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Register a new userRemoval of Batch Effects using Generative Adversarial Networks
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Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due to difference in handling the batches possibly at different times, by different experimenters or under other different conditions. This adds variation to the batches coming from the same source sample. These variations are known as Batch Effects. It is possible that these variations and natural variations due to biology confound but such situations can be avoided by performing experiments in a carefully planned manner. Batch effects can hamper downstream analysis and may also cause results to be inconclusive. Thus, it is essential to correct for these effects. This can be solved using a novel Generative Adversarial Networks (GANs) based framework that is proposed here, advantage of using this framework over other prior approaches is that here it is not required to choose a reproducing kernel and define its parameters. Results of the framework on a mass cytometry dataset are reported.
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A Triangle Generative Adversarial Network ($Delta$-GAN) is developed for semi-supervised cross-domain joint distribution matching, where the training data consists of samples from each domain, and supervision of domain correspondence is provided by only a few paired samples. $Delta$-GAN consists of four neural networks, two generators and two discriminators. The generators are designed to learn the two-way conditional distributions between the two domains, while the discriminators implicitly define a ternary discriminative function, which is trained to distinguish real data pairs and two kinds of fake data pairs. The generators and discriminators are trained together using adversarial learning. Under mild assumptions, in theory the joint distributions characterized by the two generators concentrate to the data distribution. In experiments, three different kinds of domain pairs are considered, image-label, image-image and image-attribute pairs. Experiments on semi-supervised image classification, image-to-image translation and attribute-based image generation demonstrate the superiority of the proposed approach.
Time series anomalies can offer information relevant to critical situations facing various fields, from finance and aerospace to the IT, security, and medical domains. However, detecting anomalies in time series data is particularly challenging due to the vague definition of anomalies and said datas frequent lack of labels and highly complex temporal correlations. Current state-of-the-art unsupervised machine learning methods for anomaly detection suffer from scalability and portability issues, and may have high false positive rates. In this paper, we propose TadGAN, an unsupervised anomaly detection approach built on Generative Adversarial Networks (GANs). To capture the temporal correlations of time series distributions, we use LSTM Recurrent Neural Networks as base models for Generators and Critics. TadGAN is trained with cycle consistency loss to allow for effective time-series data reconstruction. We further propose several novel methods to compute reconstruction errors, as well as different approaches to combine reconstruction errors and Critic outputs to compute anomaly scores. To demonstrate the performance and generalizability of our approach, we test several anomaly scoring techniques and report the best-suited one. We compare our approach to 8 baseline anomaly detection methods on 11 datasets from multiple reputable sources such as NASA, Yahoo, Numenta, Amazon, and Twitter. The results show that our approach can effectively detect anomalies and outperform baseline methods in most cases (6 out of 11). Notably, our method has the highest averaged F1 score across all the datasets. Our code is open source and is available as a benchmarking tool.
Conditional Generative Adversarial Networks (cGANs) are generative models that can produce data samples ($x$) conditioned on both latent variables ($z$) and known auxiliary information ($c$). We propose the Bidirectional cGAN (BiCoGAN), which effectively disentangles $z$ and $c$ in the generation process and provides an encoder that learns inverse mappings from $x$ to both $z$ and $c$, trained jointly with the generator and the discriminator. We present crucial techniques for training BiCoGANs, which involve an extrinsic factor loss along with an associated dynamically-tuned importance weight. As compared to other encoder-based cGANs, BiCoGANs encode $c$ more accurately, and utilize $z$ and $c$ more effectively and in a more disentangled way to generate samples.
Generative models are undoubtedly a hot topic in Artificial Intelligence, among which the most common type is Generative Adversarial Networks (GANs). These architectures let one synthesise artificial datasets by implicitly modelling the underlying probability distribution of a real-world training dataset. With the introduction of Conditional GANs and their variants, these methods were extended to generating samples conditioned on ancillary information available for each sample within the dataset. From a practical standpoint, however, one might desire to generate data conditioned on partial information. That is, only a subset of the ancillary conditioning variables might be of interest when synthesising data. In this work, we argue that standard Conditional GANs are not suitable for such a task and propose a new Adversarial Network architecture and training strategy to deal with the ensuing problems. Experiments illustrating the value of the proposed approach in digit and face image synthesis under partial conditioning information are presented, showing that the proposed method can effectively outperform the standard approach under these circumstances.
Generative adversarial networks (GANs) have shown great success in applications such as image generation and inpainting. However, they typically require large datasets, which are often not available, especially in the context of prediction tasks such as image segmentation that require labels. Therefore, methods such as the CycleGAN use more easily available unlabelled data, but do not offer a way to leverage additional labelled data for improved performance. To address this shortcoming, we show how to factorise the joint data distribution into a set of lower-dimensional distributions along with their dependencies. This allows splitting the discriminator in a GAN into multiple sub-discriminators that can be independently trained from incomplete observations. Their outputs can be combined to estimate the density ratio between the joint real and the generator distribution, which enables training generators as in the original GAN framework. We apply our method to image generation, image segmentation and audio source separation, and obtain improved performance over a standard GAN when additional incomplete training examples are available. For the Cityscapes segmentation task in particular, our method also improves accuracy by an absolute 14.9% over CycleGAN while using only 25 additional paired examples.
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