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1. Semi Supervised Segmentation And Graph-Based Tracking Of 3d Nuclei In Time-Lapse Microscopy

   https://doi.org/10.1109/ISBI48211.2021.9433831  

   Shailja, S.; Jiang, Jiaxiang; Manjunath, B.S. (April 2021, 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI))

   null (Ed.)

   We propose a novel weakly supervised method to improve the boundary of the 3D segmented nuclei utilizing an oversegmented image. This is motivated by the observation that current state-of-the-art deep learning methods do not result in accurate boundaries when the training data is weakly annotated. Towards this, a 3D U-Net is trained to get the centroid of the nuclei and integrated with a simple linear iterative clustering (SLIC) supervoxel algorithm that provides better adherence to cluster boundaries. To track these segmented nuclei, our algorithm utilizes the relative nuclei location depicting the processes of nuclei division and apoptosis. The proposed algorithmic pipeline achieves better segmentation performance compared to the state-of-the-art method in Cell Tracking Challenge (CTC) 2019 and comparable performance to state-of-the-art methods in IEEE ISBI CTC2020 while utilizing very few pixel-wise annotated data. Detailed experimental results are provided, and the source code is available on GitHub. 

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2. CaveSeg: Deep Semantic Segmentation and Scene Parsing for Autonomous Underwater Cave Exploration

   https://doi.org/10.1109/ICRA57147.2024.10611543  

   Abdullah, Adnan; Barua, Titon; Tibbetts, Reagan; Chen, Zijie; Islam, Md Jahidul; Rekleitis, Ioannis (May 2024, IEEE)

   — In this paper, we present CaveSeg - the first visual learning pipeline for semantic segmentation and scene parsing for AUV navigation inside underwater caves. We address the problem of scarce annotated training data by preparing a comprehensive dataset for semantic segmentation of underwater cave scenes. It contains pixel annotations for important navigation markers (e.g. caveline, arrows), obstacles (e.g. ground plain and overhead layers), scuba divers, and open areas for servoing. Through comprehensive benchmark analyses on cave systems in USA, Mexico, and Spain locations, we demonstrate that robust deep visual models can be developed based on CaveSeg for fast semantic scene parsing of underwater cave environments. In particular, we formulate a novel transformer-based model that is computationally light and offers near real-time execution in addition to achieving state-of-the-art performance. Finally, we explore the design choices and implications of semantic segmentation for visual servoing by AUVs inside underwater caves. The proposed model and benchmark dataset open up promising opportunities for future research in autonomous underwater cave exploration and mapping. 

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3. Image-Label Recovery on Fashion Data Using Image Similarity from Triple Siamese Network

   Banerjee, Debapriya; Kyrarini, Maria; Kim, Won Hwa (January 2021, Technologies)

   null (Ed.)

   Weakly labeled data are inevitable in various research areas in artificial intelligence (AI) where one has a modicum of knowledge about the complete dataset. One of the reasons for weakly labeled data in AI is insufficient accurately labeled data. Strict privacy control or accidental loss may also cause missing-data problems. However, supervised machine learning (ML) requires accurately labeled data in order to successfully solve a problem. Data labeling is difficult and time-consuming as it requires manual work, perfect results, and sometimes human experts to be involved (e.g., medical labeled data). In contrast, unlabeled data are inexpensive and easily available. Due to there not being enough labeled training data, researchers sometimes only obtain one or few data points per category or label. Training a supervised ML model from the small set of labeled data is a challenging task. The objective of this research is to recover missing labels from the dataset using state-of-the-art ML techniques using a semisupervised ML approach. In this work, a novel convolutional neural network-based framework is trained with a few instances of a class to perform metric learning. The dataset is then converted into a graph signal, which is recovered using a recover algorithm (RA) in graph Fourier transform. The proposed approach was evaluated on a Fashion dataset for accuracy and precision and performed significantly better than graph neural networks and other state-of-the-art methods 

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4. DeciX: Explain Deep Learning Based Code Generation Applications

   https://doi.org/10.1145/3660814  

   Chen, Simin; Li, Zexin; Yang, Wei; Liu, Cong (July 2024, Proceedings of the ACM on Software Engineering)

   Deep learning-based code generation (DL-CG) applications have shown great potential for assisting developers in programming with human-competitive accuracy. However, lacking transparency in such applications due to the uninterpretable nature of deep learning models makes the automatically generated programs untrustworthy. In this paper, we develop DeciX, a first explanation method dedicated to DL-CG applications. DeciX is motivated by observing two unique properties of DL-CG applications: output-to-output dependencies and irrelevant value and semantic space. These properties violate the fundamental assumptions made in existing explainable DL techniques and thus cause applying existing techniques to DL-CG applications rather pessimistic and even incorrect. DeciX addresses these two limitations by constructing a causal inference dependency graph, containing a novel method leveraging causal inference that can accurately quantify the contribution of each dependency edge in the graph to the end prediction result. Proved by extensive experiments assessing popular, widely-used DL-CG applications and several baseline methods, DeciX is able to achieve significantly better performance compared to state-of-the-art in terms of several critical performance metrics, including correctness, succinctness, stability, and overhead. Furthermore, DeciX can be applied to practical scenarios since it does not require any knowledge of the DL-CG model under explanation. We have also conducted case studies that demonstrate the applicability of DeciX in practice. 

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5. Clustering Augmented Self-Supervised Learning: An Application to Land Cover Mapping

   Ghosh, Rahul; Jia, Xiaowei; Chenxi, Lin; Jin, Zhenong; Kumar, Vipin (August 2021, DEEPSPATIA 2021: 2nd ACM SIGKDD Workshop on Deep Learning for Spatiotemporal Data, Applications, and Systems)

   null (Ed.)

   Collecting large annotated datasets in Remote Sensing is often expensive and thus can become a major obstacle for training advanced machine learning models. Common techniques of addressing this issue, based on the underlying idea of pre-training the Deep Neural Networks (DNN) on freely available large datasets, cannot be used for Remote Sensing due to the unavailability of such large-scale labeled datasets and the heterogeneity of data sources caused by the varying spatial and spectral resolution of different sensors. Self-supervised learning is an alternative approach that learns feature representation from unlabeled images without using any human annotations. In this paper, we introduce a new method for land cover mapping by using a clustering-based pretext task for self-supervised learning. We demonstrate the effectiveness of the method on two societally relevant applications from the aspect of segmentation performance, discriminative feature representation learning, and the underlying cluster structure. We also show the effectiveness of the active sampling using the clusters obtained from our method in improving the mapping accuracy given a limited budget of annotating. 

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