Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration

Muilti-modality data are ubiquitous in biology, especially that we have entered the multi-omics era, when we can measure the same biological object (cell) from different aspects (omics) to provide a more comprehensive insight into the cellular system. When dealing with such multi-omics data, the first step is to determine the correspondence among different modalities. In other words, we should match data from different spaces corresponding to the same object. This problem is particularly challenging in the single-cell multi-omics scenario because such data are very sparse with extremely high dimensions. Secondly, matched single-cell multi-omics data are rare and hard to collect. Furthermore, due to the limitations of the experimental environment, the data are usually highly noisy. To promote the single-cell multi-omics research, we overcome the above challenges, proposing a novel framework to align and integrate single-cell RNA-seq data and single-cell ATAC-seq data. Our approach can efficiently map the above data with high sparsity and noise from different spaces to a low-dimensional manifold in a unified space, making the downstream alignment and integration straightforward. Compared with the other state-of-the-art methods, our method performs better in both simulated and real single-cell data. The proposed method is helpful for the single-cell multi-omics research. The improvement for integration on the simulated data is significant.

CLMB: deep contrastive learning for robust metagenomic binning

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic binning, clustering the assembled contigs into draft genomes. Despite the existing computational tools, most of them neglect one important property of the metagenomic data, that is, the noise. To further improve the metagenomic binning step and reconstruct better metagenomes, we propose a deep Contrastive Learning framework for Metagenome Binning (CLMB), which can efficiently eliminate the disturbance of noise and produce more stable and robust results. Essentially, instead of denoising the data explicitly, we add simulated noise to the training data and force the deep learning model to produce similar and stable representations for both the noise-free data and the distorted data. Consequently, the trained model will be robust to noise and handle it implicitly during usage. CLMB outperforms the previous state-of-the-art binning methods significantly, recovering the most near-complete genomes on almost all the benchmarking datasets (up to 17\% more reconstructed genomes compared to the second-best method). It also improves the performance of bin refinement, reconstructing 8-22 more high-quality genomes and 15-32 more middle-quality genomes than the second-best result. Impressively, in addition to being compatible with the binning refiner, single CLMB even recovers on average 15 more HQ genomes than the refiner of VAMB and Maxbin on the benchmarking datasets. CLMB is open-source and available at https://github.com/zpf0117b/CLMB/.

HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides

Identifying the targets of an antimicrobial peptide is a fundamental step in studying the innate immune response and combating antibiotic resistance, and more broadly, precision medicine and public health. There have been extensive studies on the statistical and computational approaches to identify (i) whether a peptide is an antimicrobial peptide (AMP) or a non-AMP and (ii) which targets are these sequences effective to (Gram-positive, Gram-negative, etc.). Despite the existing deep learning methods on this problem, most of them are unable to handle the small AMP classes (anti-insect, anti-parasite, etc.). And more importantly, some AMPs can have multiple targets, which the previous methods fail to consider. In this study, we build a diverse and comprehensive multi-label protein sequence database by collecting and cleaning amino acids from various AMP databases. To generate efficient representations and features for the small classes dataset, we take advantage of a protein language model trained on 250 million protein sequences. Based on that, we develop an end-to-end hierarchical multi-label deep forest framework, HMD-AMP, to annotate AMP comprehensively. After identifying an AMP, it further predicts what targets the AMP can effectively kill from eleven available classes. Extensive experiments suggest that our framework outperforms state-of-the-art models in both the binary classification task and the multi-label classification task, especially on the minor classes.The model is robust against reduced features and small perturbations and produces promising results. We believe HMD-AMP contributes to both the future wet-lab investigations of the innate structural properties of different antimicrobial peptides and build promising empirical underpinnings for precise medicine with antibiotics.

Generalized Anomaly Detection

We study anomaly detection for the case when the normal class consists of more than one object category. This is an obvious generalization of the standard one-class anomaly detection problem. However, we show that jointly using multiple one-class anomaly detectors to solve this problem yields poorer results as compared to training a single one-class anomaly detector on all normal object categories together. We further develop a new anomaly detector called DeepMAD that learns compact distinguishing features by exploiting the multiple normal objects categories. This algorithm achieves higher AUC values for different datasets compared to two top performing one-class algorithms that either are trained on each normal object category or jointly trained on all normal object categories combined. In addition to theoretical results we present empirical results using the CIFAR-10, fMNIST, CIFAR-100, and a new dataset we developed called RECYCLE.

Show Me the Whole World: Towards Entire Item Space Exploration for Interactive Personalized Recommendations

User interest exploration is an important and challenging topic in recommender systems, which alleviates the closed-loop effects between recommendation models and user-item interactions. Contextual bandit (CB) algorithms strive to make a good trade-off between exploration and exploitation so that users' potential interests have chances to expose. However, classical CB algorithms can only be applied to a small, sampled item set (usually hundreds), which forces the typical applications in recommender systems limited to candidate post-ranking, homepage top item ranking, ad creative selection, or online model selection (A/B test). In this paper, we introduce two simple but effective hierarchical CB algorithms to make a classical CB model (such as LinUCB and Thompson Sampling) capable to explore users' interest in the entire item space without limiting it to a small item set. We first construct a hierarchy item tree via a bottom-up clustering algorithm to organize items in a coarse-to-fine manner. Then we propose a hierarchical CB (HCB) algorithm to explore users' interest in the hierarchy tree. HCB takes the exploration problem as a series of decision-making processes, where the goal is to find a path from the root to a leaf node, and the feedback will be back-propagated to all the nodes in the path. We further propose a progressive hierarchical CB (pHCB) algorithm, which progressively extends visible nodes which reach a confidence level for exploration, to avoid misleading actions on upper-level nodes in the sequential decision-making process. Extensive experiments on two public recommendation datasets demonstrate the effectiveness and flexibility of our methods.

Orthogonal Graph Neural Networks

Graph neural networks (GNNs) have received tremendous attention due to their superiority in learning node representations. These models rely on message passing and feature transformation functions to encode the structural and feature information from neighbors. However, stacking more convolutional layers significantly decreases the performance of GNNs. Most recent studies attribute this limitation to the over-smoothing issue, where node embeddings converge to indistinguishable vectors. Through a number of experimental observations, we argue that the main factor degrading the performance is the unstable forward normalization and backward gradient resulted from the improper design of the feature transformation, especially for shallow GNNs where the over-smoothing has not happened. Therefore, we propose a novel orthogonal feature transformation, named Ortho-GConv, which could generally augment the existing GNN backbones to stabilize the model training and improve the model's generalization performance. Specifically, we maintain the orthogonality of the feature transformation comprehensively from three perspectives, namely hybrid weight initialization, orthogonal transformation, and orthogonal regularization. By equipping the existing GNNs (e.g. GCN, JKNet, GCNII) with Ortho-GConv, we demonstrate the generality of the orthogonal feature transformation to enable stable training, and show its effectiveness for node and graph classification tasks.

Crash Report Data Analysis for Creating Scenario-Wise, Spatio-Temporal Attention Guidance to Support Computer Vision-based Perception of Fatal Crash Risks

Reducing traffic fatalities and serious injuries is a top priority of the US Department of Transportation. The computer vision (CV)-based crash anticipation in the near-crash phase is receiving growing attention. The ability to perceive fatal crash risks earlier is also critical because it will improve the reliability of crash anticipation. Yet, annotated image data for training a reliable AI model for the early visual perception of crash risks are not abundant. The Fatality Analysis Reporting System contains big data of fatal crashes. It is a reliable data source for learning the relationship between driving scene characteristics and fatal crashes to compensate for the limitation of CV. Therefore, this paper develops a data analytics model, named scenario-wise, Spatio-temporal attention guidance, from fatal crash report data, which can estimate the relevance of detected objects to fatal crashes from their environment and context information. First, the paper identifies five sparse variables that allow for decomposing the 5-year fatal crash dataset to develop scenario-wise attention guidance. Then, exploratory analysis of location- and time-related variables of the crash report data suggests reducing fatal crashes to spatially defined groups. The group's temporal pattern is an indicator of the similarity of fatal crashes in the group. Hierarchical clustering and K-means clustering merge the spatially defined groups into six clusters according to the similarity of their temporal patterns. After that, association rule mining discovers the statistical relationship between the temporal information of driving scenes with crash features, for each cluster. The paper shows how the developed attention guidance supports the design and implementation of a preliminary CV model that can identify objects of a possibility to involve in fatal crashes from their environment and context information.

A Virtual Reality-based Training and Assessment System for Bridge Inspectors with an Assistant Drone

Over 600,000 bridges in the U.S. must be inspected every two years to identify flaws, defects, or potential problems that may need follow-up maintenance. An aerial robotic technology, Unmanned Aerial Vehicles (drones), has been adopted for bridge inspection for improving safety, efficiency, and cost-effectiveness. Although drones have an autonomous operation mode, keeping inspectors in the loop is still necessary for complex tasks like bridge inspection. Therefore, inspectors need to develop the skill and confidence in operating drones in their jobs. This paper presents the design and development of a virtual reality-based system for training inspectors who are assisted by a drone in the bridge inspection. The system is composed of four integrated modules: a simulated bridge inspection developed in Unity, an interface that allows a trainee to operate the drone in simulation using a remote controller, monitoring and analysis that analyzes data to provide real-time, in-task feedback to trainees to assist their learning, and a post-study assessment for accelerating the learning of trainees. The paper also conducts a small-size experimental study to illustrate the functionality of this system and its helpfulness for establishing the inspector-drone partnership. The developed system has built a modeling and analysis foundation for exploring advanced solutions to human-drone cooperative inspection and human sensor-based human-drone interaction.

Towards Vivid and Diverse Image Colorization with Generative Color Prior

Colorization has attracted increasing interest in recent years. Classic reference-based methods usually rely on external color images for plausible results. A large image database or online search engine is inevitably required for retrieving such exemplars. Recent deep-learning-based methods could automatically colorize images at a low cost. However, unsatisfactory artifacts and incoherent colors are always accompanied. In this work, we aim at recovering vivid colors by leveraging the rich and diverse color priors encapsulated in a pretrained Generative Adversarial Networks (GAN). Specifically, we first "retrieve" matched features (similar to exemplars) via a GAN encoder and then incorporate these features into the colorization process with feature modulations. Thanks to the powerful generative color prior and delicate designs, our method could produce vivid colors with a single forward pass. Moreover, it is highly convenient to obtain diverse results by modifying GAN latent codes. Our method also inherits the merit of interpretable controls of GANs and could attain controllable and smooth transitions by walking through GAN latent space. Extensive experiments and user studies demonstrate that our method achieves superior performance than previous works.