Modeling Gene Networks in Saccharomyces cerevisiae

Detailed and innovative analysis of gene regulatory network structures may reveal novel insights to biological mechanisms. Here we study how gene regulatory network in Saccharomyces cerevisiae can differ under aerobic and anaerobic conditions. To achieve this, we discretized the gene expression profiles and calculated the self-entropy of down- and upregulation of gene expression as well as joint entropy. Based on these quantities the uncertainty coefficient was calculated for each gene triplet, following which, separate gene logic networks were constructed for the aerobic and anaerobic conditions. Four structural parameters such as average degree, average clustering coefficient, average shortest path, and average betweenness were used to compare the structure of the corresponding aerobic and anaerobic logic networks. Five genes were identified to be putative key components of the two energy metabolisms. Furthermore, community analysis using the Newman fast algorithm revealed two significant communities for the aerobic but only one for the anaerobic network. David Gene Functional Classification suggests that, under aerobic conditions, one such community reflects the cell cycle and cell replication, while the other one is linked to the mitochondrial respiratory chain function

Bilateral-Fuser: A Novel Multi-cue Fusion Architecture with Anatomical-aware Tokens for Fovea Localization

Accurate localization of fovea is one of the primary steps in analyzing retinal diseases since it helps prevent irreversible vision loss. Although current deep learning-based methods achieve better performance than traditional methods, there still remain challenges such as utilizing anatomical landmarks insufficiently, sensitivity to diseased retinal images and various image conditions. In this paper, we propose a novel transformer-based architecture (Bilateral-Fuser) for multi-cue fusion. This architecture explicitly incorporates long-range connections and global features using retina and vessel distributions for robust fovea localization. We introduce a spatial attention mechanism in the dual-stream encoder for extracting and fusing self-learned anatomical information. This design focuses more on features distributed along blood vessels and significantly decreases computational costs by reducing token numbers. Our comprehensive experiments show that the proposed architecture achieves state-of-the-art performance on two public and one large-scale private datasets. We also present that the Bilateral-Fuser is more robust on both normal and diseased retina images and has better generalization capacity in cross-dataset experiments.Comment: This paper is prepared for IEEE TRANSACTIONS ON MEDICAL IMAGIN

An Event-Triggered Low-Cost Tactile Perception System for Social Robot's Whole Body Interaction

The social interaction is one of the necessary skills for social robots to better integrate into human society. However, current social robots interact mainly through audio and visual means with little reliance on haptic interaction. There still exist many obstacles for social robots to interact through touch: 1) the complex manufacturing process of the tactile sensor array is the main obstacle to lowering the cost of production; 2) the haptic interaction mode is complex and diverse. There are no social robot interaction standards and data sets for tactile interactive behavior in the public domain. In view of this, our research looks into the following aspects of tactile perception system: 1) Development of low-cost tactile sensor array, including sensor principle, simulation, manufacture, front-end electronics, examination, then applied to the social robot's whole body; 2) Establishment of the tactile interactive model and an event-triggered perception model in a social interactive application for the social robot, then design preprocessing and classification algorithm. In this research, we use k-nearest neighbors, tree, support vector machine and other classification algorithms to classify touch behaviors into six different classes. In particular, the cosine k-nearest neighbors and quadratic support vector machine achieve an overall mean accuracy rate of more than 68%, with an individual accuracy rate of more than 80%. In short, our research provides new directions in achieving low-cost intelligent touch interaction for social robots in a real environment. The low-cost tactile sensor array solution and interactive models are expected to be applied to social robots on a large scale

Intention Understanding in Human-Robot Interaction Based on Visual-NLP Semantics

With the rapid development of robotic and AI technology in recent years, human-robot interaction has made great advancement, making practical social impact. Verbal commands are one of the most direct and frequently used means for human-robot interaction. Currently, such technology can enable robots to execute pre-defined tasks based on simple and direct and explicit language instructions, e.g., certain keywords must be used and detected. However, that is not the natural way for human to communicate. In this paper, we propose a novel task-based framework to enable the robot to comprehend human intentions using visual semantics information, such that the robot is able to satisfy human intentions based on natural language instructions (total three types, namely clear, vague, and feeling, are defined and tested). The proposed framework includes a language semantics module to extract the keywords despite the explicitly of the command instruction, a visual object recognition module to identify the objects in front of the robot, and a similarity computation algorithm to infer the intention based on the given task. The task is then translated into the commands for the robot accordingly. Experiments are performed and validated on a humanoid robot with a defined task: to pick the desired item out of multiple objects on the table, and hand over to one desired user out of multiple human participants. The results show that our algorithm can interact with different types of instructions, even with unseen sentence structures

Stepwise Feature Fusion: Local Guides Global

Colonoscopy, currently the most efficient and recognized colon polyp detection technology, is necessary for early screening and prevention of colorectal cancer. However, due to the varying size and complex morphological features of colonic polyps as well as the indistinct boundary between polyps and mucosa, accurate segmentation of polyps is still challenging. Deep learning has become popular for accurate polyp segmentation tasks with excellent results. However, due to the structure of polyps image and the varying shapes of polyps, it is easy for existing deep learning models to overfit the current dataset. As a result, the model may not process unseen colonoscopy data. To address this, we propose a new state-of-the-art model for medical image segmentation, the SSFormer, which uses a pyramid Transformer encoder to improve the generalization ability of models. Specifically, our proposed Progressive Locality Decoder can be adapted to the pyramid Transformer backbone to emphasize local features and restrict attention dispersion. The SSFormer achieves state-of-the-art performance in both learning and generalization assessment

Down Syndrome detection with Swin Transformer architecture

Objective: Down Syndrome, also known as Trisomy 21, is a severe genetic disease caused by an extra chromosome 21. For the detection of Trisomy 21, despite those statistical methods have been widely used for screening, karyotyping remains the gold standard and the first level of testing for diagnosis. Due to karyotyping being a time-consuming and labour-intensive procedure, Computer Vision methodologies have been explored to automate the karyotyping process for decades. However, few studies have focused on Down Syndrome detection with the Transformer technique. This study develops a Down-Syndrome-Detector (DSD) architecture based on the Transformer structure, which includes a segmentation module, an alignment module, a classification module, and a Down Syndrome indicator. Methods: The segmentation and classification modules are designed by homogeneous transfer learning at the model level. Transfer learning techniques enable a network to share weights learned from the source domain (e.g., millions of data in ImageNet) and optimize the weights with limited labeled data in the target domain (e.g., less than 6,000 images in BioImLab). The Align-Module is designed to process the segmentation output to fit the classification dataset, and the Down Syndrome Indicator identifies a Down Syndrome case from the classification output. Results: Experiments are first performed on two public datasets BioImLab (119 cases) and Advanced Digital Imaging Research (ADIR, 180 cases). Our performance metrics indicate the good ability of segmentation and classification modules of DSD. Then, the DS detection performance of DSD is evaluated on a private dataset consisting of 1084 cells (including 20 DS cells from 2 singleton cases): 90.0% and 86.1% for cell-level TPR and TNR; 100% and 96.08% for case-level TPR and TNR, respectively. Conclusion: This study develops a pipeline based on the modern Transformer architecture for the detection of Down Syndrome from original metaphase micrographs. Both segmentation and classification models developed in this study are assessed using public datasets with commonly used metrics, and both achieved good results. The DSDproposed in this study reported satisfactory singleton case-specific DS detection results. Significance: As verified by a medical specialist, the developed method may improve Down Syndrome detection efficiency by saving human labor and improving clinical practice

Film-GAN: towards realistic analog film photo generation

In recent years, the art of film photography has reemerged as a topic of interest for both researchers and the community. Unlike digital photography, which relies on pixels to capture and store information, film photography employs silver halide to capture the scene. This process imbues film photos with a unique colour and textured graininess not present in digital photography. In this paper, we propose Film-GAN, the first Generative Adversarial Network (GAN)-based method for translating digital images to film. Film-GAN generates a corresponding film transformation of the input image based on the desired reference film style. To improve the realism of the generated images, we introduce the colour-noise-encoding (CNE) network, which extracts the colour and graininess of the reference image separately. Our experimental simulations demonstrate that Film-GAN outperforms other state-of-the-art approaches on multiple datasets. Based on evaluations from both professional photographers and amateur photography enthusiasts, the images generated by Film-GAN also received a higher number of votes, indicating its ability to produce better film-effect images