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Nesreen K. Ahmed

Nesreen K. Ahmed appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningSocial and Information Networksphysics.soc-phArtificial IntelligenceDistributed, Parallel, and Cluster ComputingHuman-Computer InteractionApplicationsData Structures and AlgorithmsDatabasesInformation RetrievalDigital LibrariesPerformanceProgramming Languages

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Published work

18 published item(s)

preprint2026arXiv

D3-Gym: Constructing Real-World Verifiable Environments for Data-Driven Discovery

Despite recent progress in language models and agents for scientific data-driven discovery, further advancing their capabilities is held back by the absence of verifiable environments representing real-world scientific tasks. To fill this gap, we introduce D3-Gym, the first automatically constructed dataset with verifiable environments for scientific Data-Driven Discovery. D3-Gym comprises (1) 565 tasks sourced from 239 real scientific repositories across four disciplines where (2) each task is equipped with a natural language instruction, an executable environment with pre-installed dependencies, input dataset and artifact previews, a reference code solution, and an automatically synthesized evaluation script. Rigorous evaluation of the quality of the verification signal in D3-Gym confirms that our evaluation scripts achieve 87.5% agreement with human-annotated gold standards and strong alignment in domain-specific evaluation logic, showing their scientific soundness. Further, training on trajectories sampled from D3-Gym yields consistent and substantial gains across Qwen3 models of varying sizes on ScienceAgentBench, boosting Qwen3-32B by 7.8 absolute points and substantially shrinking the gap with strong proprietary models. All D3-Gym artifacts (environments, creation workflow, trajectories, and models) can be found at https://github.com/OSU-NLP-Group/D3-Gym.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

End-to-end Mapping in Heterogeneous Systems Using Graph Representation Learning

To enable heterogeneous computing systems with autonomous programming and optimization capabilities, we propose a unified, end-to-end, programmable graph representation learning (PGL) framework that is capable of mining the complexity of high-level programs down to the universal intermediate representation, extracting the specific computational patterns and predicting which code segments would run best on a specific core in heterogeneous hardware platforms. The proposed framework extracts multi-fractal topological features from code graphs, utilizes graph autoencoders to learn how to partition the graph into computational kernels, and exploits graph neural networks (GNN) to predict the correct assignment to a processor type. In the evaluation, we validate the PGL framework and demonstrate a maximum speedup of 6.42x compared to the thread-based execution, and 2.02x compared to the state-of-the-art technique.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Joint Learning of Hierarchical Community Structure and Node Representations: An Unsupervised Approach

Graph representation learning has demonstrated improved performance in tasks such as link prediction and node classification across a range of domains. Research has shown that many natural graphs can be organized in hierarchical communities, leading to approaches that use these communities to improve the quality of node representations. However, these approaches do not take advantage of the learned representations to also improve the quality of the discovered communities and establish an iterative and joint optimization of representation learning and community discovery. In this work, we present Mazi, an algorithm that jointly learns the hierarchical community structure and the node representations of the graph in an unsupervised fashion. To account for the structure in the node representations, Mazi generates node representations at each level of the hierarchy, and utilizes them to influence the node representations of the original graph. Further, the communities at each level are discovered by simultaneously maximizing the modularity metric and minimizing the distance between the representations of a node and its community. Using multi-label node classification and link prediction tasks, we evaluate our method on a variety of synthetic and real-world graphs and demonstrate that Mazi outperforms other hierarchical and non-hierarchical methods.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Personalized Visualization Recommendation

Visualization recommendation work has focused solely on scoring visualizations based on the underlying dataset and not the actual user and their past visualization feedback. These systems recommend the same visualizations for every user, despite that the underlying user interests, intent, and visualization preferences are likely to be fundamentally different, yet vitally important. In this work, we formally introduce the problem of personalized visualization recommendation and present a generic learning framework for solving it. In particular, we focus on recommending visualizations personalized for each individual user based on their past visualization interactions (e.g., viewed, clicked, manually created) along with the data from those visualizations. More importantly, the framework can learn from visualizations relevant to other users, even if the visualizations are generated from completely different datasets. Experiments demonstrate the effectiveness of the approach as it leads to higher quality visualization recommendations tailored to the specific user intent and preferences. To support research on this new problem, we release our user-centric visualization corpus consisting of 17.4k users exploring 94k datasets with 2.3 million attributes and 32k user-generated visualizations.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Temporal Network Sampling

Temporal networks representing a stream of timestamped edges are seemingly ubiquitous in the real-world. However, the massive size and continuous nature of these networks make them fundamentally challenging to analyze and leverage for descriptive and predictive modeling tasks. In this work, we propose a general framework for temporal network sampling with unbiased estimation. We develop online, single-pass sampling algorithms and unbiased estimators for temporal network sampling. The proposed algorithms enable fast, accurate, and memory-efficient statistical estimation of temporal network patterns and properties. In addition, we propose a temporally decaying sampling algorithm with unbiased estimators for studying networks that evolve in continuous time, where the strength of links is a function of time, and the motif patterns are temporally-weighted. In contrast to the prior notion of a $\bigtriangleup t$-temporal motif, the proposed formulation and algorithms for counting temporally weighted motifs are useful for forecasting tasks in networks such as predicting future links, or a future time-series variable of nodes and links. Finally, extensive experiments on a variety of temporal networks from different domains demonstrate the effectiveness of the proposed algorithms. A detailed ablation study is provided to understand the impact of the various components of the proposed framework.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Dynamic Node Embeddings from Edge Streams

Networks evolve continuously over time with the addition, deletion, and changing of links and nodes. Such temporal networks (or edge streams) consist of a sequence of timestamped edges and are seemingly ubiquitous. Despite the importance of accurately modeling the temporal information, most embedding methods ignore it entirely or approximate the temporal network using a sequence of static snapshot graphs. In this work, we propose using the notion of temporal walks for learning dynamic embeddings from temporal networks. Temporal walks capture the temporally valid interactions (e.g., flow of information, spread of disease) in the dynamic network in a lossless fashion. Based on the notion of temporal walks, we describe a general class of embeddings called continuous-time dynamic network embeddings (CTDNEs) that completely avoid the issues and problems that arise when approximating the temporal network as a sequence of static snapshot graphs. Unlike previous work, CTDNEs learn dynamic node embeddings directly from the temporal network at the finest temporal granularity and thus use only temporally valid information. As such CTDNEs naturally support online learning of the node embeddings in a streaming real-time fashion. Finally, the experiments demonstrate the effectiveness of this class of embedding methods that leverage temporal walks as it achieves an average gain in AUC of 11.9% across all methods and graphs.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

NeuroVectorizer: End-to-End Vectorization with Deep Reinforcement Learning

One of the key challenges arising when compilers vectorize loops for today's SIMD-compatible architectures is to decide if vectorization or interleaving is beneficial. Then, the compiler has to determine how many instructions to pack together and how many loop iterations to interleave. Compilers are designed today to use fixed-cost models that are based on heuristics to make vectorization decisions on loops. However, these models are unable to capture the data dependency, the computation graph, or the organization of instructions. Alternatively, software engineers often hand-write the vectorization factors of every loop. This, however, places a huge burden on them, since it requires prior experience and significantly increases the development time. In this work, we explore a novel approach for handling loop vectorization and propose an end-to-end solution using deep reinforcement learning (RL). We conjecture that deep RL can capture different instructions, dependencies, and data structures to enable learning a sophisticated model that can better predict the actual performance cost and determine the optimal vectorization factors. We develop an end-to-end framework, from code to vectorization, that integrates deep RL in the LLVM compiler. Our proposed framework takes benchmark codes as input and extracts the loop codes. These loop codes are then fed to a loop embedding generator that learns an embedding for these loops. Finally, the learned embeddings are used as input to a Deep RL agent, which determines the vectorization factors for all the loops. We further extend our framework to support multiple supervised learning methods. We evaluate our approaches against the currently used LLVM vectorizer and loop polyhedral optimization techniques. Our experiments show 1.29X-4.73X performance speedup compared to baseline and only 3% worse than the brute-force search on a wide range of benchmarks.

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
preprint2016arXiv

Graphlet Decomposition: Framework, Algorithms, and Applications

From social science to biology, numerous applications often rely on graphlets for intuitive and meaningful characterization of networks at both the global macro-level as well as the local micro-level. While graphlets have witnessed a tremendous success and impact in a variety of domains, there has yet to be a fast and efficient approach for computing the frequencies of these subgraph patterns. However, existing methods are not scalable to large networks with millions of nodes and edges, which impedes the application of graphlets to new problems that require large-scale network analysis. To address these problems, we propose a fast, efficient, and parallel algorithm for counting graphlets of size k={3,4}-nodes that take only a fraction of the time to compute when compared with the current methods used. The proposed graphlet counting algorithms leverages a number of proven combinatorial arguments for different graphlets. For each edge, we count a few graphlets, and with these counts along with the combinatorial arguments, we obtain the exact counts of others in constant time. On a large collection of 300+ networks from a variety of domains, our graphlet counting strategies are on average 460x faster than current methods. This brings new opportunities to investigate the use of graphlets on much larger networks and newer applications as we show in the experiments. To the best of our knowledge, this paper provides the largest graphlet computations to date as well as the largest systematic investigation on over 300+ networks from a variety of domains.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Relational Similarity Machines

This paper proposes Relational Similarity Machines (RSM): a fast, accurate, and flexible relational learning framework for supervised and semi-supervised learning tasks. Despite the importance of relational learning, most existing methods are hard to adapt to different settings, due to issues with efficiency, scalability, accuracy, and flexibility for handling a wide variety of classification problems, data, constraints, and tasks. For instance, many existing methods perform poorly for multi-class classification problems, graphs that are sparsely labeled or network data with low relational autocorrelation. In contrast, the proposed relational learning framework is designed to be (i) fast for learning and inference at real-time interactive rates, and (ii) flexible for a variety of learning settings (multi-class problems), constraints (few labeled instances), and application domains. The experiments demonstrate the effectiveness of RSM for a variety of tasks and data.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Revisiting Role Discovery in Networks: From Node to Edge Roles

Previous work in network analysis has focused on modeling the mixed-memberships of node roles in the graph, but not the roles of edges. We introduce the edge role discovery problem and present a generalizable framework for learning and extracting edge roles from arbitrary graphs automatically. Furthermore, while existing node-centric role models have mainly focused on simple degree and egonet features, this work also explores graphlet features for role discovery. In addition, we also develop an approach for automatically learning and extracting important and useful edge features from an arbitrary graph. The experimental results demonstrate the utility of edge roles for network analysis tasks on a variety of graphs from various problem domains.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Role Discovery in Networks

Roles represent node-level connectivity patterns such as star-center, star-edge nodes, near-cliques or nodes that act as bridges to different regions of the graph. Intuitively, two nodes belong to the same role if they are structurally similar. Roles have been mainly of interest to sociologists, but more recently, roles have become increasingly useful in other domains. Traditionally, the notion of roles were defined based on graph equivalences such as structural, regular, and stochastic equivalences. We briefly revisit these early notions and instead propose a more general formulation of roles based on the similarity of a feature representation (in contrast to the graph representation). This leads us to propose a taxonomy of three general classes of techniques for discovering roles that includes (i) graph-based roles, (ii) feature-based roles, and (iii) hybrid roles. We also propose a flexible framework for discovering roles using the notion of similarity on a feature-based representation. The framework consists of two fundamental components: (a) role feature construction and (b) role assignment using the learned feature representation. We discuss the different possibilities for discovering feature-based roles and the tradeoffs of the many techniques for computing them. Finally, we discuss potential applications and future directions and challenges.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

A Web-based Interactive Visual Graph Analytics Platform

This paper proposes a web-based visual graph analytics platform for interactive graph mining, visualization, and real-time exploration of networks. GraphVis is fast, intuitive, and flexible, combining interactive visualizations with analytic techniques to reveal important patterns and insights for sense making, reasoning, and decision making. Networks can be visualized and explored within seconds by simply drag-and-dropping a graph file into the web browser. The structure, properties, and patterns of the network are computed automatically and can be instantly explored in real-time. At the heart of GraphVis lies a multi-level interactive network visualization and analytics engine that allows for real-time graph mining and exploration across multiple levels of granularity simultaneously. Both the graph analytic and visualization techniques (at each level of granularity) are dynamic and interactive, with immediate and continuous visual feedback upon every user interaction (e.g., change of a slider for filtering). Furthermore, nodes, edges, and subgraphs are easily inserted, deleted or exported via a number of novel techniques and tools that make it extremely easy and flexible for exploring, testing hypothesis, and understanding networks in real-time over the web. A number of interactive visual graph analytic techniques are also proposed including interactive role discovery methods, community detection, as well as a number of novel block models for generating graphs with community structure. Finally, we also highlight other key aspects including filtering, querying, ranking, manipulating, exporting, partitioning, as well as tools for dynamic network analysis and visualization, interactive graph generators, and a variety of multi-level network analysis, summarization, and statistical techniques.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

NetworkRepository: An Interactive Data Repository with Multi-scale Visual Analytics

Network Repository (NR) is the first interactive data repository with a web-based platform for visual interactive analytics. Unlike other data repositories (e.g., UCI ML Data Repository, and SNAP), the network data repository (networkrepository.com) allows users to not only download, but to interactively analyze and visualize such data using our web-based interactive graph analytics platform. Users can in real-time analyze, visualize, compare, and explore data along many different dimensions. The aim of NR is to make it easy to discover key insights into the data extremely fast with little effort while also providing a medium for users to share data, visualizations, and insights. Other key factors that differentiate NR from the current data repositories is the number of graph datasets, their size, and variety. While other data repositories are static, they also lack a means for users to collaboratively discuss a particular dataset, corrections, or challenges with using the data for certain applications. In contrast, we have incorporated many social and collaborative aspects into NR in hopes of further facilitating scientific research (e.g., users can discuss each graph, post observations, visualizations, etc.).

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Graph Sample and Hold: A Framework for Big-Graph Analytics

Sampling is a standard approach in big-graph analytics; the goal is to efficiently estimate the graph properties by consulting a sample of the whole population. A perfect sample is assumed to mirror every property of the whole population. Unfortunately, such a perfect sample is hard to collect in complex populations such as graphs (e.g. web graphs, social networks etc), where an underlying network connects the units of the population. Therefore, a good sample will be representative in the sense that graph properties of interest can be estimated with a known degree of accuracy. While previous work focused particularly on sampling schemes used to estimate certain graph properties (e.g. triangle count), much less is known for the case when we need to estimate various graph properties with the same sampling scheme. In this paper, we propose a generic stream sampling framework for big-graph analytics, called Graph Sample and Hold (gSH). To begin, the proposed framework samples from massive graphs sequentially in a single pass, one edge at a time, while maintaining a small state. We then show how to produce unbiased estimators for various graph properties from the sample. Given that the graph analysis algorithms will run on a sample instead of the whole population, the runtime complexity of these algorithm is kept under control. Moreover, given that the estimators of graph properties are unbiased, the approximation error is kept under control. Finally, we show the performance of the proposed framework (gSH) on various types of graphs, such as social graphs, among others.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Learning the Latent State Space of Time-Varying Graphs

From social networks to Internet applications, a wide variety of electronic communication tools are producing streams of graph data; where the nodes represent users and the edges represent the contacts between them over time. This has led to an increased interest in mechanisms to model the dynamic structure of time-varying graphs. In this work, we develop a framework for learning the latent state space of a time-varying email graph. We show how the framework can be used to find subsequences that correspond to global real-time events in the Email graph (e.g. vacations, breaks, ...etc.). These events impact the underlying graph process to make its characteristics non-stationary. Within the framework, we compare two different representations of the temporal relationships; discrete vs. probabilistic. We use the two representations as inputs to a mixture model to learn the latent state transitions that correspond to important changes in the Email graph structure over time.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Network Sampling: From Static to Streaming Graphs

Network sampling is integral to the analysis of social, information, and biological networks. Since many real-world networks are massive in size, continuously evolving, and/or distributed in nature, the network structure is often sampled in order to facilitate study. For these reasons, a more thorough and complete understanding of network sampling is critical to support the field of network science. In this paper, we outline a framework for the general problem of network sampling, by highlighting the different objectives, population and units of interest, and classes of network sampling methods. In addition, we propose a spectrum of computational models for network sampling methods, ranging from the traditionally studied model based on the assumption of a static domain to a more challenging model that is appropriate for streaming domains. We design a family of sampling methods based on the concept of graph induction that generalize across the full spectrum of computational models (from static to streaming) while efficiently preserving many of the topological properties of the input graphs. Furthermore, we demonstrate how traditional static sampling algorithms can be modified for graph streams for each of the three main classes of sampling methods: node, edge, and topology-based sampling. Our experimental results indicate that our proposed family of sampling methods more accurately preserves the underlying properties of the graph for both static and streaming graphs. Finally, we study the impact of network sampling algorithms on the parameter estimation and performance evaluation of relational classification algorithms.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Space-Efficient Sampling from Social Activity Streams

In order to efficiently study the characteristics of network domains and support development of network systems (e.g. algorithms, protocols that operate on networks), it is often necessary to sample a representative subgraph from a large complex network. Although recent subgraph sampling methods have been shown to work well, they focus on sampling from memory-resident graphs and assume that the sampling algorithm can access the entire graph in order to decide which nodes/edges to select. Many large-scale network datasets, however, are too large and/or dynamic to be processed using main memory (e.g., email, tweets, wall posts). In this work, we formulate the problem of sampling from large graph streams. We propose a streaming graph sampling algorithm that dynamically maintains a representative sample in a reservoir based setting. We evaluate the efficacy of our proposed methods empirically using several real-world data sets. Across all datasets, we found that our method produce samples that preserve better the original graph distributions.

0 citations0 reviewsNo code linkedOpen access