## 3 Results and Discussion
### Analysis of Model Prediction Results
[PERSON] inferred that the Q0 JKI9 protein has a binding function (GO:0005488) by analyzing the ARF2 gene corresponding to the Q0 JKI9 protein [31]. Auxin response factors (ARFs) generally exhibit DNA-binding activity; therefore, it can be inferred that the Q0 JKI9 protein may be involved in DNA binding (GO:0003677). The UniProt database also inferred that the Q0 JKI9 protein had a GO:0003677 function through automatic annotation. The actual annotated function of the Q6 YSJ5 (AGO16_ORYS) protein in the CC sub-dataset was correctly predicted by the model. The above shows that, in some specific cases, the key features of the data can be accurately captured, and accurate judgments can be made by the model. However, for other protein samples, the prediction results reflected the uncertainties and limitations of the functional predictions posed by the model. Models can occasionally predict functions that are not included in a label set. For example, the test protein P16081  
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(NIA1_ORYSJ) in the MF ontology dataset was manually annotated with the GO:0003824, GO:0005488, GO:1901363, GO:0097159, GO:0046914, and GO:0043168 functions. The functions GO:0003824, GO:0005488, GO:1901363, and GO:0097159 were successfully predicted by the model, whereas the annotated functions GO:0046914 and GO:0043168 were not. Additionally, the model predicted the functions of GO:0003676, GO:0003723, and GO:0016787. We mainly focused on and analyzed the function of GO:0016787 (hydrolase activity). A recent study by [PERSON] revealed transcriptome changes in rice roots in response to phosphorus starvation [32]. The study mentioned that Os08g0468100, which encodes the P16081 protein, was downregulated under phosphorus-deficient conditions and may be related to phosphoric ester hydrolase activity. In the molecular function sub-ontology hierarchy, phosphoric ester hydrolase activity was classified as a more specific functional category under hydrolase activity (GO:0016787), suggesting that the P16081 protein may be related to hydrolase activity (GO:0016787). This demonstrates the feasibility of the proposed model for predicting unknown functions. After manual annotation, Q8W0A1 (BGAL2_ORYSJ) in the BP dataset had the GO:0005975, GO:0044238, and GO:0008152 functions. In addition to the annotated functions, the two functions GO:0016051 and GO:0009058 were predicted unexpectedly, which may be due to the correlation between the additional predicted and annotated functions. The gene expression of japonica germplasms under heat stress conditions was analyzed by [PERSON] [33], who revealed that the expression of genes associated with the function of GO:0009058 was downregulated. This downregulation suggests that proteins involved in the GO:0009058 function may be present in japonica and that the GO:0009058 function is a subset of the GO:0008152 function. Therefore, in this study, a certain degree of possibility was suggested for predicting Q8W0A1 protein function. The Q84 YK8 (LOXC2_ORYSJ) protein in the CC dataset is annotated with GO:0009507, GO:0009536, GO:0043231, GO:0043227, GO:0043229, GO:0043226, and GO:0110165. The model additionally discovered the GO:0016020 function during prediction. In the CC ontology hierarchy, the membranes (GO:0016020) were categorized as functional subsets of cellular anatomical entities (GO:0110165). Membranes are a more specific and focused category of cellular components than cellular anatomical entities. A recent study on the genetic analysis of rice seedlings reported that the LOC_Os08g39850 gene, corresponding to the Q84 YK8 protein, encodes a chloroplast precursor lipoxygenase [34]. As lipoxygenases can act on the phospholipids of cell membranes, we speculate that the Q84 YK8 protein may be related to membrane function (GO:0016020). Although additional predicted labels are not explicitly included in the original label set, an intrinsic biological relationship exists between them and known labels.