A method for rapid similarity analysis of RNA secondary structures

BACKGROUND: Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. RESULTS: Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. CONCLUSION: The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis

Spatial-Temporal Convolutional Attention for Mapping Functional Brain Networks

Using functional magnetic resonance imaging (fMRI) and deep learning to explore functional brain networks (FBNs) has attracted many researchers. However, most of these studies are still based on the temporal correlation between the sources and voxel signals, and lack of researches on the dynamics of brain function. Due to the widespread local correlations in the volumes, FBNs can be generated directly in the spatial domain in a self-supervised manner by using spatial-wise attention (SA), and the resulting FBNs has a higher spatial similarity with templates compared to the classical method. Therefore, we proposed a novel Spatial-Temporal Convolutional Attention (STCA) model to discover the dynamic FBNs by using the sliding windows. To validate the performance of the proposed method, we evaluate the approach on HCP-rest dataset. The results indicate that STCA can be used to discover FBNs in a dynamic way which provide a novel approach to better understand human brain.Comment: 5 pages, 5 figures, submitted to 20th IEEE International Symposium on Biomedical Imaging (ISBI 2023

Robust Core-Periphery Constrained Transformer for Domain Adaptation

Unsupervised domain adaptation (UDA) aims to learn transferable representation across domains. Recently a few UDA works have successfully applied Transformer-based methods and achieved state-of-the-art (SOTA) results. However, it remains challenging when there exists a large domain gap between the source and target domain. Inspired by humans' exceptional transferability abilities to adapt knowledge from familiar to uncharted domains, we try to apply the universally existing organizational structure in the human functional brain networks, i.e., the core-periphery principle to design the Transformer and improve its UDA performance. In this paper, we propose a novel brain-inspired robust core-periphery constrained transformer (RCCT) for unsupervised domain adaptation, which brings a large margin of performance improvement on various datasets. Specifically, in RCCT, the self-attention operation across image patches is rescheduled by an adaptively learned weighted graph with the Core-Periphery structure (CP graph), where the information communication and exchange between images patches are manipulated and controlled by the connection strength, i.e., edge weight of the learned weighted CP graph. Besides, since the data in domain adaptation tasks can be noisy, to improve the model robustness, we intentionally add perturbations to the patches in the latent space to ensure generating robust learned weighted core-periphery graphs. Extensive evaluations are conducted on several widely tested UDA benchmarks. Our proposed RCCT consistently performs best compared to existing works, including 88.3\% on Office-Home, 95.0\% on Office-31, 90.7\% on VisDA-2017, and 46.0\% on DomainNet.Comment: Core-Periphery, ViT, Unsupervised domain adaptatio

Asymptotic enumeration of some RNA secondary structures

AbstractIn this paper, we derive recursions of some RNA secondary structures with certain properties under two new representations. Furthermore, by making use of methods of asymptotic analysis and generating functions we present asymptotic enumeration of these RNA secondary structures

Consumer Preference on Traceable Information of Dairy Products

Diary industry in China has been in deep crisis since a series of quality scandals were exposed to public in 2008. Thanks to the traceability system in dairy supply chain and the growth of the internet, providing traceable dairy product information to the public is viewed as one of the best ways, mostly in terms of feasibility , to overcome the trust crisis and to promote the development of the dairy industry in China. However, among the tons of information available from the supply chain, there is a lack of knowledge on consumer preference. Based on choice-based conjoint analysis, this paper investigated consumer preference on dairy product traceable information query service. Specifically , this paper measured the value that consumers place on the dairy product traceable information. We used a multinomial logit model to estimate the preferences and offered 3 ways to explain the value of each kind of information that consumers are concerned about. Results indicate that different consumer groups hold different preferences

MedEdit: Model Editing for Medical Question Answering with External Knowledge Bases

Large Language Models (LLMs), although powerful in general domains, often perform poorly on domain-specific tasks like medical question answering (QA). Moreover, they tend to function as "black-boxes," making it challenging to modify their behavior. Addressing this, our study delves into model editing utilizing in-context learning, aiming to improve LLM responses without the need for fine-tuning or retraining. Specifically, we propose a comprehensive retrieval strategy to extract medical facts from an external knowledge base, and then we incorporate them into the query prompt for the LLM. Focusing on medical QA using the MedQA-SMILE dataset, we evaluate the impact of different retrieval models and the number of facts provided to the LLM. Notably, our edited Vicuna model exhibited an accuracy improvement from 44.46% to 48.54%. This work underscores the potential of model editing to enhance LLM performance, offering a practical approach to mitigate the challenges of black-box LLMs.Comment: 6 page

Matching Exemplar as Next Sentence Prediction (MeNSP): Zero-shot Prompt Learning for Automatic Scoring in Science Education

Developing models to automatically score students' written responses to science problems is critical for science education. However, collecting and labeling sufficient student responses for training models is time and cost-consuming. Recent studies suggest that pre-trained language models (PLMs) can be adapted to downstream tasks without fine-tuning with prompts. However, no research has employed such a prompt approach in science education. As student responses are presented with natural language, aligning the scoring procedure as the next sentence prediction task using prompts can skip the costly fine-tuning stage. In this study, we developed a zero-shot approach to automatically score student responses via Matching Exemplars as Next Sentence Prediction (MeNSP). This approach employs no training samples. We first apply MeNSP in scoring three assessment tasks of scientific argumentation and found machine-human scoring agreements, Cohen's Kappa ranges from 0.30 to 0.57, and F1 score ranges from 0.54 to 0.81. To improve the performance, we extend our research to the few-shots setting, either randomly selecting labeled student responses or manually constructing responses to fine-tune the models. We find that one task's performance is improved with more samples, Cohen's Kappa from 0.30 to 0.38, and F1 score from 0.54 to 0.59; for the two others, scoring performance is not improved. We also find that randomly selected few-shots perform better than the human expert-crafted approach. This study suggests that MeNSP can yield referable automatic scoring for student responses while significantly reducing the cost of model training. This method can benefit low-stakes classroom assessment practices in science education. Future research should further explore the applicability of the MeNSP in different types of assessment tasks in science education and improve the model performance.Comment: 10+3 page

Recent advances for flame retardant rubber composites: Mini-review

Flame retardant rubber composites have attracted a great attention during the past decades owing to their irreplaceable roles in complex industrial systems. Large amounts of efforts have been made to improve the flame retardant ability, developing high efficiency flame retardant systems which can reduce the release of heat, smoke and toxic gases while not deteriorate overall properties is becoming more and more important. This review briefly outlines the recent developments of flame retardant natural rubbers, silicon rubbers, some kinds of artificial rubbers and polyurethane elastomer composites, focuses on the design, development, mechanism and applications of advanced high-performance flame-retardant methods. Finally, outlooks the future tendency including more environmental-friendly strategies, higher flame-retardant efficiency and development of multifunctional flame-retardant rubber composites are proposed