Bayesian modeling of ChIP-chip data using latent variables

<p>Abstract</p> <p>Background</p> <p>The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone modifications in animals and plants. Various methods have been proposed in the literature for analyzing the ChIP-chip data, such as the sliding window methods, the hidden Markov model-based methods, and Bayesian methods. Although, due to the integrated consideration of uncertainty of the models and model parameters, Bayesian methods can potentially work better than the other two classes of methods, the existing Bayesian methods do not perform satisfactorily. They usually require multiple replicates or some extra experimental information to parametrize the model, and long CPU time due to involving of MCMC simulations.</p> <p>Results</p> <p>In this paper, we propose a Bayesian latent model for the ChIP-chip data. The new model mainly differs from the existing Bayesian models, such as the joint deconvolution model, the hierarchical gamma mixture model, and the Bayesian hierarchical model, in two respects. Firstly, it works on the difference between the averaged treatment and control samples. This enables the use of a simple model for the data, which avoids the probe-specific effect and the sample (control/treatment) effect. As a consequence, this enables an efficient MCMC simulation of the posterior distribution of the model, and also makes the model more robust to the outliers. Secondly, it models the neighboring dependence of probes by introducing a latent indicator vector. A truncated Poisson prior distribution is assumed for the latent indicator variable, with the rationale being justified at length.</p> <p>Conclusion</p> <p>The Bayesian latent method is successfully applied to real and ten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results indicate that the Bayesian latent method can outperform other methods, especially when the data contain outliers.</p

Immune infiltration and a necroptosis-related gene signature for predicting the prognosis of patients with cervical cancer

Background: Cervical cancer (CC), the fourth most common cancer among women worldwide, has high morbidity and mortality. Necroptosis is a newly discovered form of cell death that plays an important role in cancer development, progression, and metastasis. However, the expression of necroptosis-related genes (NRGs) in CC and their relationship with CC prognosis remain unclear. Therefore, we screened the signature NRGs in CC and constructed a risk prognostic model.Methods: We downloaded gene data and clinical information of patients with cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) from The Cancer Genome Atlas (TCGA) database. We performed functional enrichment analysis on the differentially expressed NRGs (DENRGs). We constructed prognostic models and evaluated them by Cox and LASSO regressions for DENRGs, and validated them using the International Cancer Genome Consortium (ICGC) dataset. We used the obtained risk score to classify patients into high- and low-risk groups. We employed the ESTIMATE and single sample gene set enrichment analysis (ssGSEA) algorithms to explore the relationship between the risk score and the clinical phenotype and the tumor immune microenvironment.Results: With LASSO regression, we established a prognostic model of CC including 16 signature DENRGs (TMP3, CHMP4C, EEF1A1, FASN, TNF, S100A10, IL1A, H1.2, SLC25A5, GLTP, IFNG, H2AC13, TUBB4B, AKNA, TYK2, and H1.5). The risk score was associated with poor prognosis in CC. Survival was lower in the high-risk group than the low-risk group. The nomogram based on the risk score, T stage, and N stage showed good prognostic predictive power. We found significant differences in immune scores, immune infiltration analysis, and immune checkpoints between the high- and low-risk groups (p &lt; 0.05).Conclusion: We screened for DENRGs based on the TCGA database by using bioinformatics methods, and constructed prognostic models based on the signature DENRGs, which we confirmed as possibly having important biological functions in CC. Our study provides a new perspective on CC prognosis and immunity, and offers a series of new targets for future treatment

Recursively Summarizing Enables Long-Term Dialogue Memory in Large Language Models

Most open-domain dialogue systems suffer from forgetting important information, especially in a long-term conversation. Existing works usually train the specific retriever or summarizer to obtain key information from the past, which is time-consuming and highly depends on the quality of labeled data. To alleviate this problem, we propose to recursively generate summaries/ memory using large language models (LLMs) to enhance long-term memory ability. Specifically, our method first stimulates LLMs to memorize small dialogue contexts and then recursively produce new memory using previous memory and following contexts. Finally, the LLM can easily generate a highly consistent response with the help of the latest memory. We evaluate our method using ChatGPT and text-davinci-003, and the experiments on the widely-used public dataset show that our method can generate more consistent responses in a long-context conversation. Notably, our method is a potential solution to enable the LLM to model the extremely long context. Code and scripts will be released later

Continuously Controllable Facial Expression Editing in Talking Face Videos

Recently audio-driven talking face video generation has attracted considerable attention. However, very few researches address the issue of emotional editing of these talking face videos with continuously controllable expressions, which is a strong demand in the industry. The challenge is that speech-related expressions and emotion-related expressions are often highly coupled. Meanwhile, traditional image-to-image translation methods cannot work well in our application due to the coupling of expressions with other attributes such as poses, i.e., translating the expression of the character in each frame may simultaneously change the head pose due to the bias of the training data distribution. In this paper, we propose a high-quality facial expression editing method for talking face videos, allowing the user to control the target emotion in the edited video continuously. We present a new perspective for this task as a special case of motion information editing, where we use a 3DMM to capture major facial movements and an associated texture map modeled by a StyleGAN to capture appearance details. Both representations (3DMM and texture map) contain emotional information and can be continuously modified by neural networks and easily smoothed by averaging in coefficient/latent spaces, making our method simple yet effective. We also introduce a mouth shape preservation loss to control the trade-off between lip synchronization and the degree of exaggeration of the edited expression. Extensive experiments and a user study show that our method achieves state-of-the-art performance across various evaluation criteria.Comment: Demo video: https://youtu.be/WD-bNVya6k

Food protein-stabilized nanoemulsions as potential delivery systems for poorly water-soluble drugs: preparation, in vitro characterization, and pharmacokinetics in rats

Nanoemulsions stabilized by traditional emulsifiers raise toxicological concerns for long-term treatment. The present work investigates the potential of food proteins as safer stabilizers for nanoemulsions to deliver hydrophobic drugs. Nanoemulsions stabilized by food proteins (soybean protein isolate, whey protein isolate, β-lactoglobulin) were prepared by high-pressure homogenization. The toxicity of the nanoemulsions was tested in Caco-2 cells using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide viability assay. In vivo absorption in rats was also evaluated. Food protein-stabilized nanoemulsions, with small particle size and good size distribution, exhibited better stability and biocompatibility compared with nanoemulsions stabilized by traditional emulsifiers. Moreover, β-lactoglobulin had a better emulsifying capacity and biocompatibility than the other two food proteins. The pancreatic degradation of the proteins accelerated drug release. It is concluded that an oil/water nanoemulsion system with good biocompatibility can be prepared by using food proteins as emulsifiers, allowing better and more rapid absorption of lipophilic drugs

Unsupervised domain adaptation through transferring both the source-knowledge and target-relatedness simultaneously

Unsupervised domain adaptation (UDA) is an emerging research topic in the field of machine learning and pattern recognition, which aims to help the learning of unlabeled target domain by transferring knowledge from the source domain. To perform UDA, a variety of methods have been proposed, most of which concentrate on the scenario of single source and the single target domain (1S1T). However, in real applications, usually single source domain with multiple target domains are involved (1SmT), which cannot be handled directly by those 1S1T models. Unfortunately, although a few related works on 1SmT UDA have been proposed, nearly none of them model the source domain knowledge and leverage the target-relatedness jointly. To overcome these shortcomings, we herein propose a more general 1SmT UDA model through transferring both the source-knowledge and target-relatedness, UDA-SKTR for short. In this way, not only the supervision knowledge from the source domain but also the potential relatedness among the target domains are simultaneously modeled for exploitation in the process of 1SmT UDA. In addition, we construct an alternating optimization algorithm to solve the variables of the proposed model with a convergence guarantee. Finally, through extensive experiments on both benchmark and real datasets, we validate the effectiveness and superiority of the proposed method

Cotton boll localization method based on point annotation and multi-scale fusion

Cotton is an important source of fiber. The precise and intelligent management of cotton fields is the top priority of cotton production. Many intelligent management methods of cotton fields are inseparable from cotton boll localization, such as automated cotton picking, sustainable boll pest control, boll maturity analysis, and yield estimation. At present, object detection methods are widely used for crop localization. However, object detection methods require relatively expensive bounding box annotations for supervised learning, and some non-object regions are inevitably included in the annotated bounding boxes. The features of these non-object regions may cause misjudgment by the network model. Unlike bounding box annotations, point annotations are less expensive to label and the annotated points are only likely to belong to the object. Considering these advantages of point annotation, a point annotation-based multi-scale cotton boll localization method is proposed, called MCBLNet. It is mainly composed of scene encoding for feature extraction, location decoding for localization prediction and localization map fusion for multi-scale information association. To evaluate the robustness and accuracy of MCBLNet, we conduct experiments on our constructed cotton boll localization (CBL) dataset (300 in-field cotton boll images). Experimental results demonstrate that MCBLNet method improves by 49.4% average precision on CBL dataset compared with typically point-based localization state-of-the-arts. Additionally, MCBLNet method outperforms or at least comparable with common object detection methods