Abstract:In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of our approach is the aggregation of 3D conformers, allowing the model to account for the fact that molecules can adopt multiple conformations-an important factor for accurate molecular representation. The tokens for each modality are extracted using modality-specific encoders: a transformer for SMILES strings, a message-passing neural network for 2D graphs, and an equivariant neural network for 3D conformers. The flexibility and modularity of this framework enable easy adaptation and replacement of these encoders, making the model highly versatile for different molecular tasks. The extracted tokens are then combined into a unified multimodal sequence, which is processed by a downstream transformer for prediction tasks. To efficiently scale our model for large multimodal datasets, we utilize Flash Attention 2 and bfloat16 precision. Despite its simplicity, our approach achieves state-of-the-art results across multiple datasets, demonstrating its effectiveness as a strong baseline for multimodal molecular representation learning.
Abstract:Message-passing graph neural networks (MPNNs) have emerged as a powerful paradigm for graph-based machine learning. Despite their effectiveness, MPNNs face challenges such as under-reaching and over-squashing, where limited receptive fields and structural bottlenecks hinder information flow in the graph. While graph transformers hold promise in addressing these issues, their scalability is limited due to quadratic complexity regarding the number of nodes, rendering them impractical for larger graphs. Here, we propose \emph{implicitly rewired message-passing neural networks} (IPR-MPNNs), a novel approach that integrates \emph{implicit} probabilistic graph rewiring into MPNNs. By introducing a small number of virtual nodes, i.e., adding additional nodes to a given graph and connecting them to existing nodes, in a differentiable, end-to-end manner, IPR-MPNNs enable long-distance message propagation, circumventing quadratic complexity. Theoretically, we demonstrate that IPR-MPNNs surpass the expressiveness of traditional MPNNs. Empirically, we validate our approach by showcasing its ability to mitigate under-reaching and over-squashing effects, achieving state-of-the-art performance across multiple graph datasets. Notably, IPR-MPNNs outperform graph transformers while maintaining significantly faster computational efficiency.
Abstract:Diffusion models have been recently used for anomaly detection (AD) in images. In this paper we investigate whether they can also be leveraged for AD on multivariate time series (MTS). We test two diffusion-based models and compare them to several strong neural baselines. We also extend the PA%K protocol, by computing a ROCK-AUC metric, which is agnostic to both the detection threshold and the ratio K of correctly detected points. Our models outperform the baselines on synthetic datasets and are competitive on real-world datasets, illustrating the potential of diffusion-based methods for AD in multivariate time series.
Abstract:Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable $k$-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.
Abstract:The DarkWeb represents a hotbed for illicit activity, where users communicate on different market forums in order to exchange goods and services. Law enforcement agencies benefit from forensic tools that perform authorship analysis, in order to identify and profile users based on their textual content. However, authorship analysis has been traditionally studied using corpora featuring literary texts such as fragments from novels or fan fiction, which may not be suitable in a cybercrime context. Moreover, the few works that employ authorship analysis tools for cybercrime prevention usually employ ad-hoc experimental setups and datasets. To address these issues, we release VeriDark: a benchmark comprised of three large scale authorship verification datasets and one authorship identification dataset obtained from user activity from either Dark Web related Reddit communities or popular illicit Dark Web market forums. We evaluate competitive NLP baselines on the three datasets and perform an analysis of the predictions to better understand the limitations of such approaches. We make the datasets and baselines publicly available at https://github.com/bit-ml/VeriDark
Abstract:Analyzing the distribution shift of data is a growing research direction in nowadays Machine Learning, leading to emerging new benchmarks that focus on providing a suitable scenario for studying the generalization properties of ML models. The existing benchmarks are focused on supervised learning, and to the best of our knowledge, there is none for unsupervised learning. Therefore, we introduce an unsupervised anomaly detection benchmark with data that shifts over time, built over Kyoto-2006+, a traffic dataset for network intrusion detection. This kind of data meets the premise of shifting the input distribution: it covers a large time span ($10$ years), with naturally occurring changes over time (\eg users modifying their behavior patterns, and software updates). We first highlight the non-stationary nature of the data, using a basic per-feature analysis, t-SNE, and an Optimal Transport approach for measuring the overall distribution distances between years. Next, we propose AnoShift, a protocol splitting the data in IID, NEAR, and FAR testing splits. We validate the performance degradation over time with diverse models (MLM to classical Isolation Forest). Finally, we show that by acknowledging the distribution shift problem and properly addressing it, the performance can be improved compared to the classical IID training (by up to $3\%$, on average). Dataset and code are available at https://github.com/bit-ml/AnoShift/.
Abstract:The task of identifying the author of a text spans several decades and was tackled using linguistics, statistics, and, more recently, machine learning. Inspired by the impressive performance gains across a broad range of natural language processing tasks and by the recent availability of the PAN large-scale authorship dataset, we first study the effectiveness of several BERT-like transformers for the task of authorship verification. Such models prove to achieve very high scores consistently. Next, we empirically show that they focus on topical clues rather than on author writing style characteristics, taking advantage of existing biases in the dataset. To address this problem, we provide new splits for PAN-2020, where training and test data are sampled from disjoint topics or authors. Finally, we introduce DarkReddit, a dataset with a different input data distribution. We further use it to analyze the domain generalization performance of models in a low-data regime and how performance varies when using the proposed PAN-2020 splits for fine-tuning. We show that those splits can enhance the models' capability to transfer knowledge over a new, significantly different dataset.
Abstract:Leveraging deep learning models for Anomaly Detection (AD) has seen widespread use in recent years due to superior performances over traditional methods. Recent deep methods for anomalies in images learn better features of normality in an end-to-end self-supervised setting. These methods train a model to discriminate between different transformations applied to visual data and then use the output to compute an anomaly score. We use this approach for AD in text, by introducing a novel pretext task on text sequences. We learn our DATE model end-to-end, enforcing two independent and complementary self-supervision signals, one at the token-level and one at the sequence-level. Under this new task formulation, we show strong quantitative and qualitative results on the 20Newsgroups and AG News datasets. In the semi-supervised setting, we outperform state-of-the-art results by +13.5% and +6.9%, respectively (AUROC). In the unsupervised configuration, DATE surpasses all other methods even when 10% of its training data is contaminated with outliers (compared with 0% for the others).