Wenzheng Cheng

Hanlin Zhang, Wenzheng Cheng

Gene essentiality refers to the degree to which a gene is necessary for the survival and reproductive efficacy of a living organism. Although the essentiality of non-coding genes has been documented, there are still aspects of non-coding genes' essentiality that are unknown to us. For example, We do not know the contribution of sequence features and network spatial features to essentiality. As a consequence, in this work, we propose DeepHEN that could answer the above question. By buidling a new lncRNA-proteion-protein network and utilizing both representation learning and graph neural network, we successfully build our DeepHEN models that could predict the essentiality of lncRNA genes. Compared to other methods for predicting the essentiality of lncRNA genes, our DeepHEN model not only tells whether sequence features or network spatial features have a greater influence on essentiality but also addresses the overfitting issue of those methods caused by the low number of essential lncRNA genes, as evidenced by the results of enrichment analysis.

Hao Ding, Yuqian Zhang, Wenzheng Cheng et al.

Surgical phase recognition (SPR) is an integral component of surgical data science, enabling high-level surgical analysis. End-to-end trained neural networks that predict surgical phase directly from videos have shown excellent performance on benchmarks. However, these models struggle with robustness due to non-causal associations in the training set. Our goal is to improve model robustness to variations in the surgical videos by leveraging the digital twin (DT) paradigm -- an intermediary layer to separate high-level analysis (SPR) from low-level processing. As a proof of concept, we present a DT representation-based framework for SPR from videos. The framework employs vision foundation models with reliable low-level scene understanding to craft DT representation. We embed the DT representation in place of raw video inputs in the state-of-the-art SPR model. The framework is trained on the Cholec80 dataset and evaluated on out-of-distribution (OOD) and corrupted test samples. Contrary to the vulnerability of the baseline model, our framework demonstrates strong robustness on both OOD and corrupted samples, with a video-level accuracy of 80.3 on a highly corrupted Cholec80 test set, 67.9 on the challenging CRCD dataset, and 99.8 on an internal robotic surgery dataset, outperforming the baseline by 3.9, 16.8, and 90.9 respectively. We also find that using DT representation as an augmentation to the raw input can significantly improve model robustness. Our findings lend support to the thesis that DT representations are effective in enhancing model robustness. Future work will seek to improve the feature informativeness and incorporate interpretability for a more comprehensive framework.