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Researcher profile

Danai Koutra

Danai Koutra contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningSocial and Information NetworksArtificial IntelligenceInformation RetrievalDatabasescs.CYeess.SY

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Published work

18 published item(s)

preprint2026arXiv

Experiment-as-Code Labs: A Declarative Stack for AI-Driven Scientific Discovery

To unleash the full potential of AI for Science, we must untether the agents from a purely digital environment. The agent's ability to control and explore in real-world labs is essential because the physical lab remains foundational to scientific discovery. While some tasks can be performed on a computer (e.g., data analysis, running simulated experiments), Eureka moments could occur at any time while operating lab instruments (e.g., when a scientist notices unexpected clues, intuition may prompt a real-time course change). Although autonomous labs are on the rise, which expose programmable APIs to control scientific instruments via software, bridging the gap between increasingly powerful AI agents and automated lab equipment requires innovation that draws insights from computer systems. We propose a new paradigm called ``Experiment-as-Code (EaC) Labs,'' where a core concept is to encode experiments as declarative configurations that can be compiled down to device-level APIs. AI agents come up with hypotheses and experiments, written as an ensemble of declarative configurations. The systems layer performs program analysis, safety checks, resource assignment, and job orchestration. Finally, programmatic experimentation occurs via actuating the device APIs. This is a general stack that is science-, lab-, and instrument-independent, representing a novel synthesis across the physical, systems, and intelligence layers to unleash the next breakthrough in AI for Science.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Augmentations in Graph Contrastive Learning: Current Methodological Flaws & Towards Better Practices

Unsupervised graph representation learning is critical to a wide range of applications where labels may be scarce or expensive to procure. Contrastive learning (CL) is an increasingly popular paradigm for such settings and the state-of-the-art in unsupervised visual representation learning. Recent work attributes the success of visual CL to use of task-relevant augmentations and large, diverse datasets. Interestingly, graph CL frameworks report strong performance despite using orders of magnitude smaller datasets and employing domain-agnostic graph augmentations (DAGAs). Motivated by this discrepancy, we probe the quality of representations learnt by popular graph CL frameworks using DAGAs. We find that DAGAs can destroy task-relevant information and harm the model's ability to learn discriminative representations. On small benchmark datasets, we show the inductive bias of graph neural networks can significantly compensate for this weak discriminability. Based on our findings, we propose several sanity checks that enable practitioners to quickly assess the quality of their model's learned representations. We further propose a broad strategy for designing task-aware augmentations that are amenable to graph CL and demonstrate its efficacy on two large-scale, complex graph applications. For example, in graph-based document classification, we show task-aware augmentations improve accuracy up to 20%.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

CAPER: Coarsen, Align, Project, Refine - A General Multilevel Framework for Network Alignment

Network alignment, or the task of finding corresponding nodes in different networks, is an important problem formulation in many application domains. We propose CAPER, a multilevel alignment framework that Coarsens the input graphs, Aligns the coarsened graphs, Projects the alignment solution to finer levels and Refines the alignment solution. We show that CAPER can improve upon many different existing network alignment algorithms by enforcing alignment consistency across multiple graph resolutions: nodes matched at finer levels should also be matched at coarser levels. CAPER also accelerates the use of slower network alignment methods, at the modest cost of linear-time coarsening and refinement steps, by allowing them to be run on smaller coarsened versions of the input graphs. Experiments show that CAPER can improve upon diverse network alignment methods by an average of 33% in accuracy and/or an order of magnitude faster in runtime.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Exploring the Design of Adaptation Protocols for Improved Generalization and Machine Learning Safety

While directly fine-tuning (FT) large-scale, pretrained models on task-specific data is well-known to induce strong in-distribution task performance, recent works have demonstrated that different adaptation protocols, such as linear probing (LP) prior to FT, can improve out-of-distribution generalization. However, the design space of such adaptation protocols remains under-explored and the evaluation of such protocols has primarily focused on distribution shifts. Therefore, in this work, we evaluate common adaptation protocols across distributions shifts and machine learning safety metrics (e.g., anomaly detection, calibration, robustness to corruptions). We find that protocols induce disparate trade-offs that were not apparent from prior evaluation. Further, we demonstrate that appropriate pairing of data augmentation and protocol can substantially mitigate this trade-off. Finally, we hypothesize and empirically see that using hardness-promoting augmentations during LP and then FT with augmentations may be particularly effective for trade-off mitigation.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

How do Quadratic Regularizers Prevent Catastrophic Forgetting: The Role of Interpolation

Catastrophic forgetting undermines the effectiveness of deep neural networks (DNNs) in scenarios such as continual learning and lifelong learning. While several methods have been proposed to tackle this problem, there is limited work explaining why these methods work well. This paper has the goal of better explaining a popularly used technique for avoiding catastrophic forgetting: quadratic regularization. We show that quadratic regularizers prevent forgetting of past tasks by interpolating current and previous values of model parameters at every training iteration. Over multiple training iterations, this interpolation operation reduces the learning rates of more important model parameters, thereby minimizing their movement. Our analysis also reveals two drawbacks of quadratic regularization: (a) dependence of parameter interpolation on training hyperparameters, which often leads to training instability and (b) assignment of lower importance to deeper layers, which are generally the place forgetting occurs in DNNs. Via a simple modification to the order of operations, we show these drawbacks can be easily avoided, resulting in 6.2\% higher average accuracy at 4.5\% lower average forgetting. We confirm the robustness of our results by training over 2000 models in different settings. Code available at \url{https://github.com/EkdeepSLubana/QRforgetting}

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning node embeddings via summary graphs: a brief theoretical analysis

Graph representation learning plays an important role in many graph mining applications, but learning embeddings of large-scale graphs remains a problem. Recent works try to improve scalability via graph summarization -- i.e., they learn embeddings on a smaller summary graph, and then restore the node embeddings of the original graph. However, all existing works depend on heuristic designs and lack theoretical analysis. Different from existing works, we contribute an in-depth theoretical analysis of three specific embedding learning methods based on introduced kernel matrix, and reveal that learning embeddings via graph summarization is actually learning embeddings on a approximate graph constructed by the configuration model. We also give analysis about approximation error. To the best of our knowledge, this is the first work to give theoretical analysis of this approach. Furthermore, our analysis framework gives interpretation of some existing methods and provides great insights for future work on this problem.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

A Hidden Challenge of Link Prediction: Which Pairs to Check?

The traditional setup of link prediction in networks assumes that a test set of node pairs, which is usually balanced, is available over which to predict the presence of links. However, in practice, there is no test set: the ground-truth is not known, so the number of possible pairs to predict over is quadratic in the number of nodes in the graph. Moreover, because graphs are sparse, most of these possible pairs will not be links. Thus, link prediction methods, which often rely on proximity-preserving embeddings or heuristic notions of node similarity, face a vast search space, with many pairs that are in close proximity, but that should not be linked. To mitigate this issue, we introduce LinkWaldo, a framework for choosing from this quadratic, massively-skewed search space of node pairs, a concise set of candidate pairs that, in addition to being in close proximity, also structurally resemble the observed edges. This allows it to ignore some high-proximity but low-resemblance pairs, and also identify high-resemblance, lower-proximity pairs. Our framework is built on a model that theoretically combines Stochastic Block Models (SBMs) with node proximity models. The block structure of the SBM maps out where in the search space new links are expected to fall, and the proximity identifies the most plausible links within these blocks, using locality sensitive hashing to avoid expensive exhaustive search. LinkWaldo can use any node representation learning or heuristic definition of proximity, and can generate candidate pairs for any link prediction method, allowing the representation power of current and future methods to be realized for link prediction in practice. We evaluate LinkWaldo on 13 networks across multiple domains, and show that on average it returns candidate sets containing 7-33% more missing and future links than both embedding-based and heuristic baselines' sets.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Node Proximity Is All You Need: Unified Structural and Positional Node and Graph Embedding

While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Refining Network Alignment to Improve Matched Neighborhood Consistency

Network alignment, or the task of finding meaningful node correspondences between nodes in different graphs, is an important graph mining task with many scientific and industrial applications. An important principle for network alignment is matched neighborhood consistency (MNC): nodes that are close in one graph should be matched to nodes that are close in the other graph. We theoretically demonstrate a close relationship between MNC and alignment accuracy. As many existing network alignment methods struggle to preserve topological consistency in difficult scenarios, we show how to refine their solutions by improving their MNC. Our refinement method, RefiNA, is straightforward to implement, admits scalable sparse approximation, and can be paired post hoc with any network alignment method. Extensive experiments show that RefiNA increases the accuracy of diverse unsupervised network alignment methods by up to 90%, making them robust enough to align graphs that are 5x more topologically different than were considered in prior work.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Towards Understanding and Evaluating Structural Node Embeddings

While most network embedding techniques model the proximity between nodes in a network, recently there has been significant interest in structural embeddings that are based on node equivalences, a notion rooted in sociology: equivalences or positions are collections of nodes that have similar roles--i.e., similar functions, ties or interactions with nodes in other positions--irrespective of their distance or reachability in the network. Unlike the proximity-based methods that are rigorously evaluated in the literature, the evaluation of structural embeddings is less mature. It relies on small synthetic or real networks with labels that are not perfectly defined, and its connection to sociological equivalences has hitherto been vague and tenuous. With new node embedding methods being developed at a breakneck pace, proper evaluation and systematic characterization of existing approaches will be essential to progress. To fill in this gap, we set out to understand what types of equivalences structural embeddings capture. We are the first to contribute rigorous intrinsic and extrinsic evaluation methodology for structural embeddings, along with carefully-designed, diverse datasets of varying sizes. We observe a number of different evaluation variables that can lead to different results (e.g., choice of similarity measure, classifier, label definitions). We find that degree distributions within nodes' local neighborhoods can lead to simple yet effective baselines in their own right and guide the future development of structural embedding. We hope that our findings can influence the design of further node embedding methods and also pave the way for more comprehensive and fair evaluation of structural embedding methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

CONE-Align: Consistent Network Alignment with Proximity-Preserving Node Embedding

Network alignment, the process of finding correspondences between nodes in different graphs, has many scientific and industrial applications. Existing unsupervised network alignment methods find suboptimal alignments that break up node neighborhoods, i.e. do not preserve matched neighborhood consistency. To improve this, we propose CONE-Align, which models intra-network proximity with node embeddings and uses them to match nodes across networks after aligning the embedding subspaces. Experiments on diverse, challenging datasets show that CONE-Align is robust and obtains 19.25% greater accuracy on average than the best-performing state-of-the-art graph alignment algorithm in highly noisy settings.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Driving with Data in the Motor City: Mining and Modeling Vehicle Fleet Maintenance Data

The City of Detroit maintains an active fleet of over 2500 vehicles, spending an annual average of over \$5 million on purchases and over \$7.7 million on maintenance. Modeling patterns and trends in this data is of particular importance to a variety of stakeholders, particularly as Detroit emerges from Chapter 9 bankruptcy, but the structure in such data is complex, and the city lacks dedicated resources for in-depth analysis. The City of Detroit's Operations and Infrastructure Group and the University of Michigan initiated a collaboration which seeks to address this unmet need by analyzing data from the City of Detroit's vehicle fleet. This work presents a case study and provides the first data-driven benchmark, demonstrating a suite of methods to aid in data understanding and prediction for large vehicle maintenance datasets. We present analyses to address three key questions raised by the stakeholders, related to discovering multivariate maintenance patterns over time; predicting maintenance; and predicting vehicle- and fleet-level costs. We present a novel algorithm, PRISM, for automating multivariate sequential data analyses using tensor decomposition. This work is a first of its kind that presents both methodologies and insights to guide future civic data research.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

From Static to Dynamic Node Embeddings

We introduce a general framework for leveraging graph stream data for temporal prediction-based applications. Our proposed framework includes novel methods for learning an appropriate graph time-series representation, modeling and weighting the temporal dependencies, and generalizing existing embedding methods for such data. While previous work on dynamic modeling and embedding has focused on representing a stream of timestamped edges using a time-series of graphs based on a specific time-scale (e.g., 1 month), we propose the notion of an $ε$-graph time-series that uses a fixed number of edges for each graph, and show its superiority over the time-scale representation used in previous work. In addition, we propose a number of new temporal models based on the notion of temporal reachability graphs and weighted temporal summary graphs. These temporal models are then used to generalize existing base (static) embedding methods by enabling them to incorporate and appropriately model temporal dependencies in the data. From the 6 temporal network models investigated (for each of the 7 base embedding methods), we find that the top-3 temporal models are always those that leverage the new $ε$-graph time-series representation. Furthermore, the dynamic embedding methods from the framework almost always achieve better predictive performance than existing state-of-the-art dynamic node embedding methods that are developed specifically for such temporal prediction tasks. Finally, the findings of this work are useful for designing better dynamic embedding methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

G-CREWE: Graph CompREssion With Embedding for Network Alignment

Network alignment is useful for multiple applications that require increasingly large graphs to be processed. Existing research approaches this as an optimization problem or computes the similarity based on node representations. However, the process of aligning every pair of nodes between relatively large networks is time-consuming and resource-intensive. In this paper, we propose a framework, called G-CREWE (Graph CompREssion With Embedding) to solve the network alignment problem. G-CREWE uses node embeddings to align the networks on two levels of resolution, a fine resolution given by the original network and a coarse resolution given by a compressed version, to achieve an efficient and effective network alignment. The framework first extracts node features and learns the node embedding via a Graph Convolutional Network (GCN). Then, node embedding helps to guide the process of graph compression and finally improve the alignment performance. As part of G-CREWE, we also propose a new compression mechanism called MERGE (Minimum dEgRee neiGhbors comprEssion) to reduce the size of the input networks while preserving the consistency in their topological structure. Experiments on all real networks show that our method is more than twice as fast as the most competitive existing methods while maintaining high accuracy.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Mining Persistent Activity in Continually Evolving Networks

Frequent pattern mining is a key area of study that gives insights into the structure and dynamics of evolving networks, such as social or road networks. However, not only does a network evolve, but often the way that it evolves, itself evolves. Thus, knowing, in addition to patterns' frequencies, for how long and how regularly they have occurred---i.e., their persistence---can add to our understanding of evolving networks. In this work, we propose the problem of mining activity that persists through time in continually evolving networks---i.e., activity that repeatedly and consistently occurs. We extend the notion of temporal motifs to capture activity among specific nodes, in what we call activity snippets, which are small sequences of edge-updates that reoccur. We propose axioms and properties that a measure of persistence should satisfy, and develop such a persistence measure. We also propose PENminer, an efficient framework for mining activity snippets' Persistence in Evolving Networks, and design both offline and streaming algorithms. We apply PENminer to numerous real, large-scale evolving networks and edge streams, and find activity that is surprisingly regular over a long period of time, but too infrequent to be discovered by aggregate count alone, and bursts of activity exposed by their lack of persistence. Our findings with PENminer include neighborhoods in NYC where taxi traffic persisted through Hurricane Sandy, the opening of new bike-stations, characteristics of social network users, and more. Moreover, we use PENminer towards identifying anomalies in multiple networks, outperforming baselines at identifying subtle anomalies by 9.8-48% in AUC.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

On Proximity and Structural Role-based Embeddings in Networks: Misconceptions, Techniques, and Applications

Structural roles define sets of structurally similar nodes that are more similar to nodes inside the set than outside, whereas communities define sets of nodes with more connections inside the set than outside. Roles based on structural similarity and communities based on proximity are fundamentally different but important complementary notions. Recently, the notion of structural roles has become increasingly important and has gained a lot of attention due to the proliferation of work on learning representations (node/edge embeddings) from graphs that preserve the notion of roles. Unfortunately, recent work has sometimes confused the notion of structural roles and communities (based on proximity) leading to misleading or incorrect claims about the capabilities of network embedding methods. As such, this paper seeks to clarify the misconceptions and key differences between structural roles and communities, and formalize the general mechanisms (e.g., random walks, feature diffusion) that give rise to community or role-based structural embeddings. We theoretically prove that embedding methods based on these mechanisms result in either community or role-based structural embeddings. These mechanisms are typically easy to identify and can help researchers quickly determine whether a method preserves community or role-based embeddings. Furthermore, they also serve as a basis for developing new and improved methods for community or role-based structural embeddings. Finally, we analyze and discuss applications and data characteristics where community or role-based embeddings are most appropriate.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

What is Normal, What is Strange, and What is Missing in a Knowledge Graph: Unified Characterization via Inductive Summarization

Knowledge graphs (KGs) store highly heterogeneous information about the world in the structure of a graph, and are useful for tasks such as question answering and reasoning. However, they often contain errors and are missing information. Vibrant research in KG refinement has worked to resolve these issues, tailoring techniques to either detect specific types of errors or complete a KG. In this work, we introduce a unified solution to KG characterization by formulating the problem as unsupervised KG summarization with a set of inductive, soft rules, which describe what is normal in a KG, and thus can be used to identify what is abnormal, whether it be strange or missing. Unlike first-order logic rules, our rules are labeled, rooted graphs, i.e., patterns that describe the expected neighborhood around a (seen or unseen) node, based on its type, and information in the KG. Stepping away from the traditional support/confidence-based rule mining techniques, we propose KGist, Knowledge Graph Inductive SummarizaTion, which learns a summary of inductive rules that best compress the KG according to the Minimum Description Length principle---a formulation that we are the first to use in the context of KG rule mining. We apply our rules to three large KGs (NELL, DBpedia, and Yago), and tasks such as compression, various types of error detection, and identification of incomplete information. We show that KGist outperforms task-specific, supervised and unsupervised baselines in error detection and incompleteness identification, (identifying the location of up to 93% of missing entities---over 10% more than baselines), while also being efficient for large knowledge graphs.

0 citations0 reviewsNo code linkedOpen access
preprint2018arXiv

Graph Summarization Methods and Applications: A Survey

While advances in computing resources have made processing enormous amounts of data possible, human ability to identify patterns in such data has not scaled accordingly. Efficient computational methods for condensing and simplifying data are thus becoming vital for extracting actionable insights. In particular, while data summarization techniques have been studied extensively, only recently has summarizing interconnected data, or graphs, become popular. This survey is a structured, comprehensive overview of the state-of-the-art methods for summarizing graph data. We first broach the motivation behind, and the challenges of, graph summarization. We then categorize summarization approaches by the type of graphs taken as input and further organize each category by core methodology. Finally, we discuss applications of summarization on real-world graphs and conclude by describing some open problems in the field.

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