United States

Cell clustering is a critical step in analyzing single-cell RNA sequencing (scRNA-seq) data, which allows us to characterize the cellular heterogeneity of transcriptional profiling at the single-cell level. Single-cell deep embedded representation models have recently become popular since they can learn feature representation and clustering simultaneously. However, the model still suffers from a variety of significant challenges, including the massive amount of data, pervasive dropout events, and complicated noise patterns in transcriptional profiling. Here, we propose a Single-Cell Deep Embedding Fusion Representation (scDEFR) model, which develop a deep embedded fusion representation to learn fused heterogeneous latent embedding that contains both the transcriptome gene-level information and the cell topology information. We first fuse them layer by layer to obtain compressed representations of intercellular relationships and transcriptome information. After that, the zero-inflated negative binomial model (ZINB)-based decoder is proposed to capture the global probabilistic structure of the data and reconstruct the final gene expression information and cell graph. Finally, by simultaneously integrating the clustering loss, crossentropy loss, ZINB loss, and the cell graph reconstruction loss,
scDEFR can optimize clustering performance and learn the latent representation in fused information under a joint mutual supervised strategy. We conducted extensive and comprehensive experiments on 15 single-cell RNA-seq datasets from different sequencing platforms to demonstrate the superiority of scDEFR over a variety of state-of-the-art methods. 


AAAI 2023

Unsupervised Deep Embedded Fusion Representation of Single-cell Transcriptomics

deep generative models & autoencoders

bioinformatics

clustering

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-23 is the Thirty-Seventh AAAI Conference on Artificial Intelligence. The theme of this conference is to create collaborative bridges within and beyond AI. Like previous AAAI conferences, AAAI-23 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and two new activities: a Bridge Program and a Lab Program. Many of these activities are tailored to the theme of bridges and all are selected according to the highest standards, with additional programs for students and young researchers. 
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The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines.

poster

Conditional independence (CI) tests underlie many approaches to model testing and structure learning in causal inference. Most existing CI tests for categorical and ordinal data stratify the sample by the conditioning variables, perform simple independence tests in each stratum, and combine the results. Unfortunately, the statistical power of this approach degrades rapidly as the number of conditioning variables increases. Here we propose a simple unified CI test for ordinal and categorical data that maintains reasonable calibration and power in high dimensions. We show that our test outperforms existing baselines in model testing and structure learning for dense directed graphical models while being comparable for sparse models. Our approach could be attractive for causal model testing because it is easy to implement, can be used with non-parametric or parametric probability models, has the symmetry property, and has reasonable computational requirements.

A Simple Unified Approach to Testing High-Dimensional Conditional Independences for Categorical and Ordinal Data

Self-supervised learning has demonstrated remarkable capability in representation learning for skeleton-based action recognition. Existing methods mainly focus on applying global data augmentation to generate different views of the skeleton sequence for contrastive learning. However, due to the rich action clues in the skeleton sequences, existing methods may only take a global perspective to learn to discriminate different skeletons without thoroughly leveraging the local relationship between different skeleton joints and video frames, which is essential for real-world applications. In this work, we propose a Partial Spatio-Temporal Learning (PSTL) framework to exploit the local relationship from a partial skeleton sequences built by a unique spatio-temporal masking strategy.  Specifically, we construct a negative-sample-free triplet steam structure that is composed of an anchor stream without any masking, a spatial masking stream with Central Spatial Masking (CSM), and a temporal masking stream with Motion Attention Temporal Masking (MATM). The feature cross-correlation matrix is measured between the anchor stream and the other two masking streams, respectively. (1) Central Spatial Masking discards selected joints from the feature calculation process, where the joints with a higher degree of centrality have a higher possibility of being selected.  (2) Motion Attention Temporal Masking leverages the motion of action and remove frames that move faster with a higher possibility. Our method achieves state-of-the-art performance on NTURGB+D 60, NTURGB+D 120 and PKU-MMD under various downstream tasks. Furthermore, to simulate the real-world scenarios, a practical evaluation is performed where some skeleton joints are lost in downstream tasks.In contrast to previous methods that suffer from large performance drops, our PSTL can still achieve remarkable results under this challenging setting, validating the robustness of our method.

Self-supervised Action Representation Learning from Partial Spatio-Temporal Skeleton Sequences

While federated learning has shown strong results in optimizing a machine learning model without direct access to the original data, 
While federated learning has shown strong results in opti- mizing a machine learning model without direct access to the original data, its performance may be hindered by in- termittent client availability which slows down the conver- gence and biases the final learned model. There are significant challenges to achieve both stable and bias-free training un- der arbitrary client availability. To address these challenges, we propose a framework named Federated Graph-based Sam- pling (FEDGS), to stabilize the global model update and mitigate the long-term bias given arbitrary client availabil- ity simultaneously. First, we model the data correlations of clients with a Data-Distribution-Dependency Graph (3DG) that helps keep the sampled clients data apart from each other, which is theoretically shown to improve the approximation to the optimal model update. Second, constrained by the far- distance in data distribution of the sampled clients, we fur- ther minimize the variance of the numbers of times that the clients are sampled, to mitigate long-term bias. To validate the effectiveness of FEDGS, we conduct experiments on three datasets under a comprehensive set of seven client availability modes. Our experimental results confirm FEDGS’s advantage in both enabling a fair client-sampling scheme and improving the model performance under arbitrary client availability. Our code is available at https://github.com/WwZzz/FedGS.

FedGS: Federated Graph-based Sampling with Arbitrary Client Availability

Cross-view geo-localization aims to estimate the location of a query ground image by matching it to a reference geo-tagged aerial images database. As an extremely challenging task, its difficulties root in the drastic view changes and different capturing time between two views. Despite these difficulties, recent works achieve outstanding progress on cross-view geo-localization benchmarks. However, existing methods still suffer from poor performance on the cross-area benchmarks, in which the training and testing data are captured from two different regions. We attribute this deficiency to the lack of ability to extract the spatial configuration of visual feature layouts and models' overfitting on low-level details from the training set. In this paper, we propose GeoDTR which explicitly disentangles geometric information from raw features and learns the spatial correlations among visual features from aerial and ground pairs with a novel geometric layout extractor module. This module generates a set of geometric layout descriptors, modulating the raw features and producing high-quality latent representations. In addition, we elaborate on two categories of data augmentations, (i) Layout simulation, which varies the spatial configuration while keeping the low-level details intact. (ii) Semantic augmentation, which alters the low-level details and encourages the model to capture spatial configurations. These augmentations help to improve the performance of the cross-view geo-localization models, especially on the cross-area benchmarks. Moreover, we propose a counterfactual-based learning process to benefit the geometric layout extractor in exploring spatial information. Extensive experiments show that GeoDTR not only achieves state-of-the-art results but also significantly boosts the performance on same-area and cross-area benchmarks. Our code can be found at https://gitlab.com/vail-uvm/geodtr.

Cross-view Geo-localization via Learning Disentangled Geometric Layout Correspondence

Federated learning aims to collaboratively train models without accessing their client's local private data. The data may be Non-IID for different clients and thus resulting in poor performance. Recently, personalized federated learning (PFL) has achieved great success in handling Non-IID data by enforcing regularization in local optimization or improving the model aggregation scheme on the server. However, most of the PFL approaches do not take into account the unfair competition issue caused by the imbalanced data distribution and lack of positive samples for some classes in each client. To address this issue, we propose a novel and generic PFL framework termed Federated Averaging via Binary Classification, dubbed FedABC. In particular, we adopt the ``one-vs-all'' training strategy in each client to alleviate the unfair competition between classes by constructing a personalized binary classification problem for each class. This may aggravate the class imbalance challenge and thus a novel personalized binary classification loss that incorporates both the under-sampling and hard sample mining strategies is designed. Extensive experiments are conducted on two popular datasets under different settings, and the results demonstrate that our FedABC can significantly outperform the existing counterparts.

FedABC: Targeting Fair Competition in Personalized Federated Learning

Access to a representative sample from the population is an assumption that underpins all of machine learning. Selection effects can cause observations to instead come from a subpopulation, by which our inferences may be subject to bias. 
It is therefore important to know whether or not a sample is affected by selection effects. We study under which conditions we can identify selection bias and give results for both parametric and non-parametric families of distributions. Based on these results we develop two practical methods to determine whether or not an observed sample comes from a distribution subject to selection bias. Through extensive evaluation on synthetic and real world data we verify that our methods beat the state of the art both in detecting as well as characterizing selection bias.

Identifying Selection Bias from Observational Data

The world is currently seeing frequent local outbreaks of epidemics, such as COVID-19 and Monkeypox. Preventing further propagation of the outbreak requires prompt implementation of control measures, and a critical step is to quickly infer patient zero. This backtracking task is challenging for two reasons. First, due to the sudden emergence of local epidemics, information recording the spreading process is limited. Second, the spreading process has strong randomness. To address these challenges, we tailor a gnn-based model to establish the inverse statistical association between the current and initial state implicitly. This model uses contact topology and the current state of the local population to determine the possibility that each individual could be patient zero. We benchmark our model on data from important epidemiological models on five real temporal networks, showing performance significantly superior to previous methods. We also demonstrate that our method is robust to missing information about contact structure or current state. Further, we find the individuals assigned higher inferred possibility by model are closer to patient zero in terms of core number and the activity sequence recording the times at which the individual had contact with other nodes.

Inferring Patient Zero on Temporal Networks via Graph Neural Networks

Embedding tables are usually huge in click-through rate (CTR) prediction models. To train and deploy the CTR models efficiently and economically, it is necessary to compress their embedding tables at the training stage. To this end, we formulate a novel quantization training framework to compress the embeddings from the training stage, termed low-precision training. Further, we provide theoretical analysis on its convergence. The results show that stochastic weight quantization is more suitable for low-precision training than deterministic weight quantization. To reduce the accuracy degradation, we propose adaptive low-precision training (ALPT) to learn the step size (i.e., the quantization resolution) adaptively. Experiments with CTR models on two real-world datasets confirm our analysis and show that ALPT can significantly improve prediction accuracy, especially at extremely low bit widths. For the first time in CTR models, we successfully train 8-bit embeddings without sacrificing prediction accuracy. The code of ALPT is publicly available.

Adaptive Low-Precision Training for Embeddings in Click-Through Rate Prediction

Adversarial attacks on thermal infrared imaging expose the risk of related applications. Estimating the security of these systems is essential for safely deploying them in the real world. In many cases, realizing the attacks in the physical space requires elaborate special perturbations. These solutions are often \emph{impractical} and \emph{attention-grabbing}. To address the need for a physically practical and stealthy adversarial attack, we introduce \textsc{HotCold} Block, a novel physical attack for infrared detectors that hide persons utilizing the wearable Warming Paste and Cooling Paste. By attaching these readily available temperature-controlled materials to the body, \textsc{HotCold} Block evades human eyes efficiently. Moreover, unlike existing methods that build adversarial patches with complex texture and structure features, \textsc{HotCold} Block utilizes an SSP-oriented adversarial optimization algorithm that enables attacks with pure color blocks and explores the influence of size, shape, and position on attack performance. Extensive experimental results in both digital and physical environments demonstrate the performance of our proposed \textsc{HotCold} Block. \emph{Code is available: https://github.com/weihui1308/HOTCOLDBlock}.

Unsupervised Deep Embedded Fusion Representation of Single-cell Transcriptomics

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