arXiv subjects

Zohair Shafi

Publications and source records attributed to Zohair Shafi.

13 recordsLinked to original sources

arXiv2026

Beat the Counter First: A Baseline for Temporal-Graph Anomaly Detectors

Progress in streaming, edge-level graph anomaly detection (GAD) has been marked by increasingly elaborate architectures, from count-min-sketch chi square tests to memory-augmented attention networks. Yet the empirical gains attributable to this added complexity have not been systematically evaluated. We propose SimpleCount, a reference with no parameter fitting that selects one scalar feature per dataset from a fixed pool of counts, recencies, first-occurrence indicators, and count-derived transforms. We compare SimpleCount with two temporal-graph detector models and an IsoForest control fitted to the complete feature vector across five public datasets and one synthetic dataset. SimpleCount matches or exceeds SLADE on three of six datasets and exceeds IsoForest on all six. We report paired statistical tests and five-seed SLADE evaluations. SLADE requires 23 to 133x more wall-clock time than SimpleCount. On Synth-Triangle and an additional Synth-Quad probe, pre-event structural scores recover the planted signal at AUC up to 0.955, while all evaluated detector models remain near random. The benefit of complexity is dataset-dependent, and every claimed gain should be reported against a strong one-feature reference together with its compute cost.

cs.LG↗

arXiv2026

DeepWeightFlow: Re-Basined Flow Matching for Generating Neural Network Weights

Building efficient and effective generative models for neural network weights has been a research focus of significant interest that faces challenges posed by the high-dimensional weight spaces of modern neural networks and their symmetries. Several prior generative models are limited to generating partial neural network weights, particularly for larger models, such as ResNet and ViT. Those that do generate complete weights struggle with generation speed or require finetuning of the generated models. In this work, we present DeepWeightFlow, a Flow Matching model that operates directly in weight space to generate diverse and high-accuracy neural network weights for a variety of architectures, neural network sizes, and data modalities. The neural networks generated by DeepWeightFlow do not require fine-tuning to perform well and can scale to large networks. We apply Git Re-Basin and TransFusion for neural network canonicalization in the context of generative weight models to account for the impact of neural network permutation symmetries and to improve generation efficiency for larger model sizes. The generated networks excel at transfer learning, and ensembles of hundreds of neural networks can be generated in minutes, far exceeding the efficiency of diffusion-based methods. DeepWeightFlow models pave the way for more efficient and scalable generation of diverse sets of neural networks.

cs.LG↗

arXiv2025

Graph-SCP: Accelerating Set Cover Problems with Graph Neural Networks

Machine learning (ML) approaches are increasingly being used to accelerate combinatorial optimization (CO) problems. We investigate the Set Cover Problem (SCP) and propose Graph-SCP, a graph neural network method that augments existing optimization solvers by learning to identify a smaller sub-problem that contains the solution space. Graph-SCP uses both supervised learning from prior solved instances and unsupervised learning to minimize the SCP objective. We evaluate the performance of Graph-SCP on synthetically weighted and unweighted SCP instances with diverse problem characteristics and complexities, and on instances from the OR Library, a canonical benchmark for SCP. We show that Graph-SCP reduces the problem size by 60-80% and achieves runtime speedups of up to 10x on average when compared to Gurobi (a state-of-the-art commercial solver), while maintaining solution quality. This is in contrast to fast greedy solutions that significantly compromise solution quality to achieve guaranteed polynomial runtime. We showcase Graph-SCP's ability to generalize to larger problem sizes, training on SCP instances with up to 3,000 subsets and testing on SCP instances with up to 10,000 subsets.

cs.LG↗

arXiv2025

FORGE: Foundational Optimization Representations from Graph Embeddings

Combinatorial optimization problems are ubiquitous in science and engineering. Still, learning-based approaches to accelerate combinatorial optimization often require solving a large number of difficult instances to collect training data, incurring significant computational cost. Existing learning-based methods require training dedicated models for each problem distribution, for each downstream task, severely limiting their scalability and generalization. We introduce Forge: Foundational Optimization Representations from Graph Embeddings, a framework that pre-trains a vector-quantized graph autoencoder on a large, diverse collection of mixed-integer programming (MIP) instances in an unsupervised manner, without relying on optimization solvers or optimal solutions. Vector quantization produces discrete code assignments that serve as a vocabulary for representing optimization instances. We evaluate Forge in both unsupervised and supervised settings. In the unsupervised setting, Forge embeddings effectively cluster unseen instances across problem domains and sizes. In the supervised setting, we fine-tune Forge embeddings and show that a single pre-trained model helps predicting both the integrality gap for cut-generation and variable hints for search guidance across multiple problem and size distributions. In both tasks, we improve the performance of a commercial optimization solver and outperform state-of-the-art learning-based methods. Finally, we open-source our training code, pre-trained Forge weights, and embeddings for multiple MIP distributions to foster further research in representation learning for optimization problems https://skadio.github.io/forge/

cs.LG↗

arXiv2025

Defense Against Shortest Path Attacks

Identifying shortest paths between nodes in a network is an important task in many applications. Recent work has shown that a malicious actor can manipulate a graph to make traffic between two nodes of interest follow their target path. In this paper, we develop a defense against such attacks by modifying the edge weights that users observe. The defender must balance inhibiting the attacker against any negative effects on benign users. Specifically, the defender's goals are: (a) recommend the shortest paths to users, (b) make the lengths of the shortest paths in the published graph close to those of the same paths in the true graph, and (c) minimize the probability of an attack. We formulate the defense as a Stackelberg game in which the defender is the leader and the attacker is the follower. We also consider a zero-sum version of the game in which the defender's goal is to minimize cost while achieving the minimum possible attack probability. We show that the defense problem is NP-hard and propose heuristic solutions for both the zero-sum and non-zero-sum settings. By relaxing some constraints of the original problem, we formulate a linear program for local optimization around a feasible point. We present defense results with both synthetic and real networks and show that our methods often reach the lower bound of the defender's cost.

cs.SI↗

arXiv2024

REGE: A Method for Incorporating Uncertainty in Graph Embeddings

Machine learning models for graphs in real-world applications are prone to two primary types of uncertainty: (1) those that arise from incomplete and noisy data and (2) those that arise from uncertainty of the model in its output. These sources of uncertainty are not mutually exclusive. Additionally, models are susceptible to targeted adversarial attacks, which exacerbate both of these uncertainties. In this work, we introduce Radius Enhanced Graph Embeddings (REGE), an approach that measures and incorporates uncertainty in data to produce graph embeddings with radius values that represent the uncertainty of the model's output. REGE employs curriculum learning to incorporate data uncertainty and conformal learning to address the uncertainty in the model's output. In our experiments, we show that REGE's graph embeddings perform better under adversarial attacks by an average of 1.5% (accuracy) against state-of-the-art methods.

cs.LG↗

arXiv2024

Generating Human Understandable Explanations for Node Embeddings

Node embedding algorithms produce low-dimensional latent representations of nodes in a graph. These embeddings are often used for downstream tasks, such as node classification and link prediction. In this paper, we investigate the following two questions: (Q1) Can we explain each embedding dimension with human-understandable graph features (e.g. degree, clustering coefficient and PageRank). (Q2) How can we modify existing node embedding algorithms to produce embeddings that can be easily explained by human-understandable graph features? We find that the answer to Q1 is yes and introduce a new framework called XM (short for eXplain eMbedding) to answer Q2. A key aspect of XM involves minimizing the nuclear norm of the generated explanations. We show that by minimizing the nuclear norm, we minimize the lower bound on the entropy of the generated explanations. We test XM on a variety of real-world graphs and show that XM not only preserves the performance of existing node embedding methods, but also enhances their explainability.

cs.LG↗

arXiv2023

GRASP: Accelerating Shortest Path Attacks via Graph Attention

Recent advances in machine learning (ML) have shown promise in aiding and accelerating classical combinatorial optimization algorithms. ML-based speed ups that aim to learn in an end to end manner (i.e., directly output the solution) tend to trade off run time with solution quality. Therefore, solutions that are able to accelerate existing solvers while maintaining their performance guarantees, are of great interest. We consider an APX-hard problem, where an adversary aims to attack shortest paths in a graph by removing the minimum number of edges. We propose the GRASP algorithm: Graph Attention Accelerated Shortest Path Attack, an ML aided optimization algorithm that achieves run times up to 10x faster, while maintaining the quality of solution generated. GRASP uses a graph attention network to identify a smaller subgraph containing the combinatorial solution, thus effectively reducing the input problem size. Additionally, we demonstrate how careful representation of the input graph, including node features that correlate well with the optimization task, can highlight important structure in the optimization solution.

cs.LG↗

arXiv2022

Attacking Shortest Paths by Cutting Edges

Identifying shortest paths between nodes in a network is a common graph analysis problem that is important for many applications involving routing of resources. An adversary that can manipulate the graph structure could alter traffic patterns to gain some benefit (e.g., make more money by directing traffic to a toll road). This paper presents the Force Path Cut problem, in which an adversary removes edges from a graph to make a particular path the shortest between its terminal nodes. We prove that this problem is APX-hard, but introduce PATHATTACK, a polynomial-time approximation algorithm that guarantees a solution within a logarithmic factor of the optimal value. In addition, we introduce the Force Edge Cut and Force Node Cut problems, in which the adversary targets a particular edge or node, respectively, rather than an entire path. We derive a nonconvex optimization formulation for these problems, and derive a heuristic algorithm that uses PATHATTACK as a subroutine. We demonstrate all of these algorithms on a diverse set of real and synthetic networks, illustrating the network types that benefit most from the proposed algorithms.

cs.SI↗

arXiv2022

AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We first unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Then, we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training, allowing us to limit the annotation imbalance and improve binding predictions for novel proteins and ligands. We illustrate the value of AI-Bind by predicting drugs and natural compounds with binding affinity to SARS-CoV-2 viral proteins and the associated human proteins. We also validate these predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. Overall, AI-Bind offers a powerful high-throughput approach to identify drug-target combinations, with the potential of becoming a powerful tool in drug discovery.

q-bio.QM↗

arXiv2021

Optimal Edge Weight Perturbations to Attack Shortest Paths

Finding shortest paths in a given network (e.g., a computer network or a road network) is a well-studied task with many applications. We consider this task under the presence of an adversary, who can manipulate the network by perturbing its edge weights to gain an advantage over others. Specifically, we introduce the Force Path Problem as follows. Given a network, the adversary's goal is to make a specific path the shortest by adding weights to edges in the network. The version of this problem in which the adversary can cut edges is NP-complete. However, we show that Force Path can be solved to within arbitrary numerical precision in polynomial time. We propose the PATHPERTURB algorithm, which uses constraint generation to build a set of constraints that require paths other than the adversary's target to be sufficiently long. Across a highly varied set of synthetic and real networks, we show that the optimal solution often reduces the required perturbation budget by about half when compared to a greedy baseline method.

cs.SI↗

arXiv2021

PATHATTACK: Attacking Shortest Paths in Complex Networks

Shortest paths in complex networks play key roles in many applications. Examples include routing packets in a computer network, routing traffic on a transportation network, and inferring semantic distances between concepts on the World Wide Web. An adversary with the capability to perturb the graph might make the shortest path between two nodes route traffic through advantageous portions of the graph (e.g., a toll road he owns). In this paper, we introduce the Force Path Cut problem, in which there is a specific route the adversary wants to promote by removing a minimum number of edges in the graph. We show that Force Path Cut is NP-complete, but also that it can be recast as an instance of the Weighted Set Cover problem, enabling the use of approximation algorithms. The size of the universe for the set cover problem is potentially factorial in the number of nodes. To overcome this hurdle, we propose the PATHATTACK algorithm, which via constraint generation considers only a small subset of paths -- at most 5% of the number of edges in 99% of our experiments. Across a diverse set of synthetic and real networks, the linear programming formulation of Weighted Set Cover yields the optimal solution in over 98% of cases. We also demonstrate a time/cost tradeoff using two approximation algorithms and greedy baseline methods. This work provides a foundation for addressing similar problems and expands the area of adversarial graph mining beyond recent work on node classification and embedding.

cs.SI↗

arXiv2021

RAWLSNET: Altering Bayesian Networks to Encode Rawlsian Fair Equality of Opportunity

We present RAWLSNET, a system for altering Bayesian Network (BN) models to satisfy the Rawlsian principle of fair equality of opportunity (FEO). RAWLSNET's BN models generate aspirational data distributions: data generated to reflect an ideally fair, FEO-satisfying society. FEO states that everyone with the same talent and willingness to use it should have the same chance of achieving advantageous social positions (e.g., employment), regardless of their background circumstances (e.g., socioeconomic status). Satisfying FEO requires alterations to social structures such as school assignments. Our paper describes RAWLSNET, a method which takes as input a BN representation of an FEO application and alters the BN's parameters so as to satisfy FEO when possible, and minimize deviation from FEO otherwise. We also offer guidance for applying RAWLSNET, including on recognizing proper applications of FEO. We demonstrate the use of our system with publicly available data sets. RAWLSNET's altered BNs offer the novel capability of generating aspirational data for FEO-relevant tasks. Aspirational data are free from the biases of real-world data, and thus are useful for recognizing and detecting sources of unfairness in machine learning algorithms besides biased data.

cs.CY↗