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1. InfoGAN-CR and ModelCentrality: Self-supervised Model Training and Selection for Disentangling GANs

   Zinan Lin, Kiran Thekumparampil (January 2020, International Conference on Machine Learning)

   null (Ed.)

   Disentangled generative models map a latent code vector to a target space, while enforcing that a subset of the learned latent codes are interpretable and associated with distinct properties of the target distribution. Recent advances have been dominated by Variational AutoEncoder (VAE)-based methods, while training disentangled generative adversarial networks (GANs) remains challenging. In this work, we show that the dominant challenges facing disentangled GANs can be mitigated through the use of self-supervision. We make two main contributions: first, we design a novel approach for training disentangled GANs with self-supervision. We propose contrastive regularizer, which is inspired by a natural notion of disentanglement: latent traversal. This achieves higher disentanglement scores than state-of-the-art VAE- and GAN-based approaches. Second, we propose an unsupervised model selection scheme called ModelCentrality, which uses generated synthetic samples to compute the medoid (multi-dimensional generalization of median) of a collection of models. The current common practice of hyper-parameter tuning requires using ground-truths samples, each labelled with known perfect disentangled latent codes. As real datasets are not equipped with such labels, we propose an unsupervised model selection scheme and show that it finds a model close to the best one, for both VAEs and GANs. Combining contrastive regularization with ModelCentrality, we improve upon the state-of-the-art disentanglement scores significantly, without accessing the supervised data. 

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2. Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders

   https://doi.org/10.1371/journal.pcbi.1009439  

   Whiteway, Matthew R.; Biderman, Dan; Friedman, Yoni; Dipoppa, Mario; Buchanan, E. Kelly; Wu, Anqi; Zhou, John; Bonacchi, Niccolò; Miska, Nathaniel J.; Noel, Jean-Paul; et al (September 2021, PLOS Computational Biology)

   Theunissen, Frédéric E. (Ed.)

   Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting in an increased need for computer vision algorithms that extract useful information from video data. Here we introduce a new video analysis tool that combines the output of supervised pose estimation algorithms (e.g. DeepLabCut) with unsupervised dimensionality reduction methods to produce interpretable, low-dimensional representations of behavioral videos that extract more information than pose estimates alone. We demonstrate this tool by extracting interpretable behavioral features from videos of three different head-fixed mouse preparations, as well as a freely moving mouse in an open field arena, and show how these interpretable features can facilitate downstream behavioral and neural analyses. We also show how the behavioral features produced by our model improve the precision and interpretation of these downstream analyses compared to using the outputs of either fully supervised or fully unsupervised methods alone. 

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3. Beyond Images: Label Noise Transition Matrix Estimation for Tasks with Lower-Quality Features

   Zhu, Zhaowei; Wang, Jialu; Liu, Yang (January 2022, International Conference on Machine Learning)

   The label noise transition matrix, denoting the transition probabilities from clean labels to noisy labels, is crucial for designing statistically robust solutions. Existing estimators for noise transition matrices, e.g., using either anchor points or clusterability, focus on computer vision tasks that are relatively easier to obtain high-quality representations. We observe that tasks with lower-quality features fail to meet the anchor-point or clusterability condition, due to the coexistence of both uninformative and informative representations. To handle this issue, we propose a generic and practical information-theoretic approach to down-weight the less informative parts of the lower-quality features. This improvement is crucial to identifying and estimating the label noise transition matrix. The salient technical challenge is to compute the relevant information-theoretical metrics using only noisy labels instead of clean ones. We prove that the celebrated f-mutual information measure can often preserve the order when calculated using noisy labels. We then build our transition matrix estimator using this distilled version of features. The necessity and effectiveness of the proposed method are also demonstrated by evaluating the estimation error on a varied set of tabular data and text classification tasks with lower-quality features. 

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4. GAGE: Geometry Preserving Attributed Graph Embeddings

   https://doi.org/10.1145/3488560.3498467  

   Kanatsoulis, Charilaos I.; Sidiropoulos, Nicholas D. (February 2022, 15th ACM Conference on Web Search and Data Mining (WSDM))

   Node embedding is the task of extracting concise and informative representations of certain entities that are connected in a network. Various real-world networks include information about both node connectivity and certain node attributes, in the form of features or time-series data. Modern representation learning techniques employ both the connectivity and attribute information of the nodes to produce embeddings in an unsupervised manner. In this context, deriving embeddings that preserve the geometry of the network and the attribute vectors would be highly desirable, as they would reflect both the topological neighborhood structure and proximity in feature space. While this is fairly straightforward to maintain when only observing the connectivity or attribute information of the network, preserving the geometry of both types of information is challenging. A novel tensor factorization approach for node embedding in attributed networks is proposed in this paper, that preserves the distances of both the connections and the attributes. Furthermore, an effective and lightweight algorithm is developed to tackle the learning task and judicious experiments with multiple state-of-the-art baselines suggest that the proposed algorithm offers significant performance improvements in downstream tasks. 

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5. Discovering a sparse set of pairwise discriminating features in high-dimensional data

   https://doi.org/10.1093/bioinformatics/btaa690  

   Melton, Samuel; Ramanathan, Sharad (July 2020, Bioinformatics)

   Luigi Martelli, Pier (Ed.)

   Abstract Motivation Recent technological advances produce a wealth of high-dimensional descriptions of biological processes, yet extracting meaningful insight and mechanistic understanding from these data remains challenging. For example, in developmental biology, the dynamics of differentiation can now be mapped quantitatively using single-cell RNA sequencing, yet it is difficult to infer molecular regulators of developmental transitions. Here, we show that discovering informative features in the data is crucial for statistical analysis as well as making experimental predictions. Results We identify features based on their ability to discriminate between clusters of the data points. We define a class of problems in which linear separability of clusters is hidden in a low-dimensional space. We propose an unsupervised method to identify the subset of features that define a low-dimensional subspace in which clustering can be conducted. This is achieved by averaging over discriminators trained on an ensemble of proposed cluster configurations. We then apply our method to single-cell RNA-seq data from mouse gastrulation, and identify 27 key transcription factors (out of 409 total), 18 of which are known to define cell states through their expression levels. In this inferred subspace, we find clear signatures of known cell types that eluded classification prior to discovery of the correct low-dimensional subspace. Availability and implementation https://github.com/smelton/SMD. Supplementary information Supplementary data are available at Bioinformatics online. 

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