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Informed Deep Abstaining Classifier: Investigating noise-robust training for diagnostic decision support systems
Authors:
Helen Schneider,
Sebastian Nowak,
Aditya Parikh,
Yannik C. Layer,
Maike Theis,
Wolfgang Block,
Alois M. Sprinkart,
Ulrike Attenberger,
Rafet Sifa
Abstract:
Image-based diagnostic decision support systems (DDSS) utilizing deep learning have the potential to optimize clinical workflows. However, developing DDSS requires extensive datasets with expert annotations and is therefore costly. Leveraging report contents from radiological data bases with Natural Language Processing to annotate the corresponding image data promises to replace labor-intensive ma…
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Image-based diagnostic decision support systems (DDSS) utilizing deep learning have the potential to optimize clinical workflows. However, developing DDSS requires extensive datasets with expert annotations and is therefore costly. Leveraging report contents from radiological data bases with Natural Language Processing to annotate the corresponding image data promises to replace labor-intensive manual annotation. As mining "real world" databases can introduce label noise, noise-robust training losses are of great interest. However, current noise-robust losses do not consider noise estimations that can for example be derived based on the performance of the automatic label generator used. In this study, we expand the noise-robust Deep Abstaining Classifier (DAC) loss to an Informed Deep Abstaining Classifier (IDAC) loss by incorporating noise level estimations during training. Our findings demonstrate that IDAC enhances the noise robustness compared to DAC and several state-of-the-art loss functions. The results are obtained on various simulated noise levels using a public chest X-ray data set. These findings are reproduced on an in-house noisy data set, where labels were extracted from the clinical systems of the University Hospital Bonn by a text-based transformer. The IDAC can therefore be a valuable tool for researchers, companies or clinics aiming to develop accurate and reliable DDSS from routine clinical data.
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Submitted 28 October, 2024;
originally announced October 2024.
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Automated Pruning of Polyculture Plants
Authors:
Mark Presten,
Rishi Parikh,
Shrey Aeron,
Sandeep Mukherjee,
Simeon Adebola,
Satvik Sharma,
Mark Theis,
Walter Teitelbaum,
Ken Goldberg
Abstract:
Polyculture farming has environmental advantages but requires substantially more pruning than monoculture farming. We present novel hardware and algorithms for automated pruning. Using an overhead camera to collect data from a physical scale garden testbed, the autonomous system utilizes a learned Plant Phenotyping convolutional neural network and a Bounding Disk Tracking algorithm to evaluate the…
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Polyculture farming has environmental advantages but requires substantially more pruning than monoculture farming. We present novel hardware and algorithms for automated pruning. Using an overhead camera to collect data from a physical scale garden testbed, the autonomous system utilizes a learned Plant Phenotyping convolutional neural network and a Bounding Disk Tracking algorithm to evaluate the individual plant distribution and estimate the state of the garden each day. From this garden state, AlphaGardenSim selects plants to autonomously prune. A trained neural network detects and targets specific prune points on the plant. Two custom-designed pruning tools, compatible with a FarmBot gantry system, are experimentally evaluated and execute autonomous cuts through controlled algorithms. We present results for four 60-day garden cycles. Results suggest the system can autonomously achieve 0.94 normalized plant diversity with pruning shears while maintaining an average canopy coverage of 0.84 by the end of the cycles. For code, videos, and datasets, see https://sites.google.com/berkeley.edu/pruningpolyculture.
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Submitted 22 August, 2022;
originally announced August 2022.
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AlphaGarden: Learning to Autonomously Tend a Polyculture Garden
Authors:
Mark Presten,
Yahav Avigal,
Mark Theis,
Satvik Sharma,
Rishi Parikh,
Shrey Aeron,
Sandeep Mukherjee,
Sebastian Oehme,
Simeon Adebola,
Walter Teitelbaum,
Varun Kamat,
Ken Goldberg
Abstract:
This paper presents AlphaGarden: an autonomous polyculture garden that prunes and irrigates living plants in a 1.5m x 3.0m physical testbed. AlphaGarden uses an overhead camera and sensors to track the plant distribution and soil moisture. We model individual plant growth and interplant dynamics to train a policy that chooses actions to maximize leaf coverage and diversity. For autonomous pruning,…
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This paper presents AlphaGarden: an autonomous polyculture garden that prunes and irrigates living plants in a 1.5m x 3.0m physical testbed. AlphaGarden uses an overhead camera and sensors to track the plant distribution and soil moisture. We model individual plant growth and interplant dynamics to train a policy that chooses actions to maximize leaf coverage and diversity. For autonomous pruning, AlphaGarden uses two custom-designed pruning tools and a trained neural network to detect prune points. We present results for four 60-day garden cycles. Results suggest AlphaGarden can autonomously achieve 0.96 normalized diversity with pruning shears while maintaining an average canopy coverage of 0.86 during the peak of the cycle. Code, datasets, and supplemental material can be found at https://github.com/BerkeleyAutomation/AlphaGarden.
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Submitted 22 August, 2022; v1 submitted 10 November, 2021;
originally announced November 2021.