ADCNet: a unified framework for predicting the activity of antibody-drug conjugates

Antibody-drug conjugate (ADC) has revolutionized the field of cancer treatment in the era of precision medicine due to their ability to precisely target cancer cells and release highly effective drug. Nevertheless, the realization of rational design of ADC is very difficult because the relationship between their structures and activities is difficult to understand. In the present study, we introduce a unified deep learning framework called ADCNet to help design potential ADCs. The ADCNet highly integrates the protein representation learning language model ESM-2 and small-molecule representation learning language model FG-BERT models to achieve activity prediction through learning meaningful features from antigen and antibody protein sequences of ADC, SMILES strings of linker and payload, and drug-antibody ratio (DAR) value. Based on a carefully designed and manually tailored ADC data set, extensive evaluation results reveal that ADCNet performs best on the test set compared to baseline machine learning models across all evaluation metrics. For example, it achieves an average prediction accuracy of 87.12%, a balanced accuracy of 0.8689, and an area under receiver operating characteristic curve of 0.9293 on the test set. In addition, cross-validation, ablation experiments, and external independent testing results further prove the stability, advancement, and robustness of the ADCNet architecture. For the convenience of the community, we develop the first online platform (https://ADCNet.idruglab.cn) for the prediction of ADCs activity based on the optimal ADCNet model, and the source code is publicly available at https://github.com/idrugLab/ADCNet.

Improving Human Annotation in Single Object Tracking

Human annotation is always considered as ground truth in video object tracking tasks. It is used in both training and evaluation purposes. Thus, ensuring its high quality is an important task for the success of trackers and evaluations between them. In this paper, we give a qualitative and quantitative analysis of the existing human annotations. We show that human annotation tends to be non-smooth and is prone to partial visibility and deformation. We propose a smoothing trajectory strategy with the ability to handle moving scenes. We use a two-step adaptive image alignment algorithm to find the canonical view of the video sequence. We then use different techniques to smooth the trajectories at certain degree. Once we convert back to the original image coordination, we can compare with the human annotation. With the experimental results, we can get more consistent trajectories. At a certain degree, it can also slightly improve the trained model. If go beyond a certain threshold, the smoothing error will start eating up the benefit. Overall, our method could help extrapolate the missing annotation frames or identify and correct human annotation outliers as well as help improve the training data quality.