annotated from farmer declarations collected via the Land Parcel Identification System (LPIS) for harmonizing country wide labels. These declarations have only recently been made available as open data, allowing for the first time the labeling of satellite imagery from ground truth data. We proceed to propose and standardise a new crop type taxonomy across Europe that address Common Agriculture Policy (CAP) needs, based on the Food and Agriculture Organization (FAO) Indicative Crop Classification scheme. Sen4AgriNet is the only multi-country, multi-year dataset that includes all spectral information. It is constructed to cover the period 2016-2020 for Catalonia and France, while it can be extended to include additional countries. Currently, it contains 42.5 million parcels, which makes it significantly larger than other available archives. We extract two sub-datasets to highlight its value for diverse Deep Learning applications; the Object Aggregated Dataset (OAD) and the Patches Assembled Dataset (PAD). OAD capitalizes zonal statistics of each parcel, thus creating a powerful label-to-features instance for classification algorithms. On the other hand, PAD structure generalizes the classification problem to parcel extraction and semantic segmentation and labeling. The PAD and OAD are examined under three different scenarios to showcase and model the effects of spatial and temporal variability across different years and different countries.

  • 4 authors
·
Apr 2, 2022

HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

  • 13 authors
·
Jun 27, 2023 2

AsyncPatch Diffusion: spatially-flexible image generation

Standard diffusion models corrupt an entire sample with a single shared noise level, forcing all spatial regions to follow the same denoising trajectory. We introduce AsyncPatch Diffusion, a joint-diffusion framework that assigns distinct noise levels to different input dimensions, such as image pixels, or latent tokens. We show how this asynchronous corruption defines a valid generative process while supporting a richer family of spatially heterogeneous denoising trajectories, and prove the first valid ELBO for this process. We show that a single pretrained model can perform spatially adaptive generation, where different regions are denoised on different schedules. A key challenge is training: naive independent noise-level sampling overemphasizes highly heterogeneous configurations and underrepresents homogeneous noise levels, that are crucial during sampling. We address this with a controlled noise-level sampler that regulates both the average corruption level and its spatial variability. AsyncPatch achieves generation quality comparable to conventional diffusion on ImageNet 256 and LSUN, while being natively suited for inpainting without task-specific fine-tuning. We further introduce input guidance, which uses clean or partially corrupted regions to guide the generation of unknown regions, improving local consistency and texture matching. Finally, we demonstrate adaptive generation strategies including uncertainty-guided acceleration and autoregressive sampling.

  • 6 authors
·
Jun 4