Weixian Deng

Zhiwei Xu, Weixian Deng, Xuyang Liu et al.

Code clone detection has been extensively studied for decades, and recent approaches have begun reporting remarkably high performance for semantic (Type-4) clones on benchmark datasets. However, it remains unclear whether these results reflect a genuine ability to capture semantic equivalence between programs, or simply an ability to exploit dataset-specific patterns. In this paper, we present the first systematic empirical study investigating the generalizability of state-of-the-art (SOTA) semantic code clone detectors beyond benchmark evaluation settings. Inspired by the inherent inclusion relationship among clone types, we propose a clone operator framework consisting of eight transformation operators derived from Type-2 and Type-3 clone variations. Using these operators, we construct distribution-shifted yet semantically equivalent Type-4 clone instances and evaluate 11 representative detectors spanning token-based, tree-based, and graph-based paradigms on the real-world BigCloneBench dataset. Our results reveal substantial performance degradation across all evaluated approaches, despite their strong benchmark performance. Further analyses show that existing detectors heavily rely on shortcut learning based on lexical and structural cues rather than robust semantic understanding. Our findings suggest that current SOTA semantic code clone detectors exhibit limited generalizability in real-world scenarios, highlighting important avenues for future research.

Fanglei Xue, Meihan Zhang, Shuqi Li et al.

Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the primary small molecules that induce TPD. Both types of molecules form a ternary complex linking an E3 ligase with a target protein, a crucial step for drug discovery. While significant advances have been made in binary structure prediction for proteins and small molecules, ternary structure prediction remains challenging due to obscure interaction mechanisms and insufficient training data. Traditional methods relying on manually assigned rules perform poorly and are computationally demanding due to extensive random sampling. In this work, we introduce DeepTernary, a novel deep learning-based approach that directly predicts ternary structures in an end-to-end manner using an encoder-decoder architecture. DeepTernary leverages an SE(3)-equivariant graph neural network (GNN) with both intra-graph and ternary inter-graph attention mechanisms to capture intricate ternary interactions from our collected high-quality training dataset, TernaryDB. The proposed query-based Pocket Points Decoder extracts the 3D structure of the final binding ternary complex from learned ternary embeddings, demonstrating state-of-the-art accuracy and speed in existing PROTAC benchmarks without prior knowledge from known PROTACs. It also achieves notable accuracy on the more challenging MGD benchmark under the blind docking protocol. Remarkably, our experiments reveal that the buried surface area calculated from predicted structures correlates with experimentally obtained degradation potency-related metrics. Consequently, DeepTernary shows potential in effectively assisting and accelerating the development of TPDs for previously undruggable targets.