Add to Chrome
Add to Firefox
Add to EdgePytorch-Wildlife: A Collaborative Deep Learning Framework for Conservation
May 21, 2024
The alarming decline in global biodiversity, driven by various factors, underscores the urgent need for large-scale wildlife monitoring. In response, scientists have turned to automated deep learning methods for data processing in wildlife monitoring. However, applying these advanced methods in real-world scenarios is challenging due to their complexity and the need for specialized knowledge, primarily because of technical challenges and interdisciplinary barriers. To address these challenges, we introduce Pytorch-Wildlife, an open-source deep learning platform built on PyTorch. It is designed for creating, modifying, and sharing powerful AI models. This platform emphasizes usability and accessibility, making it accessible to individuals with limited or no technical background. It also offers a modular codebase to simplify feature expansion and further development. Pytorch-Wildlife offers an intuitive, user-friendly interface, accessible through local installation or Hugging Face, for animal detection and classification in images and videos. As two real-world applications, Pytorch-Wildlife has been utilized to train animal classification models for species recognition in the Amazon Rainforest and for invasive opossum recognition in the Galapagos Islands. The Opossum model achieves 98% accuracy, and the Amazon model has 92% recognition accuracy for 36 animals in 90% of the data. As Pytorch-Wildlife evolves, we aim to integrate more conservation tasks, addressing various environmental challenges. Pytorch-Wildlife is available at https://github.com/microsoft/CameraTraps.
Analyzing Decades-Long Environmental Changes in Namibia Using Archival Aerial Photography and Deep Learning
Apr 12, 2024This study explores object detection in historical aerial photographs of Namibia to identify long-term environmental changes. Specifically, we aim to identify key objects -- \textit{Waterholes}, \textit{Omuti homesteads}, and \textit{Big trees} -- around Oshikango in Namibia using sub-meter gray-scale aerial imagery from 1943 and 1972. In this work, we propose a workflow for analyzing historical aerial imagery using a deep semantic segmentation model on sparse hand-labels. To this end, we employ a number of strategies including class-weighting, pseudo-labeling and empirical p-value-based filtering to balance skewed and sparse representations of objects in the ground truth data. Results demonstrate the benefits of these different training strategies resulting in an average $F_1=0.661$ and $F_1=0.755$ over the three objects of interest for the 1943 and 1972 imagery, respectively. We also identified that the average size of Waterhole and Big trees increased while the average size of Omutis decreased between 1943 and 1972 reflecting some of the local effects of the massive post-Second World War economic, agricultural, demographic, and environmental changes. This work also highlights the untapped potential of historical aerial photographs in understanding long-term environmental changes beyond Namibia (and Africa). With the lack of adequate satellite technology in the past, archival aerial photography offers a great alternative to uncover decades-long environmental changes.
A slice classification neural network for automated classification of axial PET/CT slices from a multi-centric lymphoma dataset
Mar 11, 2024Automated slice classification is clinically relevant since it can be incorporated into medical image segmentation workflows as a preprocessing step that would flag slices with a higher probability of containing tumors, thereby directing physicians attention to the important slices. In this work, we train a ResNet-18 network to classify axial slices of lymphoma PET/CT images (collected from two institutions) depending on whether the slice intercepted a tumor (positive slice) in the 3D image or if the slice did not (negative slice). Various instances of the network were trained on 2D axial datasets created in different ways: (i) slice-level split and (ii) patient-level split; inputs of different types were used: (i) only PET slices and (ii) concatenated PET and CT slices; and different training strategies were employed: (i) center-aware (CAW) and (ii) center-agnostic (CAG). Model performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC), and various binary classification metrics. We observe and describe a performance overestimation in the case of slice-level split as compared to the patient-level split training. The model trained using patient-level split data with the network input containing only PET slices in the CAG training regime was the best performing/generalizing model on a majority of metrics. Our models were additionally more closely compared using the sensitivity metric on the positive slices from their respective test sets.
* 10 pages, 6 figures, 2 tables
Bootstrapping Rare Object Detection in High-Resolution Satellite Imagery
Mar 05, 2024
Rare object detection is a fundamental task in applied geospatial machine learning, however is often challenging due to large amounts of high-resolution satellite or aerial imagery and few or no labeled positive samples to start with. This paper addresses the problem of bootstrapping such a rare object detection task assuming there is no labeled data and no spatial prior over the area of interest. We propose novel offline and online cluster-based approaches for sampling patches that are significantly more efficient, in terms of exposing positive samples to a human annotator, than random sampling. We apply our methods for identifying bomas, or small enclosures for herd animals, in the Serengeti Mara region of Kenya and Tanzania. We demonstrate a significant enhancement in detection efficiency, achieving a positive sampling rate increase from 2% (random) to 30%. This advancement enables effective machine learning mapping even with minimal labeling budgets, exemplified by an F1 score on the boma detection task of 0.51 with a budget of 300 total patches.
Weak Labeling for Cropland Mapping in Africa
Jan 13, 2024Cropland mapping can play a vital role in addressing environmental, agricultural, and food security challenges. However, in the context of Africa, practical applications are often hindered by the limited availability of high-resolution cropland maps. Such maps typically require extensive human labeling, thereby creating a scalability bottleneck. To address this, we propose an approach that utilizes unsupervised object clustering to refine existing weak labels, such as those obtained from global cropland maps. The refined labels, in conjunction with sparse human annotations, serve as training data for a semantic segmentation network designed to identify cropland areas. We conduct experiments to demonstrate the benefits of the improved weak labels generated by our method. In a scenario where we train our model with only 33 human-annotated labels, the F_1 score for the cropland category increases from 0.53 to 0.84 when we add the mined negative labels.
Seeing the roads through the trees: A benchmark for modeling spatial dependencies with aerial imagery
Jan 12, 2024Fully understanding a complex high-resolution satellite or aerial imagery scene often requires spatial reasoning over a broad relevant context. The human object recognition system is able to understand object in a scene over a long-range relevant context. For example, if a human observes an aerial scene that shows sections of road broken up by tree canopy, then they will be unlikely to conclude that the road has actually been broken up into disjoint pieces by trees and instead think that the canopy of nearby trees is occluding the road. However, there is limited research being conducted to understand long-range context understanding of modern machine learning models. In this work we propose a road segmentation benchmark dataset, Chesapeake Roads Spatial Context (RSC), for evaluating the spatial long-range context understanding of geospatial machine learning models and show how commonly used semantic segmentation models can fail at this task. For example, we show that a U-Net trained to segment roads from background in aerial imagery achieves an 84% recall on unoccluded roads, but just 63.5% recall on roads covered by tree canopy despite being trained to model both the same way. We further analyze how the performance of models changes as the relevant context for a decision (unoccluded roads in our case) varies in distance. We release the code to reproduce our experiments and dataset of imagery and masks to encourage future research in this direction -- https://github.com/isaaccorley/ChesapeakeRSC.
Comprehensive Evaluation and Insights into the Use of Deep Neural Networks to Detect and Quantify Lymphoma Lesions in PET/CT Images
Nov 16, 2023
This study performs comprehensive evaluation of four neural network architectures (UNet, SegResNet, DynUNet, and SwinUNETR) for lymphoma lesion segmentation from PET/CT images. These networks were trained, validated, and tested on a diverse, multi-institutional dataset of 611 cases. Internal testing (88 cases; total metabolic tumor volume (TMTV) range [0.52, 2300] ml) showed SegResNet as the top performer with a median Dice similarity coefficient (DSC) of 0.76 and median false positive volume (FPV) of 4.55 ml; all networks had a median false negative volume (FNV) of 0 ml. On the unseen external test set (145 cases with TMTV range: [0.10, 2480] ml), SegResNet achieved the best median DSC of 0.68 and FPV of 21.46 ml, while UNet had the best FNV of 0.41 ml. We assessed reproducibility of six lesion measures, calculated their prediction errors, and examined DSC performance in relation to these lesion measures, offering insights into segmentation accuracy and clinical relevance. Additionally, we introduced three lesion detection criteria, addressing the clinical need for identifying lesions, counting them, and segmenting based on metabolic characteristics. We also performed expert intra-observer variability analysis revealing the challenges in segmenting ``easy'' vs. ``hard'' cases, to assist in the development of more resilient segmentation algorithms. Finally, we performed inter-observer agreement assessment underscoring the importance of a standardized ground truth segmentation protocol involving multiple expert annotators. Code is available at: https://github.com/microsoft/lymphoma-segmentation-dnn
Multimodal Foundation Models for Zero-shot Animal Species Recognition in Camera Trap Images
Nov 02, 2023Due to deteriorating environmental conditions and increasing human activity, conservation efforts directed towards wildlife is crucial. Motion-activated camera traps constitute an efficient tool for tracking and monitoring wildlife populations across the globe. Supervised learning techniques have been successfully deployed to analyze such imagery, however training such techniques requires annotations from experts. Reducing the reliance on costly labelled data therefore has immense potential in developing large-scale wildlife tracking solutions with markedly less human labor. In this work we propose WildMatch, a novel zero-shot species classification framework that leverages multimodal foundation models. In particular, we instruction tune vision-language models to generate detailed visual descriptions of camera trap images using similar terminology to experts. Then, we match the generated caption to an external knowledge base of descriptions in order to determine the species in a zero-shot manner. We investigate techniques to build instruction tuning datasets for detailed animal description generation and propose a novel knowledge augmentation technique to enhance caption quality. We demonstrate the performance of WildMatch on a new camera trap dataset collected in the Magdalena Medio region of Colombia.
Assessment of Differentially Private Synthetic Data for Utility and Fairness in End-to-End Machine Learning Pipelines for Tabular Data
Oct 30, 2023Differentially private (DP) synthetic data sets are a solution for sharing data while preserving the privacy of individual data providers. Understanding the effects of utilizing DP synthetic data in end-to-end machine learning pipelines impacts areas such as health care and humanitarian action, where data is scarce and regulated by restrictive privacy laws. In this work, we investigate the extent to which synthetic data can replace real, tabular data in machine learning pipelines and identify the most effective synthetic data generation techniques for training and evaluating machine learning models. We investigate the impacts of differentially private synthetic data on downstream classification tasks from the point of view of utility as well as fairness. Our analysis is comprehensive and includes representatives of the two main types of synthetic data generation algorithms: marginal-based and GAN-based. To the best of our knowledge, our work is the first that: (i) proposes a training and evaluation framework that does not assume that real data is available for testing the utility and fairness of machine learning models trained on synthetic data; (ii) presents the most extensive analysis of synthetic data set generation algorithms in terms of utility and fairness when used for training machine learning models; and (iii) encompasses several different definitions of fairness. Our findings demonstrate that marginal-based synthetic data generators surpass GAN-based ones regarding model training utility for tabular data. Indeed, we show that models trained using data generated by marginal-based algorithms can exhibit similar utility to models trained using real data. Our analysis also reveals that the marginal-based synthetic data generator MWEM PGM can train models that simultaneously achieve utility and fairness characteristics close to those obtained by models trained with real data.
Poverty rate prediction using multi-modal survey and earth observation data
Jul 21, 2023
This work presents an approach for combining household demographic and living standards survey questions with features derived from satellite imagery to predict the poverty rate of a region. Our approach utilizes visual features obtained from a single-step featurization method applied to freely available 10m/px Sentinel-2 surface reflectance satellite imagery. These visual features are combined with ten survey questions in a proxy means test (PMT) to estimate whether a household is below the poverty line. We show that the inclusion of visual features reduces the mean error in poverty rate estimates from 4.09% to 3.88% over a nationally representative out-of-sample test set. In addition to including satellite imagery features in proxy means tests, we propose an approach for selecting a subset of survey questions that are complementary to the visual features extracted from satellite imagery. Specifically, we design a survey variable selection approach guided by the full survey and image features and use the approach to determine the most relevant set of small survey questions to include in a PMT. We validate the choice of small survey questions in a downstream task of predicting the poverty rate using the small set of questions. This approach results in the best performance -- errors in poverty rate decrease from 4.09% to 3.71%. We show that extracted visual features encode geographic and urbanization differences between regions.