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1. Self-supervised maize kernel classification and segmentation for embryo identification

   https://doi.org/10.3389/fpls.2023.1108355  

   Dong, David ; Nagasubramanian, Koushik ; Wang, Ruidong ; Frei, Ursula K. ; Jubery, Talukder Z. ; Lübberstedt, Thomas ; Ganapathysubramanian, Baskar ( April 2023 , Frontiers in Plant Science)

   Computer vision and deep learning (DL) techniques have succeeded in a wide range of diverse fields. Recently, these techniques have been successfully deployed in plant science applications to address food security, productivity, and environmental sustainability problems for a growing global population. However, training these DL models often necessitates the large-scale manual annotation of data which frequently becomes a tedious and time-and-resource- intensive process. Recent advances in self-supervised learning (SSL) methods have proven instrumental in overcoming these obstacles, using purely unlabeled datasets to pre-train DL models.

   Here, we implement the popular self-supervised contrastive learning methods of NNCLR Nearest neighbor Contrastive Learning of visual Representations) and SimCLR (Simple framework for Contrastive Learning of visual Representations) for the classification of spatial orientation and segmentation of embryos of maize kernels. Maize kernels are imaged using a commercial high-throughput imaging system. This image data is often used in multiple downstream applications across both production and breeding applications, for instance, sorting for oil content based on segmenting and quantifying the scutellum’s size and for classifying haploid and diploid kernels.

   We show that in both classification and segmentation problems, SSL techniques outperform their purely supervised transfer learning-based counterparts and are significantly more annotation efficient. Additionally, we show that a single SSL pre-trained model can be efficiently finetuned for both classification and segmentation, indicating good transferability across multiple downstream applications. Segmentation models with SSL-pretrained backbones produce DICE similarity coefficients of 0.81, higher than the 0.78 and 0.73 of those with ImageNet-pretrained and randomly initialized backbones, respectively. We observe that finetuning classification and segmentation models on as little as 1% annotation produces competitive results. These results show SSL provides a meaningful step forward in data efficiency with agricultural deep learning and computer vision.

    

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2. Data-Efficient Double-Win Lottery Tickets from Robust Pre-training

   Chen, Tianlong ; Zhang, Zhenyu ; Liu, Sijia ; Zhang, Yang ; Chang, Shiyu ; Wang, Zhangyang ( July 2022 , International Conference on Machine Learning (ICML))

   Pre-training serves as a broadly adopted starting point for transfer learning on various downstream tasks. Recent investigations of lottery tickets hypothesis (LTH) demonstrate such enormous pre-trained models can be replaced by extremely sparse subnetworks (a.k.a. matching subnetworks) without sacrificing transferability. However, practical security-crucial applications usually pose more challenging requirements beyond standard transfer, which also demand these subnetworks to overcome adversarial vulnerability. In this paper, we formulate a more rigorous concept, Double-Win Lottery Tickets, in which a located subnetwork from a pre-trained model can be independently transferred on diverse downstream tasks, to reach BOTH the same standard and robust generalization, under BOTH standard and adversarial training regimes, as the full pre-trained model can do. We comprehensively examine various pre-training mechanisms and find that robust pre-training tends to craft sparser double-win lottery tickets with superior performance over the standard counterparts. For example, on downstream CIFAR-10/100 datasets, we identify double-win matching subnetworks with the standard, fast adversarial, and adversarial pre-training from ImageNet, at 89.26%/73.79%, 89.26%/79.03%, and 91.41%/83.22% sparsity, respectively. Furthermore, we observe the obtained double-win lottery tickets can be more data-efficient to transfer, under practical data-limited (e.g., 1% and 10%) downstream schemes. Our results show that the benefits from robust pre-training are amplified by the lottery ticket scheme, as well as the data-limited transfer setting. 

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3. The lottery ticket hypothesis for pre-trained BERT networks

   Chen, Tianlong ; Frankle, Jonathan ; Chang, Shiyu ; Liu, Sijia ; Zhang, Yang ; Wang, Zhangyang ; Carbin, Michael ( December 2020 , Advances in neural information processing systems)

   null (Ed.)

   In natural language processing (NLP), enormous pre-trained models like BERT have become the standard starting point for training on a range of downstream tasks, and similar trends are emerging in other areas of deep learning. In parallel, work on the lottery ticket hypothesis has shown that models for NLP and computer vision contain smaller matching subnetworks capable of training in isolation to full accuracy and transferring to other tasks. In this work, we combine these observations to assess whether such trainable, transferrable subnetworks exist in pre-trained BERT models. For a range of downstream tasks, we indeed find matching subnetworks at 40% to 90% sparsity. We find these subnetworks at (pre-trained) initialization, a deviation from prior NLP research where they emerge only after some amount of training. Subnetworks found on the masked language modeling task (the same task used to pre-train the model) transfer universally; those found on other tasks transfer in a limited fashion if at all. As large-scale pre-training becomes an increasingly central paradigm in deep learning, our results demonstrate that the main lottery ticket observations remain relevant in this context. 

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4. Self‐supervised learning improves classification of agriculturally important insect pests in plants

   https://doi.org/10.1002/ppj2.20079  

   Kar, Soumyashree ; Nagasubramanian, Koushik ; Elango, Dinakaran ; Carroll, Matthew E. ; Abel, Craig A. ; Nair, Ajay ; Mueller, Daren S. ; O'Neal, Matthew E. ; Singh, Asheesh K. ; Sarkar, Soumik ; et al ( July 2023 , The Plant Phenome Journal)

   Insect pests cause significant damage to food production, so early detection and efficient mitigation strategies are crucial. There is a continual shift toward machine learning (ML)‐based approaches for automating agricultural pest detection. Although supervised learning has achieved remarkable progress in this regard, it is impeded by the need for significant expert involvement in labeling the data used for model training. This makes real‐world applications tedious and oftentimes infeasible. Recently, self‐supervised learning (SSL) approaches have provided a viable alternative to training ML models with minimal annotations. Here, we present an SSL approach to classify 22 insect pests. The framework was assessed on raw and segmented field‐captured images using three different SSL methods, Nearest Neighbor Contrastive Learning of Visual Representations (NNCLR), Bootstrap Your Own Latent, and Barlow Twins. SSL pre‐training was done on ResNet‐18 and ResNet‐50 models using all three SSL methods on the original RGB images and foreground segmented images. The performance of SSL pre‐training methods was evaluated using linear probing of SSL representations and end‐to‐end fine‐tuning approaches. The SSL‐pre‐trained convolutional neural network models were able to perform annotation‐efficient classification. NNCLR was the best performing SSL method for both linear and full model fine‐tuning. With just 5% annotated images, transfer learning with ImageNet initialization obtained 74% accuracy, whereas NNCLR achieved an improved classification accuracy of 79% for end‐to‐end fine‐tuning. Models created using SSL pre‐training consistently performed better, especially under very low annotation, and were robust to object class imbalances. These approaches help overcome annotation bottlenecks and are resource efficient.

    

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5. Strategies For Pre-training Graph Neural Networks

   Hu, W. ; Liu, B. ; Gomes, J. ; Zitnik, M. ; Liang, P. ; Pande, V. ; Leskovec, J. ( April 2020 , International Conference on Learning Representations (ICLR))

   Many applications of machine learning require a model to make accurate predictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naïve strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction. 

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