Graph mining has become crucial in fields such as social science, finance, and cybersecurity. Many large-scale real-world networks exhibit both heterogeneity, where multiple node and edge types exist in the graph, and heterophily, where connected nodes may have dissimilar labels and attributes. However, existing benchmarks primarily focus on either heterophilic homogeneous graphs or homophilic heterogeneous graphs, leaving a significant gap in understanding how models perform on graphs with both heterogeneity and heterophily. To bridge this gap, we introduce H2GB, a large-scale node-classification graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of real-world graphs. H2GB encompasses 9 real-world datasets spanning 5 diverse domains, 28 baseline models, and a unified benchmarking library with a standardized data loader, evaluator, unified modeling framework, and an extensible framework for reproducibility. We establish a standardized workflow supporting both model selection and development, enabling researchers to easily benchmark graph learning methods. Extensive experiments across 28 baselines reveal that current methods struggle with heterophilic and heterogeneous graphs, underscoring the need for improved approaches. Finally, we present a new variant of the model, H2G-former, developed following our standardized workflow, that excels at this challenging benchmark. Both the benchmark and the framework are publicly available at Github and PyPI, with documentation hosted at https://junhongmit.github.io/H2GB.
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Massive datasets related to infectious diseases became available after the COVID-19 pandemic, supporting data-driven approaches in modeling and forecasting infectious diseases. However, these approaches are known to exacerbate data biases present in the training data such as having certain demographic groups being over or underrepresented in the data. Such data collection biases may propagate through the modeling and prediction pipelines to decision-making, and the consequences are relatively unknown. Therefore, efforts are needed to understand how data collection bias affects data-driven infectious disease models. This datasets and benchmarks paper provides a suite of datasets, each corresponding to a simulated disease spread among a population of 5000 simulated agents over 90 days in Atlanta and San Francisco. For each dataset, we provide not only the full (simulated ground truth) of the disease spread in terms of when, where, and by whom the disease spreads, but also information on which cases are observed when different types and degrees of data collection bias are applied. The agents' characteristics, check-ins, and social network data are also available to support downstream tasks. Additionally, we also describe how to use the simulation to re-generate the data and to generate new datasets in different regions and with different parameters. With the provided datasets and the simulation tools, researchers studying the spread of infectious diseases may better understand, account for, and correct the systematic bias caused by the inherent real-world data bias, and hence improve the prediction of infectious diseases.
Flavor development in the food industry is increasingly challenged by the need for rapid innovation and precise flavor profile creation. Traditional flavor research methods typically rely on iterative, subjective testing, which lacks the efficiency and scalability required for modern demands. This paper presents three contributions to address these challenges. Firstly, we define a new problem domain for scientific agents in flavor science, conceptualized as the generation of hypotheses for flavor profile sourcing and understanding. By leveraging their capacity to identify relevant evidence and reason within large context spaces, language model-backed agents can perform the labor-intensive tasks of flavor sourcing and understanding with enhanced efficiency and precision. To facilitate research in this area, we introduce the FoodPuzzle dataset, a challenging benchmark consisting of 978 food items and 1,766 flavor molecule profiles. We propose a novel Scientific Agent approach, integrating in-context learning and retrieval augmented techniques to generate grounded hypotheses in the domain of food science. Experimental results indicate that our model significantly surpasses traditional methods in flavor profile prediction tasks, demonstrating its potential to transform flavor development practices.
Bridging the Binary Analysis Gap: A Cross-Compiler Dataset and Neural Framework for Industrial Control Systems
PDF ↗Industrial Control Systems (ICS) rely heavily on Programmable Logic Controllers (PLCs) to manage critical infrastructure, yet analyzing PLC executables remains challenging due to diverse proprietary compilers and limited access to source code.To bridge this gap, we introduce PLC-BEAD, a comprehensive dataset containing 2431 compiled binaries from 700+ PLC programs across four major industrial compilers (CoDeSys, GEB, OpenPLC-V2, OpenPLC-V3). This novel dataset uniquely pairs each binary with its original Structured Text source code and standardized functionality labels, enabling both binary-level and source-level analysis. We demonstrate the dataset's utility through PLCEmbed, a transformer-based framework for binary code analysis that achieves 93% accuracy in compiler provenance identification and 42% accuracy in fine-grained functionality classification across 22 industrial control categories. Through comprehensive ablation studies, we analyze how compiler optimization levels, code patterns, and class distributions influence model performance. We provide detailed documentation of the dataset creation process, labeling taxonomy, and benchmark protocols to ensure reproducibility. Both PLC-BEAD and PLCEmbed are released as open-source resources to foster research in PLC security, reverse engineering, and ICS forensics, establishing new baselines for data-driven approaches to industrial cybersecurity.
Recent advances in graph machine learning (ML) with the introduction of Graph Neural Networks (GNNs) have led to a widespread interest in applying these approaches to business applications at scale. GNNs enable differentiable end-to-end (E2E) learning of model parameters given graph structure which enables optimization towards popular node, edge (link) and graph-level tasks. While the research innovation in new GNN layers and training strategies has been rapid, industrial adoption and utility of GNNs has lagged considerably due to the unique scale challenges that large-scale graph ML problems create. In this work, we share our approach to training, inference, and utilization of GNNs at Snapchat. To this end, we present GiGL (Gigantic Graph Learning), an open-source library to enable large-scale distributed graph ML to the benefit of researchers, ML engineers, and practitioners. We use GiGL internally at Snapchat to manage the heavy lifting of GNN workflows, including graph data preprocessing from relational DBs, subgraph sampling, distributed training, inference, and orchestration. GiGL is designed to interface cleanly with open-source GNN modeling libraries prominent in academia like PyTorch Geometric (PyG), while handling scaling and productionization challenges that make it easier for internal practitioners to focus on modeling. GiGL is used in multiple production settings, and has powered over 35 launches across multiple business domains in the last 2 years in the contexts of friend recommendation, content recommendation and advertising. This work details high-level design and tools the library provides, scaling properties, case studies in diverse business settings with large-scale graphs up to hundreds of millions of nodes, tens of billions of edges, and hundreds of node and edge features, and several key lessons learned in employing graph ML at scale on large social data. GiGL is open-sourced at https://github.com/Snapchat/GiGL.
Millions of smart meters have been deployed worldwide, collecting the total power consumed by individual households. Based on these data, electricity suppliers offer their clients energy monitoring solutions to provide feedback on the consumption of their individual appliances. Historically, such estimates have relied on statistical methods that use coarse-grained total monthly consumption and static customer data, such as appliance ownership. Non-Intrusive Load Monitoring (NILM) is the problem of disaggregating a household's collected total power consumption to retrieve the consumed power for individual appliances. Current state-of-the-art (SotA) solutions for NILM are based on deep-learning (DL) and operate on subsequences of an entire household consumption reading. However, the non-stationary nature of real-world smart meter data leads to a drift in the data distribution within each segmented window, which significantly affects model performance. This paper introduces NILMFormer, a Transformer-based architecture that incorporates a new subsequence stationarization/de-stationarization scheme to mitigate the distribution drift and that uses a novel positional encoding that relies only on the subsequence's timestamp information. Experiments with 4 real-world datasets show that NILMFormer significantly outperforms the SotA approaches. Our solution has been deployed as the backbone algorithm for EDF's (Electricité De France) consumption monitoring service, delivering detailed insights to millions of customers about their individual appliances' power consumption.
MAD: Multicriteria Anomaly Detection of Suspicious Financial Accounts from Billions of Cash Transactions
PDF ↗This paper presents a real-world deployment case study on using unsupervised anomaly detection for Anti-Money Laundering (AML). Using more than 2 billion anonymized bank transactions that Intesa Sanpaolo, a primary Italian financial institution, registered over 8 months, we developed, tuned and deployed a machine learning pipeline in production. Experts from Intesa Sanpaolo validated the performance of our approach against the institution's traditional rule-based system and checked new real-world cases the system allowed them to identify. Besides increasing both precision and recall by a factor of 6 in the detection of high-risk cases, our pipeline raises 200+ additional alerts during the 8-month period, manually identified by branch managers, but missed by the rule-based system. More importantly, a manual inspection of 100 new unseen cases revealed 28 significant previously unreported cases. The pipeline, now fully deployed in Intesa Sanpaolo's Transaction Monitoring system, highlights the advantages of machine learning over traditional approaches typically adopted in this traditionally very conservative sector.
COEF-VQ: Cost-Efficient Video Quality Understanding through a Cascaded Multimodal LLM Framework
PDF ↗Recently, with the emergence of recent Multimodal Large Language Model (MLLM) technology, it has become possible to exploit its video understanding capability on different classification tasks. In practice, we face the difficulty of huge requirements for GPU resource if we need to deploy MLLMs online. In this paper, we propose COEF-VQ, a novel cascaded MLLM framework designed to enhance video quality understanding on the short-video platform while optimizing computational efficiency. Our approach integrates an entropy-based pre-filtering stage, where a lightweight model assesses uncertainty and selectively filters cases before passing them to the more computationally intensive MLLM for final evaluation. By prioritizing high-uncertainty samples for deeper analysis, our framework significantly reduces GPU usage while maintaining the strong classification performance of a full MLLM deployment. To demonstrate the effectiveness of COEF-VQ, we deploy this new framework onto the video management platform (VMP) at the short-video platform, and perform a series of detailed experiments on two in-house tasks related to video quality understanding. We show that COEF-VQ leads to substantial performance gains from the offline evaluation in these two tasks and effectively enhances platform safety with limit resource consumption, significantly reducing inappropriate content video view rate by 9.9% in a online A/B test without affecting engagement. Post-launch monitoring confirmed sustained improvements, validating its real-world impact.
Technology firms conduct randomized controlled experiments (''A/B tests'') to learn which actions to take to improve business outcomes. In firms with mature experimentation platforms, experimentation programs can consist of many thousands of tests. To effectively scale experimentation, firms rely on decision rules: standard operating procedures for mapping the results of an experiment to a choice of treatment arm to launch to the general user population. Despite the critical role of decision rules in translating experimentation into business decisions, rigorous guidance on how to evaluate and choose decision rules is scarce. This paper proposes to evaluate decision rules based on their cumulative returns to business north star metrics. Although intuitive and easy to explain to decision-makers, this quantity can be difficult to estimate, especially when experiments have weak signal-to-noise ratios. We develop a cross-validation estimator that is much less biased than the naive plug-in estimator under conditions realistic to digital experimentation. We demonstrate the efficacy of our approach via a case study of 123 historical A/B tests at Netflix, where we used it to show that a new decision rule would have increased cumulative returns to the north star metric by an estimated 33%, directly leading to the adoption of the new rule.
Retrievers, which form one of the most important recommendation stages, are responsible for efficiently selecting possible positive samples to the later stages under strict latency limitations. Because of this, large-scale systems always rely on approximate calculations and indexes to roughly shrink candidate scale, with a simple ranking model. Most of the existing methods mainly focus on incorporating complicated ranking models. However, index structure is not improved, which also bottlenecks the whole effectiveness. In this paper, we propose a novel index structure: streaming Vector Quantization model, as a new generation of retrieval paradigm. Streaming VQ attaches items with indexes in real time, granting it immediacy. Moreover, through meticulous verification of possible variants, it achieves additional benefits like index balancing and reparability, enabling it to support complicated ranking models as existing approaches. Streaming VQ has been deployed and replaced all major retrievers in Douyin and Douyin Lite, resulting in remarkable user engagement gain.
Managing evolving graph data presents substantial challenges in storage and privacy, and training graph neural networks (GNNs) on such data often leads to catastrophic forgetting, impairing performance on earlier tasks. Despite existing continual graph learning (CGL) methods mitigating this to some extent, they rely on centralized architectures and ignore the potential of distributed graph databases to leverage collective intelligence. To this end, we propose Federated Continual Graph Learning (FCGL) to adapt GNNs across multiple evolving graphs under storage and privacy constraints. Our empirical study highlights two core challenges: local graph forgetting (LGF), where clients lose prior knowledge when adapting to new tasks, and global expertise conflict (GEC), where the global GNN exhibits sub-optimal performance in both adapting to new tasks and retaining old ones, arising from inconsistent client expertise during server-side parameter aggregation. To address these, we introduce POWER, a framework that preserves experience nodes with maximum local-global coverage locally to mitigate LGF, and leverages pseudo-prototype reconstruction with trajectory-aware knowledge transfer to resolve GEC. Experiments on various graph datasets demonstrate POWER's superiority over federated adaptations of CGL baselines and vision-centric federated continual learning approaches.
Many existing models for clinical trial outcome prediction are optimized using task-specific loss functions on trial phase-specific data. While this scheme may boost prediction for common diseases and drugs, it can hinder the learning of generalizable representations, leading to more false positives/negatives. To address this limitation, we introduce CLaDMoP, a new pre-training approach for clinical trial outcome prediction, alongside the Successful Clinical Trials dataset (SCT), specifically designed for this task. CLaDMoP leverages a Large Language Model-to encode trials' eligibility criteria-linked to a lightweight Drug-Molecule branch through a novel multi-level fusion technique. To efficiently fuse long embeddings across levels, we incorporate a grouping block, drastically reducing computational overhead. CLaDMoP avoids reliance on task-specific objectives by pre-training on a ''pair matching'' proxy task. Compared to established zero-shot and few-shot baselines, our method significantly improves both PR-AUC and ROC-AUC, especially for phase I and phase II trials. We further evaluate and perform ablation on CLaDMoP after Parameter-Efficient Fine-Tuning, comparing it to state-of-the-art supervised baselines, including MEXA-CTP, on the Trial Outcome Prediction (TOP) benchmark. CLaDMoP achieves up to 10.5% improvement in PR-AUC and 3.6% in ROC-AUC, while attaining comparable F1 score to MEXA-CTP, highlighting its potential for clinical trial outcome prediction. Code and SCT dataset can be downloaded from https://github.com/murai-lab/CLaDMoP.
With the advent of large language models (LLMs), managing scientific literature via LLMs has become a promising direction of research. However, existing approaches often overlook the rich structural and semantic relevance among scientific literature, limiting their ability to discern the relationships between pieces of scientific knowledge, and suffer from various types of hallucinations. These methods also focus narrowly on individual downstream tasks, limiting their applicability across use cases. We propose LitFM, the first literature foundation model designed for a wide variety of practical downstream tasks on domain-specific literature, with a focus on citation information. At its core, LitFM contains a novel graph retriever that can provide accurate and diverse recommendations for LLM to integrate graph structure information and relevant literature. LitFM also leverages a knowledge-infused LLM, fine-tuned through a well-developed instruction paradigm. It enables LitFM to extract domain-specific knowledge from literature and reason relationships among them. By integrating citation graphs during both training and inference, LitFM can generalize to unseen papers and accurately assess their relevance within existing literature. Additionally, we introduce new large-scale literature citation benchmark datasets on three academic fields, featuring sentence-level citation information and local context. Extensive experiments validate the superiority of LitFM, achieving 28.1% improvement on retrieval task in precision, and an average improvement of 7.52% over state-of-the-art across six downstream literature-related tasks.
Self-supervised learning (SSL) has emerged as a promising paradigm that presents supervisory signals to real-world problems, bypassing the extensive cost of manual labeling. Consequently, self-supervised anomaly detection (SSAD) has seen a recent surge of interest, since SSL is especially attractive for unsupervised tasks. However, recent works have reported that the choice of a data augmentation function has significant impact on the accuracy of SSAD, posing augmentation search as an essential but nontrivial problem due to lack of labeled validation data. In this paper, we introduce ST-SSAD, the first unsupervised approach to end-to-end augmentation tuning for SSAD. To this end, our work presents two key contributions. The first is a new unsupervised validation loss that quantifies the alignment between augmented training data and unlabeled validation data. The second is new differentiable augmentation functions, allowing data augmentation hyperparameter(s) to be tuned in an end-to-end manner. Experiments on two testbeds with semantic class anomalies and subtle industrial defects show that ST-SSAD gives significant performance gains over existing works. All our code and testbeds are available at https://github.com/jaeminyoo/ST-SSAD.
Track and Tweak: Monitoring and Improving Group Fairness for Temporal Graph Neural Networks in Real Time
PDF ↗The prevalence of temporal networks in real-world applications, like financial transaction networks for loan approval prediction, poses significant challenges for ensuring fairness across different groups. These dynamic systems increasingly rely on Temporal Graph Neural Networks (TGNNs) to model evolving interactions between users over time, but TGNNs can inadvertently produce unfair outcomes across different demographic groups. In this work, we are the first to investigate group fairness on temporal graphs and propose a novel real-time framework for monitoring and improving group fairness in TGNNs. We begin by incorporating a fixed fairness regularization term into the TGNN framework, named FTGNN-R, which operates in real-time but exhibits several critical limitations. To address this, we propose FTGNN-M, a new monitoring-based approach that assesses fairness on the fly, without relying on unseen test data. By conducting a sensitivity analysis, FTGNN-M further identifies the specific channels of node embeddings responsible for unfairness and adaptively adjusts the corresponding subset of model parameters. This approach enables a trade-off between fairness and utility in dynamic settings. FTGNN-M offers theoretical guarantees for both fairness assessment and fairness promotion. Extensive experiments on five temporal transaction network datasets demonstrate the effectiveness of our proposed FTGNN-M model in terms of both utility and fairness metrics.
Large language models (LLMs) have significantly improved various aspects of our daily lives. These models have impacted numerous domains, from healthcare to education, enhancing productivity, decision-making processes, and accessibility. However, the quadratic complexity of attention in transformer architectures makes it impractical to train very large models on lengthy texts or use them efficiently during inference. While a recent study by [Kacham, Mirrokni and Zhong 2023] introduced a technique that replaces the softmax with a polynomial function and polynomial sketching to speed up attention mechanisms, the theoretical understandings of this new approach are not yet well understood. In this paper, we offer a theoretical analysis of the expressive capabilities of polynomial attention. Our study reveals a disparity in the ability of high-degree and low-degree polynomial attention. Specifically, we construct two carefully designed datasets, namely D 0 and D 1, where D 1 includes a feature with a significantly larger value compared to D 0. We demonstrate that with a sufficiently high degree β, a single-layer polynomial attention network can distinguish between D 0 and D 1. However, with a low degree β, the network cannot effectively separate the two datasets. This analysis underscores the greater effectiveness of high-degree polynomials in amplifying large values and distinguishing between datasets. Our analysis offers insight into the representational capacity of polynomial attention and provides a rationale for incorporating higher-degree polynomials in attention mechanisms to capture intricate linguistic correlations.
Predicting changes in binding free energy (ΔΔ G) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between ΔΔ G and entropy, using probabilities of biologically important objects such as side chain angles and residue identities to estimate ΔΔ G. However, estimating the full conformational distribution of a protein complex is generally considered intractable. In this work, we propose a new approach to ΔΔ G prediction that avoids this issue by instead leveraging energy-based models for estimating the probability of a complex's conformation. Specifically, we novelly decompose ΔΔ G into a sequence-based component estimated by an inverse folding model and a structure-based component estimated by an energy model. This decomposition is made tractable by assuming equilibrium between the bound and unbound states, allowing us to simplify the estimation of degeneracies associated with each state. Unlike previous deep learning-based methods, our method incorporates an energy-based physical inductive bias by connecting the often-used sequence log-odds ratio-based approach to ΔΔ G prediction with a new ΔΔ E term grounded in statistical mechanics. We demonstrate superiority over existing state-of-the-art structure and sequence-based deep learning methods in ΔΔ G prediction and antibody optimization against SARS-CoV-2.
Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Molecular Graph Learning
PDF ↗Graph Neural Networks (GNNs) have gained considerable traction for modeling molecular structures and predicting properties, but their interpretability remains a significant challenge in understanding chemical behaviors. Current interpretation methods often rely on post-hoc explanations, which aim to provide transparency in GNN decisions. However, these approaches struggle with interpreting complex subgraphs and fail to leverage explanations to enhance predictive capabilities. While transparent methods can enhance GNN predictions, they typically compromise on explanation precision. This limitation underscores the need for a new strategy that effectively integrates GNN explanations and predictions. In this study, we have developed a novel interpretable causal GNN framework that combines retrieval-based causal learning with Graph Information Bottleneck (GIB) theory. Our framework semi-parametrically identifies crucial subgraphs through GIB and compresses explanatory subgraphs using a causal module. The framework consistently outperformed state-of-the-art methods, achieving a 32.72% increase in precision for scientific explanation tasks involving diverse substructures. More importantly, the learned explanations were also shown to be able to improve GNN prediction performance. This advancement is particularly vital for molecular graph learning, as it addresses the critical need to interpret how molecular structures influence predicted properties, thereby aiding drug discovery and materials science by providing insights into chemical mechanisms.
The rapid expansion in the size of new datasets has created a need for fast and efficient parameter-learning techniques. Compressive learning is a framework that enables efficient processing by using random, nonlinear features to project large-scale databases onto compact, information-preserving representations whose dimensionality is independent of the number of samples and can be easily stored, transferred, and processed. These database-level summaries are then used to decode parameters of interest from the underlying data distribution without requiring access to the original samples, offering an efficient and privacy-friendly learning framework. However, both the encoding and decoding techniques are typically randomized and data-independent, failing to exploit the underlying structure of the data. In this work, we propose a framework that meta-learns both the encoding and decoding stages of compressive learning methods by using neural networks that provide faster and more accurate systems than the current state-of-the-art approaches. To demonstrate the potential of the presented Compressive Meta-Learning framework, we explore multiple applications--including neural network-based compressive PCA, compressive ridge regression, compressive k-means, and autoencoders.
Differentially private stochastic gradient descent (DP-SGD) is broadly considered to be the gold standard for training and fine-tuning neural networks under differential privacy (DP). With the increasing availability of high-quality pre-trained model checkpoints (e.g., vision and language models), fine-tuning has become a popular strategy. However, despite recent progress in understanding and applying DP-SGD for private transfer learning tasks, significant challenges remain - most notably, the performance gap between models fine-tuned with DP-SGD and their non-private counterparts. Sparse fine-tuning on private data has emerged as an alternative to full-model fine-tuning -- recent work has shown that privately fine-tuning only a small subset of model weights and keeping the rest of the weights fixed can lead to better performance. In this work, we propose a new approach for sparse fine-tuning of neural networks under DP. Existing work on private sparse finetuning often used fixed choice of trainable weights (e.g., updating only the last layer), or relied on public model's weights to choose the subset of weights to modify. Such choice of weights remains suboptimal. In contrast, we explore an optimization-based approach, where our selection method makes use of the private gradient information, while using off the shelf privacy accounting techniques. Our numerical experiments on several computer vision models and datasets show that our parameter selection method leads to better prediction accuracy, compared to full-model private fine-tuning or existing private sparse fine-tuning approaches. Our code is available here: https://github.com/mazumder-lab/SPARTA/tree/main