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For many RNA molecules, the secondary structure is essential for the correct function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time. Traditional RNA secondary structure prediction algorithms are primarily based on thermodynamic models through free energy minimization, which imposes strong prior assumptions and is slow to run. Here, we propose a deep learning-based method, called UFold, for RNA secondary structure prediction, trained directly on annotated data and base-pairing rules. UFold proposes a novel image-like representation of RNA sequences, which can be efficiently processed by Fully Convolutional Networks (FCNs). We benchmark the performance of UFold on both within- and cross-family RNA datasets. It significantly outperforms previous methods on within-family datasets, while achieving a similar performance as the traditional methods when trained and tested on distinct RNA families. UFold is also able to predict pseudoknots accurately. Its prediction is fast with an inference time of about 160 ms per sequence up to 1500 bp in length. An online web server running UFold is available at https://ufold.ics.uci.edu. Code is available at https://github.com/uci-cbcl/UFold.

 

This paper presents a policy-driven sequential image augmentation approach for image-related tasks. Our approach applies a sequence of image transformations (e.g., translation, rotation) over a training image, one transformation at a time, with the augmented image from the previous time step treated as the input for the next transformation. This sequential data augmentation substantially improves sample diversity, leading to improved test performance, especially for data-hungry models (e.g., deep neural networks). However, the search for the optimal transformation of each image at each time step of the sequence has high complexity due to its combination nature. To address this challenge, we formulate the search task as a sequential decision process and introduce a deep policy network that learns to produce transformations based on image content. We also develop an iterative algorithm to jointly train a classifier and the policy network in the reinforcement learning setting. The immediate reward of a potential transformation is defined to encourage transformations producing hard samples for the current classifier. At each iteration, we employ the policy network to augment the training dataset, train a classifier with the augmented data, and train the policy net with the aid of the classifier. We apply the above approach to both public image classification benchmarks and a newly collected image dataset for material recognition. Comparisons to alternative augmentation approaches show that our policy-driven approach achieves comparable or improved classification performance while using significantly fewer augmented images. The code is available at https://github.com/Paul-LiPu/rl_autoaug. 

Abstract Motivation Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) provides new opportunities to dissect epigenomic heterogeneity and elucidate transcriptional regulatory mechanisms. However, computational modeling of scATAC-seq data is challenging due to its high dimension, extreme sparsity, complex dependencies and high sensitivity to confounding factors from various sources. Results Here, we propose a new deep generative model framework, named SAILER, for analyzing scATAC-seq data. SAILER aims to learn a low-dimensional nonlinear latent representation of each cell that defines its intrinsic chromatin state, invariant to extrinsic confounding factors like read depth and batch effects. SAILER adopts the conventional encoder-decoder framework to learn the latent representation but imposes additional constraints to ensure the independence of the learned representations from the confounding factors. Experimental results on both simulated and real scATAC-seq datasets demonstrate that SAILER learns better and biologically more meaningful representations of cells than other methods. Its noise-free cell embeddings bring in significant benefits in downstream analyses: clustering and imputation based on SAILER result in 6.9% and 18.5% improvements over existing methods, respectively. Moreover, because no matrix factorization is involved, SAILER can easily scale to process millions of cells. We implemented SAILER into a software package, freely available to all for large-scale scATAC-seq data analysis. Availability and implementation The software is publicly available at https://github.com/uci-cbcl/SAILER. Supplementary information Supplementary data are available at Bioinformatics online. 

Knowledge Distillation (KD) is a widely used technique to transfer knowledge from pre-trained teacher models to (usually more lightweight) student models. However, in certain situations, this technique is more of a curse than a blessing. For instance, KD poses a potential risk of exposing intellectual properties (IPs): even if a trained machine learning model is released in ``black boxes'' (e.g., as executable software or APIs without open-sourcing code), it can still be replicated by KD through imitating input-output behaviors. To prevent this unwanted effect of KD, this paper introduces and investigates a concept called : a specially trained teacher network that yields nearly the same performance as a normal one, but would significantly degrade the performance of student models learned by imitating it. We propose a simple yet effective algorithm to build the nasty teacher, called . Specifically, we aim to maximize the difference between the output of the nasty teacher and a normal pre-trained network. Extensive experiments on several datasets demonstrate that our method is effective on both standard KD and data-free KD, providing the desirable KD-immunity to model owners for the first time. We hope our preliminary study can draw more awareness and interest in this new practical problem of both social and legal importance. Our codes and pre-trained models can be found at: $\url{https://github.com/VITA-Group/Nasty-Teacher}$. 

Characterizing genome-wide binding profiles of transcription factors (TFs) is essential for understanding biological processes. Although techniques have been developed to assess binding profiles within a population of cells, determining them at a single-cell level remains elusive. Here, we report scFAN (single-cell factor analysis network), a deep learning model that predicts genome-wide TF binding profiles in individual cells. scFAN is pretrained on genome-wide bulk assay for transposase-accessible chromatin sequencing (ATAC-seq), DNA sequence, and chromatin immunoprecipitation sequencing (ChIP-seq) data and uses single-cell ATAC-seq to predict TF binding in individual cells. We demonstrate the efficacy of scFAN by both studying sequence motifs enriched within predicted binding peaks and using predicted TFs for discovering cell types. We develop a new metric “TF activity score” to characterize each cell and show that activity scores can reliably capture cell identities. scFAN allows us to discover and study cellular identities and heterogeneity based on chromatin accessibility profiles.