arXiv subjects

Sayan Ranu

Publications and source records attributed to Sayan Ranu.

At least 19 recordsLinked to original sources

arXiv2026

SC3: The Multi-Solvent Solubility Challenge and Benchmark

Solubility prediction is a standard benchmark in computational chemistry, yet multi-solvent models which reportedly approach the experimental-noise ceiling (i.e. the aleatoric limit) are not yet reliable enough to be deployed. We argue that this gap is partly artefactual: published benchmarks differ in curation policies, evaluate on count-weighted RMSE that hides failure on tail-heavy solvent distributions, and treat the widely cited 0.6-0.8 log S inter-laboratory figure as the aleatoric ceiling even though it reflects worst-case, not expected, disagreement. We introduce SC3, a multi-solvent solubility benchmark built on BigSolDB v2.1 with three contributions: (i) a reproducible curation pipeline yielding 101,535 measurements over 1,327 solutes and 206 solvents, with a recalibrated aleatoric floor of 0.106 log S-roughly 6 times tighter than the conventional figure; (ii) nested Gold/Silver/Bronze consensus tiers with per-point standard deviation, three leakage-checked splits, and a multi-solvent metric suite (PS-RMSE, Z-RMSE); and (iii) a 31-model benchmark across six families, whose best Bronze PS-RMSE sits at 5 times the aleatoric limit, and we observe this is a gap unclosed by any deep alternative tested. We perform three follow-on analyses: data scaling, transfer from quantum-chemistry solvation energies, and feature-level attribution, which demonstrates that calibrated per-point uncertainty is a reusable infrastructure for diagnosis beyond point prediction.

physics.chem-ph↗

arXiv2026

GFFMERGE: Efficient Merging of Graph Neural Force Fields and Beyond

Graph Neural Networks (GNNs) have revolutionized Neural Force Fields for atomistic simulations, achieving near-quantum accuracy at reduced cost, yet adapting these models to new chemical systems requires expensive retraining of foundation models. Inspired by model merging in vision and language processing, we introduce GFFMERGE, the first principled framework for closed-form model merging in GNNs. We exploit the linear structure of message-passing layers and formulate merging as a convex embedding-alignment problem with an analytical solution. Through the first systematic benchmarking of model merging for GNNs, we show that existing methods designed for vision and language catastrophically fail on force field regression, while GFFMERGE recovers performance approaching gold standard joint training. Across molecular (MD17, MD22), solid-state (LiPS20), and large-scale graph benchmarks, GFFMERGE and GNNMERGE (its generic GNN counterpart) achieve 5-27$\times$ speedups while enabling modular composition of specialized models. Remarkably, our closed-form solution alone outperforms all baseline methods before fine-tuning and provides superior initialization for faster, data-efficient convergence.

cs.LG↗

arXiv2026

Position: Graph Condensation Needs a Reset -- Move Beyond Full-dataset Training and Model-Dependence

Graph Neural Networks (GNNs) are powerful tools for learning from graph-structured data, but their scalability is increasingly strained by the size of real-world graphs in domains like recommender systems, fraud detection, and molecular biology. Graph condensation -- the task of generating a smaller synthetic graph that retains the performance of models trained on the original -- has emerged as a promising solution. However, the dominant approach of gradient matching introduces a fundamental contradiction: it requires training on the full dataset to create the compressed version, thereby undermining the goal of efficiency. Worse still, these methods suffer from high computational overhead, poor generalization across GNN architectures, and brittle reliance on specific model configurations. Equally concerning is the community's reliance on misleading evaluation protocols such as node compression ratios, which fail to reflect true resource savings, condensation overhead, and illusory application to neural architecture search. These shortcomings are not incidental -- they are systemic, and they obstruct meaningful progress. In this position paper, we argue that graph condensation, in its current form, needs a reset. We call for moving beyond full-dataset training and model-dependent design, and instead advocate for methods that are lightweight, architecture-agnostic, and practically deployable. By identifying key methodological flaws and outlining concrete research directions, we aim to reorient the field toward approaches that deliver on the true promise of condensation: efficient, generalizable, and usable GNN training at scale.

cs.LG↗

arXiv2026

Revealing Interpretable Failure Modes of VLMs

Vision-Language Models (VLMs) are increasingly used in safety-critical applications because of their broad reasoning capabilities and ability to generalize with minimal task-specific engineering. Despite these advantages, they can exhibit catastrophic failures in specific real-world situations, constituting failure modes. We introduce REVELIO, a framework for systematically uncovering interpretable failure modes in VLMs. We define a failure mode as a composition of interpretable, domain-relevant concepts-such as pedestrian proximity or adverse weather conditions-under which a target VLM consistently behaves incorrectly. Identifying such failures requires searching over an exponentially large discrete combinatorial space. To address this challenge, REVELIO combines two search procedures: a diversity-aware beam search that efficiently maps the failure landscape, and a Gaussian-process Thompson Sampling strategy that enables broader exploration of complex failure modes. We apply REVELIO to autonomous driving and indoor robotics domains, uncovering previously unreported vulnerabilities in state-of-the-art VLMs. In driving environments, the models often demonstrate weak spatial grounding and fail to account for major obstructions, leading to recommendations that would result in simulated crashes. In indoor robotics tasks, VLMs either miss safety hazards or behave excessively conservatively, producing false alarms and reducing operational efficiency. By identifying structured and interpretable failure modes, REVELIO offers actionable insights that can support targeted VLM safety improvements.

cs.AI↗

arXiv2025

Lumos: Let there be Language Model System Certification

We introduce the first principled framework, Lumos, for specifying and formally certifying Language Model System (LMS) behaviors. Lumos is an imperative probabilistic programming DSL over graphs, with constructs to generate independent and identically distributed prompts for LMS. It offers a structured view of prompt distributions via graphs, forming random prompts from sampled subgraphs. Lumos supports certifying LMS for arbitrary prompt distributions via integration with statistical certifiers. We provide hybrid (operational and denotational) semantics for Lumos, providing a rigorous way to interpret the specifications. Using only a small set of composable constructs, Lumos can encode existing LMS specifications, including complex relational and temporal specifications. It also facilitates specifying new properties - we present the first safety specifications for vision-language models (VLMs) in autonomous driving scenarios developed with Lumos. Using these, we show that the state-of-the-art VLM Qwen-VL exhibits critical safety failures, producing incorrect and unsafe responses with at least 90% probability in right-turn scenarios under rainy driving conditions, revealing substantial safety risks. Lumos's modular structure allows easy modification of the specifications, enabling LMS certification to stay abreast with the rapidly evolving threat landscape. We further integrate a prompt-level deterministic verifier to obtain guarantees over the privacy of the LLM generation distribution over a prompt distribution. Lumos is simple to program in, requiring only a few constructs, as evidenced by state-of-the-art large language models generating correct Lumos specifications in zero-shot settings. Lumos is the first systematic and extensible language-based framework for specifying and certifying LMS behaviors, paving the way for a wider adoption of LMS certification.

cs.PL↗

arXiv2025

Panorama: Fast-Track Nearest Neighbors

Approximate Nearest-Neighbor Search (ANNS) pipelines for high-dimensional neural embeddings spend the bulk of their query time in candidate verification, making it the primary bottleneck in the search process. In this paper, we present PANORAMA, a state-of-the-art refinement technique that accelerates verification by exploiting the inherent spectral decay of these embeddings. Using PCA to compact signal energy, PANORAMA evaluates candidate distances incrementally, computing at each step a strict lower bound on the full-vector distance and dynamically pruning candidates the moment this bound exceeds the running k-th nearest neighbor distance. While PCA's concentration of variance facilitates pruning, it breaks the uniform-variance assumption required by Product Quantization (PQ); we resolve this with a variance-shaping step that redistributes energy across subvectors, rendering accretive refinement compatible with quantized indexes. Optimized for modern memory hierarchies via vectorized bulk-pruning and cache-conscious data layouts, PANORAMA has been upstreamed into the FAISS library across major index families (IVFPQ/Flat, HNSW, and Refine). PANORAMA achieves higher QPS at any target recall with a cost that provably scales inversely with dataset spectral decay, delivering end-to-end speedups of up to 28.9x and outperforming probabilistic methods across all recall bands.

cs.LG↗

arXiv2025

GnnXemplar: Exemplars to Explanations -- Natural Language Rules for Global GNN Interpretability

Graph Neural Networks (GNNs) are widely used for node classification, yet their opaque decision-making limits trust and adoption. While local explanations offer insights into individual predictions, global explanation methods, those that characterize an entire class, remain underdeveloped. Existing global explainers rely on motif discovery in small graphs, an approach that breaks down in large, real-world settings where subgraph repetition is rare, node attributes are high-dimensional, and predictions arise from complex structure-attribute interactions. We propose GnnXemplar, a novel global explainer inspired from Exemplar Theory from cognitive science. GnnXemplar identifies representative nodes in the GNN embedding space, exemplars, and explains predictions using natural language rules derived from their neighborhoods. Exemplar selection is framed as a coverage maximization problem over reverse k-nearest neighbors, for which we provide an efficient greedy approximation. To derive interpretable rules, we employ a self-refining prompt strategy using large language models (LLMs). Experiments across diverse benchmarks show that GnnXemplar significantly outperforms existing methods in fidelity, scalability, and human interpretability, as validated by a user study with 60 participants.

cs.LG↗

arXiv2025

UniFFBench: Evaluating Universal Machine Learning Force Fields Against Experimental Measurements

Universal machine learning force fields (UMLFFs) promise to revolutionize materials science by enabling rapid atomistic simulations across the periodic table. However, their evaluation has been limited to computational benchmarks that may not reflect real-world performance. We introduce UniFFBench, a comprehensive evaluation framework featuring the MinX dataset -- a diverse collection of 1,500+ mineral systems spanning 85 elements, extreme thermodynamic conditions (0--5000 K, 0--1000 GPa), and structural complexity, including partial occupancy and disorder. This diversity, combined with experimental reference values for validation, enables assessment of UMLFF generalization across chemical space and conditions substantially beyond typical training scenarios. Our systematic evaluation of six state-of-the-art UMLFFs reveals a substantial ``reality gap'': models achieving impressive performance on computational benchmarks often fail when confronted with experimental complexity. Even the best-performing models exhibit higher density prediction error than the threshold required for practical applications. We observe disconnects between simulation stability and mechanical property accuracy, with prediction errors correlating with training data representation rather than the modeling method.

cond-mat.mtrl-sci↗

arXiv2025

GRAIL: Graph Edit Distance and Node Alignment Using LLM-Generated Code

Graph Edit Distance (GED) is a widely used metric for measuring similarity between two graphs. Computing the optimal GED is NP-hard, leading to the development of various neural and non-neural heuristics. While neural methods have achieved improved approximation quality compared to non-neural approaches, they face significant challenges: (1) They require large amounts of ground truth data, which is itself NP-hard to compute. (2) They operate as black boxes, offering limited interpretability. (3) They lack cross-domain generalization, necessitating expensive retraining for each new dataset. We address these limitations with GRAIL, introducing a paradigm shift in this domain. Instead of training a neural model to predict GED, GRAIL employs a novel combination of large language models (LLMs) and automated prompt tuning to generate a program that is used to compute GED. This shift from predicting GED to generating programs imparts various advantages, including end-to-end interpretability and an autonomous self-evolutionary learning mechanism without ground-truth supervision. Extensive experiments on seven datasets confirm that GRAIL not only surpasses state-of-the-art GED approximation methods in prediction quality but also achieves robust cross-domain generalization across diverse graph distributions.

cs.LG↗

arXiv2025

GNNMerge: Merging of GNN Models Without Accessing Training Data

Model merging has gained prominence in machine learning as a method to integrate multiple trained models into a single model without accessing the original training data. While existing approaches have demonstrated success in domains such as computer vision and NLP, their application to Graph Neural Networks (GNNs) remains unexplored. These methods often rely on the assumption of shared initialization, which is seldom applicable to GNNs. In this work, we undertake the first benchmarking study of model merging algorithms for GNNs, revealing their limited effectiveness in this context. To address these challenges, we propose GNNMerge, which utilizes a task-agnostic node embedding alignment strategy to merge GNNs. Furthermore, we establish that under a mild relaxation, the proposed optimization objective admits direct analytical solutions for widely used GNN architectures, significantly enhancing its computational efficiency. Empirical evaluations across diverse datasets, tasks, and architectures establish GNNMerge to be up to 24% more accurate than existing methods while delivering over 2 orders of magnitude speed-up compared to training from scratch.

cs.LG↗

arXiv2024

Bonsai: Gradient-free Graph Condensation for Node Classification

Graph condensation has emerged as a promising avenue to enable scalable training of GNNs by compressing the training dataset while preserving essential graph characteristics. Our study uncovers significant shortcomings in current graph condensation techniques. First, the majority of the algorithms paradoxically require training on the full dataset to perform condensation. Second, due to their gradient-emulating approach, these methods require fresh condensation for any change in hyperparameters or GNN architecture, limiting their flexibility and reusability. Finally, they fail to achieve substantial size reduction due to synthesizing fully-connected, edge-weighted graphs. To address these challenges, we present Bonsai, a novel graph condensation method empowered by the observation that \textit{computation trees} form the fundamental processing units of message-passing GNNs. Bonsai condenses datasets by encoding a careful selection of \textit{exemplar} trees that maximize the representation of all computation trees in the training set. This unique approach imparts Bonsai as the first linear-time, model-agnostic graph condensation algorithm for node classification that outperforms existing baselines across $7$ real-world datasets on accuracy, while being $22$ times faster on average. Bonsai is grounded in rigorous mathematical guarantees on the adopted approximation strategies making it robust to GNN architectures, datasets, and parameters.

cs.LG↗

arXiv2024

TAGMol: Target-Aware Gradient-guided Molecule Generation

3D generative models have shown significant promise in structure-based drug design (SBDD), particularly in discovering ligands tailored to specific target binding sites. Existing algorithms often focus primarily on ligand-target binding, characterized by binding affinity. Moreover, models trained solely on target-ligand distribution may fall short in addressing the broader objectives of drug discovery, such as the development of novel ligands with desired properties like drug-likeness, and synthesizability, underscoring the multifaceted nature of the drug design process. To overcome these challenges, we decouple the problem into molecular generation and property prediction. The latter synergistically guides the diffusion sampling process, facilitating guided diffusion and resulting in the creation of meaningful molecules with the desired properties. We call this guided molecular generation process as TAGMol. Through experiments on benchmark datasets, TAGMol demonstrates superior performance compared to state-of-the-art baselines, achieving a 22% improvement in average Vina Score and yielding favorable outcomes in essential auxiliary properties. This establishes TAGMol as a comprehensive framework for drug generation.

q-bio.BM↗

arXiv2024

GRAPHGINI: Fostering Individual and Group Fairness in Graph Neural Networks

Graph Neural Networks (GNNs) have demonstrated impressive performance across various tasks, leading to their increased adoption in high-stakes decision-making systems. However, concerns have arisen about GNNs potentially generating unfair decisions for underprivileged groups or individuals when lacking fairness constraints. This work addresses this issue by introducing GraphGini, a novel approach that incorporates the Gini coefficient to enhance both individual and group fairness within the GNN framework. We rigorously establish that the Gini coefficient offers greater robustness and promotes equal opportunity among GNN outcomes, advantages not afforded by the prevailing Lipschitz constant methodology. Additionally, we employ the Nash social welfare program to ensure our solution yields a Pareto optimal distribution of group fairness. Extensive experimentation on real-world datasets demonstrates GraphGini's efficacy in significantly improving individual fairness compared to state-of-the-art methods while maintaining utility and group fairness.

cs.LG↗

arXiv2024

Towards Fair Allocation in Social Commerce Platforms

Social commerce platforms are emerging businesses where producers sell products through re-sellers who advertise the products to other customers in their social network. Due to the increasing popularity of this business model, thousands of small producers and re-sellers are starting to depend on these platforms for their livelihood; thus, it is important to provide fair earning opportunities to them. The enormous product space in such platforms prohibits manual search, and motivates the need for recommendation algorithms to effectively allocate product exposure and, consequently, earning opportunities. In this work, we focus on the fairness of such allocations in social commerce platforms and formulate the problem of assigning products to re-sellers as a fair division problem with indivisible items under two-sided cardinality constraints, wherein each product must be given to at least a certain number of re-sellers and each re-seller must get a certain number of products. Our work systematically explores various well-studied benchmarks of fairness -- including Nash social welfare, envy-freeness up to one item (EF1), and equitability up to one item (EQ1) -- from both theoretical and experimental perspectives. We find that the existential and computational guarantees of these concepts known from the unconstrained setting do not extend to our constrained model. To address this limitation, we develop a mixed-integer linear program and other scalable heuristics that provide near-optimal approximation of Nash social welfare in simulated and real social commerce datasets. Overall, our work takes the first step towards achieving provable fairness alongside reasonable revenue guarantees on social commerce platforms.

cs.CY↗

arXiv2024

EUGENE: Explainable Structure-aware Graph Edit Distance Estimation with Generalized Edit Costs

The need to identify graphs with small structural distances from a query arises in domains such as biology, chemistry, recommender systems, and social network analysis. Among several methods for measuring inter-graph distance, Graph Edit Distance (GED) is preferred for its comprehensibility, though its computation is hindered by NP-hardness. Optimization based heuristic methods often face challenges in providing accurate approximations. State-of-the-art GED approximations predominantly utilize neural methods, which, however: (i) lack an explanatory edit path corresponding to the approximated GED; (ii) require the NP-hard generation of ground-truth GEDs for training; and (iii) necessitate separate training on each dataset. In this paper, we propose EUGENE, an efficient, algebraic, and structure-aware optimization based method that estimates GED and also provides edit paths corresponding to the estimated cost. Extensive experimental evaluation demonstrates that EUGENE achieves state-of-the-art GED estimation with superior scalability across diverse datasets and generalized cost settings.

cs.LG↗

arXiv2023

NeuroCUT: A Neural Approach for Robust Graph Partitioning

Graph partitioning aims to divide a graph into disjoint subsets while optimizing a specific partitioning objective. The majority of formulations related to graph partitioning exhibit NP-hardness due to their combinatorial nature. Conventional methods, like approximation algorithms or heuristics, are designed for distinct partitioning objectives and fail to achieve generalization across other important partitioning objectives. Recently machine learning-based methods have been developed that learn directly from data. Further, these methods have a distinct advantage of utilizing node features that carry additional information. However, these methods assume differentiability of target partitioning objective functions and cannot generalize for an unknown number of partitions, i.e., they assume the number of partitions is provided in advance. In this study, we develop NeuroCUT with two key innovations over previous methodologies. First, by leveraging a reinforcement learning-based framework over node representations derived from a graph neural network and positional features, NeuroCUT can accommodate any optimization objective, even those with non-differentiable functions. Second, we decouple the parameter space and the partition count making NeuroCUT inductive to any unseen number of partition, which is provided at query time. Through empirical evaluation, we demonstrate that NeuroCUT excels in identifying high-quality partitions, showcases strong generalization across a wide spectrum of partitioning objectives, and exhibits strong generalization to unseen partition count.

cs.LG↗

arXiv2023

Mirage: Model-Agnostic Graph Distillation for Graph Classification

GNNs, like other deep learning models, are data and computation hungry. There is a pressing need to scale training of GNNs on large datasets to enable their usage on low-resource environments. Graph distillation is an effort in that direction with the aim to construct a smaller synthetic training set from the original training data without significantly compromising model performance. While initial efforts are promising, this work is motivated by two key observations: (1) Existing graph distillation algorithms themselves rely on training with the full dataset, which undermines the very premise of graph distillation. (2) The distillation process is specific to the target GNN architecture and hyper-parameters and thus not robust to changes in the modeling pipeline. We circumvent these limitations by designing a distillation algorithm called Mirage for graph classification. Mirage is built on the insight that a message-passing GNN decomposes the input graph into a multiset of computation trees. Furthermore, the frequency distribution of computation trees is often skewed in nature, enabling us to condense this data into a concise distilled summary. By compressing the computation data itself, as opposed to emulating gradient flows on the original training set-a prevalent approach to date-Mirage transforms into an unsupervised and architecture-agnostic distillation algorithm. Extensive benchmarking on real-world datasets underscores Mirage's superiority, showcasing enhanced generalization accuracy, data compression, and distillation efficiency when compared to state-of-the-art baselines.

cs.LG↗

arXiv2023

GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarking

Numerous explainability methods have been proposed to shed light on the inner workings of GNNs. Despite the inclusion of empirical evaluations in all the proposed algorithms, the interrogative aspects of these evaluations lack diversity. As a result, various facets of explainability pertaining to GNNs, such as a comparative analysis of counterfactual reasoners, their stability to variational factors such as different GNN architectures, noise, stochasticity in non-convex loss surfaces, feasibility amidst domain constraints, and so forth, have yet to be formally investigated. Motivated by this need, we present a benchmarking study on perturbation-based explainability methods for GNNs, aiming to systematically evaluate and compare a wide range of explainability techniques. Among the key findings of our study, we identify the Pareto-optimal methods that exhibit superior efficacy and stability in the presence of noise. Nonetheless, our study reveals that all algorithms are affected by stability issues when faced with noisy data. Furthermore, we have established that the current generation of counterfactual explainers often fails to provide feasible recourses due to violations of topological constraints encoded by domain-specific considerations. Overall, this benchmarking study empowers stakeholders in the field of GNNs with a comprehensive understanding of the state-of-the-art explainability methods, potential research problems for further enhancement, and the implications of their application in real-world scenarios.

cs.LG↗