Yijie Ding

Yizheng Wang, Yixiao Zhai, Yijie Ding et al.

Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We introduce the Support Bio-Sequence Machine for Proteins (SBSM-Pro), a model purpose-built for the classification of biological sequences. This model starts with raw sequences and groups amino acids based on their physicochemical properties. It incorporates sequence alignment to measure the similarities between proteins and uses a novel multiple kernel learning (MKL) approach to integrate various types of information, utilizing support vector machines for classification prediction. The results indicate that our model demonstrates commendable performance across ten datasets in terms of the identification of protein function and posttranslational modification. This research not only exemplifies state-of-the-art work in protein classification but also paves avenues for new directions in this domain, representing a beneficial endeavor in the development of platforms tailored for the classification of biological sequences. SBSM-Pro is available for access at http://lab.malab.cn/soft/SBSM-Pro/.

Xiaoyi Liu, Hongpeng Yang, Chengwei Ai et al.

Incomplete knowledge of metabolic processes hinders the accuracy of GEnome-scale Metabolic models (GEMs), which in turn impedes advancements in systems biology and metabolic engineering. Existing gap-filling methods typically rely on phenotypic data to minimize the disparity between computational predictions and experimental results. However, there is still a lack of an automatic and precise gap-filling method for initial state GEMs before experimental data and annotated genomes become available. In this study, we introduce CLOSEgaps, a deep learning-driven tool that addresses the gap-filling issue by modeling it as a hyperedge prediction problem within GEMs. Specifically, CLOSEgaps maps metabolic networks as hypergraphs and learns their hyper-topology features to identify missing reactions and gaps by leveraging hypothetical reactions. This innovative approach allows for the characterization and curation of both known and hypothetical reactions within metabolic networks. Extensive results demonstrate that CLOSEgaps accurately gap-filling over 96% of artificially introduced gaps for various GEMs. Furthermore, CLOSEgaps enhances phenotypic predictions for 24 GEMs and also finds a notable improvement in producing four crucial metabolites (Lactate, Ethanol, Propionate, and Succinate) in two organisms. As a broadly applicable solution for any GEM, CLOSEgaps represents a promising model to automate the gap-filling process and uncover missing connections between reactions and observed metabolic phenotypes.

Yijie Ding, Zitian Guo, Jiacheng Li et al.

A widely held hypothesis for why generative recommendation (GR) models outperform conventional item ID-based models is that they generalize better. However, there is few systematic way to verify this hypothesis beyond a superficial comparison of overall performance. To address this gap, we categorize each data instance based on the specific capability required for a correct prediction: either memorization (reusing item transition patterns observed during training) or generalization (composing known patterns to predict unseen item transitions). Extensive experiments show that GR models perform better on instances that require generalization, whereas item ID-based models perform better when memorization is more important. To explain this divergence, we shift the analysis from the item level to the token level and show that what appears to be item-level generalization often reduces to token-level memorization for GR models. Finally, we show that the two paradigms are complementary. We propose a simple memorization-aware indicator that adaptively combines them on a per-instance basis, leading to improved overall recommendation performance.

Yuqing Qian, Ziyu Zheng, Prayag Tiwari et al.

Drug-side effect prediction has become an essential area of research in the field of pharmacology. As the use of medications continues to rise, so does the importance of understanding and mitigating the potential risks associated with them. At present, researchers have turned to data-driven methods to predict drug-side effects. Drug-side effect prediction is a link prediction problem, and the related data can be described from various perspectives. To process these kinds of data, a multi-view method, called Multiple Kronecker RLS fusion-based link propagation (MKronRLSF-LP), is proposed. MKronRLSF-LP extends the Kron-RLS by finding the consensus partitions and multiple graph Laplacian constraints in the multi-view setting. Both of these multi-view settings contribute to a higher quality result. Extensive experiments have been conducted on drug-side effect datasets, and our empirical results provide evidence that our approach is effective and robust.