Assessing bioartificial organ function: the 3P model framework and its validation.

The rapid advancement in the fabrication and culture of in vitro organs has marked a new era in biomedical research. While strides have been made in creating structurally diverse bioartificial organs, such as the liver, which serves as the focal organ in our study, the field lacks a uniform approach for the predictive assessment of liver function. Our research bridges this gap with the introduction of a novel, machine-learning-based "3P model" framework. This model draws on a decade of experimental data across diverse culture platform studies, aiming to identify critical fabrication parameters affecting liver function, particularly in terms of albumin and urea secretion. Through meticulous statistical analysis, we evaluated the functional sustainability of the in vitro liver models. Despite the diversity of research methodologies and the consequent scarcity of standardized data, our regression model effectively captures the patterns observed in experimental findings. The insights gleaned from our study shed light on optimizing culture conditions and advance the evaluation of the functional maintenance capacity of bioartificial livers. This sets a precedent for future functional evaluations of bioartificial organs using machine learning.

Bidirectional Trust-Enhanced Collaborative Filtering for Point-of-Interest Recommendation.

A personalized point-of-interest (POI) recommender system is of great significance to facilitate the daily life of users. However, it suffers from some challenges, such as trustworthiness and data sparsity problems. Existing models only consider the trust user influence and ignore the role of the trust location. Furthermore, they fail to refine the influence of context factors and fusion between the user preference and context models. To address the trustworthiness problem, we propose a novel bidirectional trust-enhanced collaborative filtering model, which investigates the trust filtering from the views of users and locations. To tackle the data sparsity problem, we introduce temporal factor into the trust filtering of users as well as geographical and textual content factors into the trust filtering of locations. To further alleviate the sparsity of user-POI rating matrices, we employ a weighted matrix factorization fused with the POI category factor to learn the user preference. To integrate the trust filtering models and the user preference model, we develop a fused framework with two kinds of integrating methods in relation to the different impacts of factors on the POIs that users have visited and the POIs that users have not visited. Finally, we conduct extensive experiments on Gowalla and Foursquare datasets to evaluate our proposed POI recommendation model, and the results show that our proposed model improves by 13.87% at precision@5 and 10.36% at recall@5 over the state-of-the-art model, which demonstrates that our proposed model outperforms the state-of-the-art method.

Insect recognition based on complementary features from multiple views.

Insect pest recognition has always been a significant branch of agriculture and ecology. The slight variance among different kinds of insects in appearance makes it hard for human experts to recognize. It is increasingly imperative to finely recognize specific insects by employing machine learning methods. In this study, we proposed a feature fusion network to synthesize feature presentations in different backbone models. Firstly, we employed one CNN-based backbone ResNet, and two attention-based backbones Vision Transformer and Swin Transformer to localize the important regions of insect images with Grad-CAM. During this process, we designed new architectures for these two Transformers to enable Grad-CAM to be applicable in such attention-based models. Then we further proposed an attention-selection mechanism to reconstruct the attention area by delicately integrating the important regions, enabling these partial but key expressions to complement each other. We only need part of the image scope that represents the most crucial decision-making information for insect recognition. We randomly selected 20 species of insects from the IP102 dataset and then adopted all 102 kinds of insects to test the classification performance. Experimental results show that the proposed approach outperforms other advanced CNN-based models. More importantly, our attention-selection mechanism demonstrates good robustness to augmented images.

Collectively encoding protein properties enriches protein language models.

Pre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to protein domains by fine-tuning specific in-domain tasks. However, few studies focused on enriching such protein language models by jointly learning protein properties from strongly-correlated protein tasks. Here we elaborately designed a multi-task learning (MTL) architecture, aiming to decipher implicit structural and evolutionary information from three sequence-level classification tasks for protein family, superfamily and fold. Considering the co-existing contextual relevance between human words and protein language, we employed BERT, pre-trained on a large natural language corpus, as our backbone to handle protein sequences. More importantly, the encoded knowledge obtained in the MTL stage can be well transferred to more fine-grained downstream tasks of TAPE. Experiments on structure- or evolution-related applications demonstrate that our approach outperforms many state-of-the-art Transformer-based protein models, especially in remote homology detection.