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Register a new userContrastive Learning of Single-Cell Phenotypic Representations for Treatment Classification
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Added by
Alexis Perakis
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Learning robust representations to discriminate cell phenotypes based on microscopy images is important for drug discovery. Drug development efforts typically analyse thousands of cell images to screen for potential treatments. Early works focus on creating hand-engineered features from these images or learn such features with deep neural networks in a fully or weakly-supervised framework. Both require prior knowledge or labelled datasets. Therefore, subsequent works propose unsupervised approaches based on generative models to learn these representations. Recently, representations learned with self-supervised contrastive loss-based methods have yielded state-of-the-art results on various imaging tasks compared to earlier unsupervised approaches. In this work, we leverage a contrastive learning framework to learn appropriate representations from single-cell fluorescent microscopy images for the task of Mechanism-of-Action classification. The proposed work is evaluated on the annotated BBBC021 dataset, and we obtain state-of-the-art results in NSC, NCSB and drop metrics for an unsupervised approach. We observe an improvement of 10% in NCSB accuracy and 11% in NSC-NSCB drop over the previously best unsupervised method. Moreover, the performance of our unsupervised approach ties with the best supervised approach. Additionally, we observe that our framework performs well even without post-processing, unlike earlier methods. With this, we conclude that one can learn robust cell representations with contrastive learning.
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Red blood cells are highly deformable and present in various shapes. In blood cell disorders, only a subset of all cells is morphologically altered and relevant for the diagnosis. However, manually labeling of all cells is laborious, complicated and introduces inter-expert variability. We propose an attention based multiple instance learning method to classify blood samples of patients suffering from blood cell disorders. Cells are detected using an R-CNN architecture. With the features extracted for each cell, a multiple instance learning method classifies patient samples into one out of four blood cell disorders. The attention mechanism provides a measure of the contribution of each cell to the overall classification and significantly improves the networks classification accuracy as well as its interpretability for the medical expert.
Environmental Sound Classification (ESC) is a challenging field of research in non-speech audio processing. Most of current research in ESC focuses on designing deep models with special architectures tailored for specific audio datasets, which usually cannot exploit the intrinsic patterns in the data. However recent studies have surprisingly shown that transfer learning from models trained on ImageNet is a very effective technique in ESC. Herein, we propose SoundCLR, a supervised contrastive learning method for effective environment sound classification with state-of-the-art performance, which works by learning representations that disentangle the samples of each class from those of other classes. Our deep network models are trained by combining a contrastive loss that contributes to a better probability output by the classification layer with a cross-entropy loss on the output of the classifier layer to map the samples to their respective 1-hot encoded labels. Due to the comparatively small sizes of the available environmental sound datasets, we propose and exploit a transfer learning and strong data augmentation pipeline and apply the augmentations on both the sound signals and their log-mel spectrograms before inputting them to the model. Our experiments show that our masking based augmentation technique on the log-mel spectrograms can significantly improve the recognition performance. Our extensive benchmark experiments show that our hybrid deep network models trained with combined contrastive and cross-entropy loss achieved the state-of-the-art performance on three benchmark datasets ESC-10, ESC-50, and US8K with validation accuracies of 99.75%, 93.4%, and 86.49% respectively. The ensemble version of our models also outperforms other top ensemble methods. The code is available at https://github.com/alireza-nasiri/SoundCLR.
Convolutional operations have two limitations: (1) do not explicitly model where to focus as the same filter is applied to all the positions, and (2) are unsuitable for modeling long-range dependencies as they only operate on a small neighborhood. While both limitations can be alleviated by attention operations, many design choices remain to be determined to use attention, especially when applying attention to videos. Towards a principled way of applying attention to videos, we address the task of spatiotemporal attention cell search. We propose a novel search space for spatiotemporal attention cells, which allows the search algorithm to flexibly explore various design choices in the cell. The discovered attention cells can be seamlessly inserted into existing backbone networks, e.g., I3D or S3D, and improve video classification accuracy by more than 2% on both Kinetics-600 and MiT datasets. The discovered attention cells outperform non-local blocks on both datasets, and demonstrate strong generalization across different modalities, backbones, and datasets. Inserting our attention cells into I3D-R50 yields state-of-the-art performance on both datasets.
A good clustering algorithm can discover natural groupings in data. These groupings, if used wisely, provide a form of weak supervision for learning representations. In this work, we present Clustering-based Contrastive Learning (CCL), a new clustering-based representation learning approach that uses labels obtained from clustering along with video constraints to learn discriminative face features. We demonstrate our method on the challenging task of learning representations for video face clustering. Through several ablation studies, we analyze the impact of creating pair-wise positive and negative labels from different sources. Experiments on three challenging video face clustering datasets: BBT-0101, BF-0502, and ACCIO show that CCL achieves a new state-of-the-art on all datasets.
We propose a self-supervised approach for learning representations of objects from monocular videos and demonstrate it is particularly useful in situated settings such as robotics. The main contributions of this paper are: 1) a self-supervising objective trained with contrastive learning that can discover and disentangle object attributes from video without using any labels; 2) we leverage object self-supervision for online adaptation: the longer our online model looks at objects in a video, the lower the object identification error, while the offline baseline remains with a large fixed error; 3) to explore the possibilities of a system entirely free of human supervision, we let a robot collect its own data, train on this data with our self-supervise scheme, and then show the robot can point to objects similar to the one presented in front of it, demonstrating generalization of object attributes. An interesting and perhaps surprising finding of this approach is that given a limited set of objects, object correspondences will naturally emerge when using contrastive learning without requiring explicit positive pairs. Videos illustrating online object adaptation and robotic pointing are available at: https://online-objects.github.io/.
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