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1. Biodiversity Image Quality Metadata Augments Convolutional Neural Network Classification of Fish Species

   Leipzig, J.; Bakis, Y; Wang, X; Elhamod, M.; Diamond, K.; Dahdul, W; Karpante, A; Maga, M; Mabee, P; Bart, H; et al (March 2021, Metadata and Semantic Research. MTSR 2020. Communications in Computer and Information Science)

   null; null (Ed.)

   Biodiversity image repositories are crucial sources of training data for machine learning approaches to biological research. Metadata, specifically metadata about object quality, is putatively an important prerequisite to selecting sample subsets for these experiments. This study demonstrates the importance of image quality metadata to a species classification experiment involving a corpus of 1935 fish specimen images which were annotated with 22 metadata quality properties. A small subset of high quality images produced an F1 accuracy of 0.41 compared to 0.35 for a taxonomically matched subset of low quality images when used by a convolutional neural network approach to species identification. Using the full corpus of images revealed that image quality differed between correctly classified and misclassified images. We found the visibility of all anatomical features was the most important quality feature for classification accuracy. We suggest biodiversity image repositories consider adopting a minimal set of image quality metadata to support future machine learning projects. 

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2. Automatic Metadata Generation for Fish Specimen Image Collections

   https://doi.org/10.1109/JCDL52503.2021.00015  

   Pepper, Joel; Greenberg, Jane; Bakis, Yasin; Wang, Xiaojun; Bart, Henry; Breen, David (September 2021, The Institute of Electrical and Electronics Engineers, Inc. (IEEE) Conference Proceedings/2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL))

   Conference Title: 2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL) Conference Start Date: 2021, Sept. 27 Conference End Date: 2021, Sept. 30 Conference Location: Champaign, IL, USAMetadata are key descriptors of research data, particularly for researchers seeking to apply machine learning (ML) to the vast collections of digitized specimens. Unfortunately, the available metadata is often sparse and, at times, erroneous. Additionally, it is prohibitively expensive to address these limitations through traditional, manual means. This paper reports on research that applies machine-driven approaches to analyzing digitized fish images and extracting various important features from them. The digitized fish specimens are being analyzed as part of the Biology Guided Neural Networks (BGNN) initiative, which is developing a novel class of artificial neural networks using phylogenies and anatomy ontologies. Automatically generated metadata is crucial for identifying the high-quality images needed for the neural network's predictive analytics. Methods that combine ML and image informatics techniques allow us to rapidly enrich the existing metadata associated with the 7,244 images from the Illinois Natural History Survey (INHS) used in our study. Results show we can accurately generate many key metadata properties relevant to the BGNN project, as well as general image quality metrics (e.g. brightness and contrast). Results also show that we can accurately generate bounding boxes and segmentation masks for fish, which are needed for subsequent machine learning analyses. The automatic process outperforms humans in terms of time and accuracy, and provides a novel solution for leveraging digitized specimens in ML. This research demonstrates the ability of computational methods to enhance the digital library services associated with the tens of thousands of digitized specimens stored in open-access repositories worldwide. 

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3. Computational metadata generation methods for biological specimen image collections

   https://doi.org/10.1007/s00799-022-00342-1  

   Karnani, Kevin; Pepper, Joel; Bakiş, Yasin; Wang, Xiaojun; Bart, Henry; Breen, David E.; Greenberg, Jane (November 2022, International Journal on Digital Libraries)

   Adam, N.; Neuhold, E.; Furuta, R. (Ed.)

   Metadata is a key data source for researchers seeking to apply machine learning (ML) to the vast collections of digitized biological specimens that can be found online. Unfortunately, the associated metadata is often sparse and, at times, erroneous. This paper extends previous research conducted with the Illinois Natural History Survey (INHS) collection (7244 specimen images) that uses computational approaches to analyze image quality, and then automatically generates 22 metadata properties representing the image quality and morphological features of the specimens. In the research reported here, we demonstrate the extension of our initial work to University of the Wisconsin Zoological Museum (UWZM) collection (4155 specimen images). Further, we enhance our computational methods in four ways: (1) augmenting the training set, (2) applying contrast enhancement, (3) upscaling small objects, and (4) refining our processing logic. Together these new methods improved our overall error rates from 4.6 to 1.1%. These enhancements also allowed us to compute an additional set of 17 image-based metadata properties. The new metadata properties provide supplemental features and information that may also be used to analyze and classify the fish specimens. Examples of these new features include convex area, eccentricity, perimeter, skew, etc. The newly refined process further outperforms humans in terms of time and labor cost, as well as accuracy, providing a novel solution for leveraging digitized specimens with ML. This research demonstrates the ability of computational methods to enhance the digital library services associated with the tens of thousands of digitized specimens stored in open-access repositories world-wide by generating accurate and valuable metadata for those repositories. 

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4. Improving plankton image classification using context metadata

   https://doi.org/10.1002/lom3.10324  

   Ellen, Jeffrey S.; Graff, Casey A.; Ohman, Mark D. (July 2019, Limnology and Oceanography: Methods)

   Abstract Advances in both hardware and software are enabling rapid proliferation of in situ plankton imaging methods, requiring more effective machine learning approaches to image classification. Deep Learning methods, such as convolutional neural networks (CNNs), show marked improvement over traditional feature‐based supervised machine learning algorithms, but require careful optimization of hyperparameters and adequate training sets. Here, we document some best practices in applying CNNs to zooplankton and marine snow images and note where our results differ from contemporary Deep Learning findings in other domains. We boost the performance of CNN classifiers by incorporating metadata of different types and illustrate how to assimilate metadata beyond simple concatenation. We utilize both geotemporal (e.g., sample depth, location, time of day) and hydrographic (e.g., temperature, salinity, chlorophylla) metadata and show that either type by itself, or both combined, can substantially reduce error rates. Incorporation of context metadata also boosts performance of the feature‐based classifiers we evaluated: Random Forest, Extremely Randomized Trees, Gradient Boosted Classifier, Support Vector Machines, and Multilayer Perceptron. For our assessments, we use an original data set of 350,000 in situ images (roughly 50% marine snow and 50% non‐snow sorted into 26 categories) from a novel in situZooglider. We document asymptotically increasing performance with more computationally intensive techniques, such as substantially deeper networks and artificially augmented data sets. Our best model achieves 92.3% accuracy with our 27‐class data set. We provide guidance for further refinements that are likely to provide additional gains in classifier accuracy. 

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5. EGIS: Entropy Guided Image Synthesis for Dataset-Agnostic Testing of RRAM-Based DNNs

   Saha, A; Amarnath, C; Ma, K; Chatterjee, A (March 2025, IEEE)

   While resistive random access memory (RRAM) based deep neural networks (DNN) are important for low-power inference in IoT and edge applications, they are vulnerable to the effects of manufacturing process variations that degrade their performance (classification accuracy). However, to test the same post-manufacture, the (image) dataset used to train the associated machine learning applications may not be available to the RRAM crossbar manufacturer for privacy reasons. As such, the performance of DNNs needs to be assessed with carefully crafted dataset-agnostic synthetic test images that expose anomalies in the crossbar manufacturing process to the maximum extent possible. In this work, we propose a dataset-agnostic post-manufacture testing framework for RRAM-based DNNs using Entropy Guided Image Synthesis (EGIS). We first create a synthetic image dataset such that the DNN outputs corresponding to the synthetic images minimize an entropy-based loss metric. Next, a small subset (consisting of 10-20 images) of the synthetic image dataset, called the compact image dataset, is created to expedite testing. The response of the device under test (DUT) to the compact image dataset is passed to a machine learning based outlier detector for pass/fail labeling of the DUT. It is seen that the test accuracy using such synthetic test images is very close to that of contemporary test methods. 

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