Interpretable Modeling of Single-cell perturbation Responses to Novel Drugs Using Cycle Consistence Learning

Phenotype-based screening has attracted much attention for identifying cell-active compounds. Transcriptional and proteomic profiles of cell population or single cells are informative phenotypic measures of cellular responses to perturbations. In this paper, we proposed a deep learning framework based on encoder-decoder architecture that maps the initial cellular states to a latent space, in which we assume the effects of drug perturbation on cellular states follow linear additivity. Next, we introduced the cycle consistency constraints to enforce that initial cellular state subjected to drug perturbations would produce the perturbed cellular responses, and, conversely, removal of drug perturbation from the perturbed cellular states would restore the initial cellular states. The cycle consistency constraints and linear modeling in latent space enable to learn interpretable and transferable drug perturbation representations, so that our model can predict cellular response to unseen drugs. We validated our model on three different types of datasets, including bulk transcriptional responses, bulk proteomic responses, and single-cell transcriptional responses to drug perturbations. The experimental results show that our model achieves better performance than existing state-of-the-art methods

RecapNet: Action Proposal Generation Mimicking Human Cognitive Process

International audienceGenerating action proposals in untrimmed videos is a challenging task, since video sequences usually contain lots of irrelevant contents and the duration of an action instance is arbitrary. The quality of action proposals is key to action detection performance. The previous methods mainly rely on sliding windows or anchor boxes to cover all ground-truth actions, but this is infeasible and computationally inefficient. To this end, this article proposes a RecapNet--a novel framework for generating action proposal, by mimicking the human cognitive process of understanding video content. Specifically, this RecapNet includes a residual causal convolution module to build a short memory of the past events, based on which the joint probability actionness density ranking mechanism is designed to retrieve the action proposals. The RecapNet can handle videos with arbitrary length and more important, a video sequence will need to be processed only in one single pass in order to generate all action proposals. The experiments show that the proposed RecapNet outperforms the state of the art under all metrics on the benchmark THUMOS14 and ActivityNet-1.3 datasets. The code is available publicly at https://github.com/tianwangbuaa/RecapNet

TVPR: Text-to-Video Person Retrieval and a New Benchmark

Most existing methods for text-based person retrieval focus on text-to-image person retrieval. Nevertheless, due to the lack of dynamic information provided by isolated frames, the performance is hampered when the person is obscured in isolated frames or variable motion details are given in the textual description. In this paper, we propose a new task called Text-to-Video Person Retrieval(TVPR) which aims to effectively overcome the limitations of isolated frames. Since there is no dataset or benchmark that describes person videos with natural language, we construct a large-scale cross-modal person video dataset containing detailed natural language annotations, such as person's appearance, actions and interactions with environment, etc., termed as Text-to-Video Person Re-identification (TVPReid) dataset, which will be publicly available. To this end, a Text-to-Video Person Retrieval Network (TVPRN) is proposed. Specifically, TVPRN acquires video representations by fusing visual and motion representations of person videos, which can deal with temporal occlusion and the absence of variable motion details in isolated frames. Meanwhile, we employ the pre-trained BERT to obtain caption representations and the relationship between caption and video representations to reveal the most relevant person videos. To evaluate the effectiveness of the proposed TVPRN, extensive experiments have been conducted on TVPReid dataset. To the best of our knowledge, TVPRN is the first successful attempt to use video for text-based person retrieval task and has achieved state-of-the-art performance on TVPReid dataset. The TVPReid dataset will be publicly available to benefit future research

A comparative photocatalytic study of TiO2 loaded on three natural clays with different morphologies

[EN] In this work, a sol-gel method was used to load TiO2 nanoparticles on three clays (kaolinite, halloysite and palygorskite) with different morphologies (plates, tubes, and rods with micro tunnels), and then the photocatalytic performance of obtained clay-TiO2 composites for degradation of methyl orange was comparatively investigated. The results surprisingly show that the trend of photocatalytic performance of composites is opposite to that of special surface area of corresponding clays. By concentrated analysis of the loading status of TiO2, the lowest photocatalytic efficiency of palygorskite-TiO2 composite is mainly ascribed to (1) the aggregation of TiO2 nanoparticles on Pal surface, not the amount of TiO2 and (2) the relatively weak adsorption of Pal to methyl orange. The additional adsorption of hydroxyl surface of Kaol to methyl orange and little TiO2 in the lumen of Hal tube leads to the better photocatalytic performance of kaolinite-TiO2 composite than halloysite-TiO2 composite. Finally, kaolinite is proved to be an excellent carrier to support nano TiO2 resulting in a good photocatalytic performance and cycle stability, and the study can provide a direct guidance to select appropriate clay-photocatalyst composites for different practical applications.This work is supported by the National Natural Science Foundation of China (41502032) and the Fundamental Research Funds for the Central Universities (2019XKQYMS76).Wu, A.; Wang, D.; Wei, C.; Zhang, X.; Liu, Z.; Feng, P.; Ou, X.... (2019). A comparative photocatalytic study of TiO2 loaded on three natural clays with different morphologies. Applied Clay Science. 183:1-12. https://doi.org/10.1016/j.clay.2019.105352S11218

Draft genome sequence of the mulberry tree Morus notabilis

Human utilization of the mulberry–silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species’ spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant–herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants

Détection et suivi de la posture humaine dans les images fixes et les vidéos

Human pose estimation is a challenging problem in computer vision and shares all the difficulties of object detection. This thesis focuses on the problems of human pose estimation in still images or video, including the diversity of appearances, changes in scene illumination and confounding background clutter. To tackle these problems, we build a robust model consisting of the following components. First, the top-down and bottom-up methods are combined to estimation human pose. We extend the Pictorial Structure (PS) model to cooperate with annealed particle filter (APF) for robust multi-view pose estimation. Second, we propose an upper body based multiple mixture parts (MMP) model for human pose estimation that contains two stages. In the pre-estimation stage, there are three steps: upper body detection, model category estimation for upper body, and full model selection for pose estimation. In the estimation stage, we address the problem of a variety of human poses and activities. Finally, a Deep Convolutional Neural Network (DCNN) is introduced for human pose estimation. A Local Multi-Resolution Convolutional Neural Network (LMR-CNN) is proposed to learn the representation for each body part. Moreover, a LMR-CNN based hierarchical model is defined to meet the structural complexity of limb parts. The experimental results demonstrate the effectiveness of the proposed modelL’estimation de la pose du corps humain est un problème difficile en vision par ordinateur et les actions de toutes les difficultés de détection d’objet. Cette thèse se concentre sur les problèmes de l’estimation de la pose du corps humain dans les images ou vidéo, y compris la diversité des apparences, les changements de scène et l’éclairage de fond de confusion encombrement. Pour résoudre ces problèmes, nous construisons un modèle robuste comprenant les éléments suivants. Tout d’abord, les méthodes top-down et bottom-up sont combinés à l’estimation pose humaine. Nous étendons le modèle structure picturale (PS) de coopérer avec filtre à particules recuit (APF) pour robuste multi-vues estimation de la pose. Deuxièmement, nous proposons plusieurs parties de mélange à base (MMP) modèle d’une partie supérieure du corps pour l’estimation de la pose qui contient deux étapes. Dans la phase de pré-estimation, il y a trois étapes: la détection du haut du corps, catégorie estimation du modèle pour le haut du corps, et la sélection de modèle complet pour pose estimation. Dans l’étape de l’estimation, nous abordons le problème d’une variété de poses et les activités humaines. Enfin, le réseau de neurones à convolution (CNN) est introduit pour l’estimation de la pose. Un Local Multi-résolution réseau de neurones à convolution (LMR-CNN) est proposé pour apprendre la représentation pour chaque partie du corps. En outre, un modèle hiérarchique sur la base LMR-CNN est défini pour faire face à la complexité structurelle des parties de branche. Les résultats expérimentaux démontrent l’efficacité du modèle propos

Hierarchical graphical-based human pose estimation via local multi-resolution convolutional neural network

This paper addresses the problems of the graphical-based human pose estimation in still images, including the diversity of appearances and confounding background clutter. We present a new architecture for estimating human pose using a Convolutional Neural Network (CNN). Firstly, a Relative Mixture Deformable Model (RMDM) is defined by each pair of connected parts to compute the relative spatial information in the graphical model. Secondly, a Local Multi-Resolution Convolutional Neural Network (LMR-CNN) is proposed to train and learn the multi-scale representation of each body parts by combining different levels of part context. Thirdly, a LMR-CNN based hierarchical model is defined to explore the context information of limb parts. Finally, the experimental results demonstrate the effectiveness of the proposed deep learning approach for human pose estimation

Articulated human motion tracking with foreground learning

International audienceTracking the articulated human body is a challenging computer vision problem because of changes in body poses and their appearance. Pictorial structure (PS) models are widely used in 2D human pose estimation. In this work, we extend the PS models for robust 3D pose estimation, which includes two stages: multi-view human body parts detection by foreground learning and pose states updating by annealed particle filter (APF) and detection. Moreover, the image dataset F-PARSE was built for foreground training and flexible mixture of parts (FMP) model was used for foreground learning. Experimental results demonstrate the effectiveness of our foreground learning-based method

Exposing image resampling forgery by using linear parametric model

International audienceResampling forgery generally refers to as the technique that utilizes interpolation algorithm to maliciously geometrically transform a digital image or a portion of an image. This paper investigates the problem of image resampling detection based on the linear parametric model. First, we expose the periodic artifact of one-dimensional 1-D) resampled signal. After dealing with the nuisance parameters, together with Bayes’ rule, the detector is designed based on the probability of residual noise extracted from resampled signal using linear parametric model. Subsequently, we mainly study the characteristic of a resampled image. Meanwhile, it is proposed to estimate the probability of pixels’ noise and establish a practical Likelihood Ratio Test (LRT). Comparison with the state-of-the-art tests, numerical experiments show the relevance of our proposed algorithm with detecting uncompressed/compressed resampled images

Articulated pose estimation via multiple mixture parts model

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