Peptides are attractive candidates for drug development because of their low toxicity and relatively small binding interfaces, making accurate protein-peptide binding prediction crucial. In this study, we propose a flexible transformer-based framework with mutual attention that integrates protein pocket structural information and can be instantiated with different pocket-structure encoders. Within this unified framework, we systematically compare three encoders: an attention-based SE(3)-Transformer, a geometric graph neural network ProtGVP, and the large-scale structure-based pretrained model ESM-IF1. Using rigorous data partitioning with strict separation of training and test sets, we show that incorporating pocket structural information consistently improves binding prediction over sequence-only models, with GVP-GNN providing particularly effective pocket representations and structure-based variants exhibiting superior robustness on previously unseen data.

Reproducing research results is important for the networking community. The current best practice typically resorts to: (1) looking for publicly available prototypes; (2) contacting the authors to get a private prototype; or (3) manually implementing a prototype following the description of the publication. However, most published network research does not have public prototypes and private ones are hard to get. As such, most reproducing efforts are spent on manual implementation based on the publications, which is both time and labor consuming and error-prone. In this paper, we boldly propose reproducing network research results using the emerging large language models (LLMs). We first prove its feasibility with a small-scale experiment, in which four students with essential networking knowledge each reproduces a different networking system published in prominent conferences and journals by prompt engineering ChatGPT. We report our observations and lessons and discuss future open research questions of this proposal.

Centralized data plane verification (DPV) faces significant scalability issues in large networks (i.e., the verifier being a performance bottleneck and single point of failure and requiring a reliable management network). We tackle this scalability challenge by introducing Tulkun, a distributed, on-device DPV framework. Our key insight is that DPV can be transformed into a counting problem on a directed acyclic graph, which can be naturally decomposed into lightweight tasks executed at network devices, enabling fast data plane checking in networks of various scales and types. With this insight, Tulkun consists of (1) a declarative invariant specification language, (2) a planner that employs a novel data structure DPVNet to systematically decompose global verification into on-device counting tasks, (3) a distributed verification messaging (DVM) protocol that specifies how on-device verifiers efficiently communicate task results to jointly verify the invariants, and (4) a mechanism to verify invariant fault-tolerance with minimal involvement of the planner. Extensive experiments with real-world datasets (WAN/LAN/DC) show that Tulkun verifies a real, large DC in 41 seconds while others tools need minutes or up to tens of hours, and shows an up to 2355× speed up on 80% quantile of incremental verification with small overhead on commodity network devices.

Current data plane verification (DPV) tools employ a centralized architecture, where a server collects the data planes of all devices and verifies them. This architecture is inherently unscalable (i.e., requiring a reliable management network, incurring a long control path and making the server a single point of failure). In this paper, we tackle this scalability challenge of DPV from an architectural perspective. In particular, we circumvent the scalability bottleneck of centralized design and advocate for a distributed, on-device DPV framework. Our key insight is that DPV can be transformed into a counting problem on DAG, which can be naturally decomposed into lightweight tasks executed at network devices, enabling scalability. Evaluation shows that a prototype of this framework achieves scalable DPV under various settings, with little overhead on commodity network devices.