DNS-GT: A Graph-based Transformer Approach to Learn Embeddings of Domain Names from DNS Queries

Classic Network Intrusion Detection Systems (NIDS) often rely on manual feature engineering to extract meaningful patterns from network traffic data. However, this approach requires domain expertise and runs counter to the widely adopted principle of modern machine learning and neural networks: that models themselves should learn meaningful representations directly from data. We investigate whether tabular representation learning techniques can improve intrusion detection performance by automatically learning robust feature representations for NetFlow data. This paper presents a systematic evaluation of state-of-the-art representation learning methods on benchmark NetFlow datasets, comparing against traditional autoencoders and end-to-end transformer baselines. We evaluate learned representations using both supervised classifiers and unsupervised anomaly detectors, with comprehensive hyperparameter exploration for each combination. Our results reveal strong dataset-model dependency, with no single approach consistently dominating across all scenarios. For supervised classification, TabICL achieves the best performance on CIDDS, while autoencoders follow closely and tie with end-to-end transformer models for the best average rank across datasets. Supervised approaches substantially outperform unsupervised anomaly detection methods, where no single combination consistently dominates as optimal choices depend on the dataset. Cross-dataset transfer experiments demonstrate that learned representations can generalize across network environments with appropriate method and classifier selection. However, transfer performance varies substantially depending on the source-target dataset combination, indicating sensitivity to distributional differences between network environments.

Recent deep learning approaches for network intrusion detection increasingly incorporate temporal architectures such as recurrent networks and Transformers, often reporting near-perfect performance on CIC-IDS2017. However, many existing studies neither supply their temporal modules with genuine sequence inputs nor evaluate under realistic, leakage-free conditions, making it unclear whether reported gains arise from true sequence-modeling capability. In this work, we reformulate CIC-IDS2017 as a temporal intrusion-detection task by constructing ordered flow sequences from network conversations and benchmarking nine classical and deep learning architectures under a random split, two leakage-free splits, and a padding-scheme ablation. The central finding is that padding convention, not architecture, determines the Transformer's performance: on genuinely sequential (non-padded) windows the Transformer achieves the highest macro-F1 of any model in the experiment (0.89); under zero-pad+mask evaluation it drops markedly (-0.24 macro-F1), while LSTM, GRU, and 1D-CNN remain stable. Under leakage-free group evaluation the Random Forest is the most robust model (+0.009), while the Transformer's false-alarm rate grows from 0.04% to 2.7%, a 67-fold increase invisible under conventional protocols. These findings demonstrate that evaluation methodology -- specifically padding convention and split protocol -- has a larger effect on reported performance than architectural choice, and that widely used random splits with repeat-last padding can overestimate model robustness by up to 0.24 macro-F1. We advocate leakage-free splits, explicit padding disclosure, and sequence-aware benchmarking as standard practice in future IDS research. Code and implementation details are available at https://github.com/zachmocz/temporal-ids-bench.

We study whether in-domain pretraining of Bidirectional Encoder Representations from Transformer (BERT) model improves subdomain-level detection of exfiltration at low false positive rates. While previous work mostly examines fine-tuned generic Transformers, it does not aim to isolate the effect of pretraining on the downstream task of classification. To address this gap, we develop a controlled pipeline where we freeze operating points on validation and transfer them to the test set, thus enabling clean ablations across different label and pretraining budgets. Our results show significant improvements in the left tail of the Receiver Operating Characteristic (ROC) curve, especially against randomly initialized baseline. Additionally, within pretrained model variants, increasing the number of pretraining steps helps the most when more labeled data are available for fine-tuning.