arXiv subjects

Can Polat

Publications and source records attributed to Can Polat.

14 recordsLinked to original sources

arXiv2026

Separating perception from reasoning in vision-language models: a model-free render ceiling for crystal structures

Multimodal evaluations cannot say whether a vision-language model misread an image or misreasoned about it, because every existing method for separating the two places a second model in the loop. We introduce the render ceiling, a model-free reference for benchmarks built by rendering known objects: inverting the frozen cameras and re-solving cross-view correspondence recovers exactly the answer the images support. We prove the ceiling fails only through an enumerable set of projection coincidences and certify that set empty on 2,160 rendered crystal structures, so every point of a model's deficit belongs to the model. Across fourteen vision-language models, supplying exact geometry as text lifts every model yet closes under half the gap for thirteen, while a supervised vision model with no language component reads the same images at 0.8952, above every vision-language model. The instrument exposes extraction-stage fabrication that downstream accuracy would misattribute to reasoning, yields camera-placement rules for benchmark builders, and transfers to any benchmark with an invertible forward rendering.

cs.CV↗

arXiv2026

A single design choice determines whether machine learning models of materials make physically impossible predictions

Machine-learned models are replacing first-principles calculations across materials discovery, and physical symmetry is the central guarantee built into them. The debate over how much symmetry to hard-wire rather than learn has run on rotations, where a symmetry error is an approximation error. Some constraints are exact: symmetry forces certain property tensors to exactly zero, so a nonzero prediction is physically impossible rather than inaccurate. Here we show that whether a model can make such predictions is decided before training by one rarely reported design bit, whether its features carry parity labels, and derive a criterion, the parity gap, that computes from group theory alone which properties and crystals are exposed. Across matched architecture pairs differing only in that bit, evaluated on two thousand centrosymmetric crystals whose piezoelectric tensor must vanish, parity-labelled arms sit at the floating-point floor while rotation-only arms predict forbidden responses on 90-96% of crystals, six orders of magnitude apart, at no accuracy cost. Training on explicit zeros does not recover exactness, and a head on a frozen universal potential inherits its backbone's symmetry group. One reflection at random initialization verifies the label in seconds.

cond-mat.mtrl-sci↗

arXiv2026

When do machine-learned exchange-correlation improvements inherit into density-functional tight binding?

Machine-learned exchange-correlation functionals correct band gaps at near-semilocal cost, while density-functional tight binding reaches the $10^3$-$10^6$-atom regime; combining them assumes that a better parent yields a better parameterization, but we show it does not. Current-generation functionals are orbital-dependent generalized Kohn-Sham operators, whereas the parameterization channel is built on a multiplicative potential, preventing exact representation. Using the transfer ratio, the surviving fraction of a parent-level change, we find anti-transfer: coherently negative ratios across four covalent semiconductors move the gap in the wrong direction, consistent with a molecular proxy and an r$^2$SCAN control. The minimal-basis overgap is dominated by the on-site convention rather than basis incompleteness; correcting the on-site block removes most of it, while one $d$-polarization shell closes a further $16$-$40%$, depending on the placement of the empty $d$ level, which no free-atom eigenvalue uniquely fixes. Occupied-manifold enhancements, ionic and closed-shell repulsive potentials, and rocksalt-oxide gaps inherit, whereas elemental and III-V covalent networks inherit neither gaps nor repulsive potentials and oxide networks inherit only the latter. We screen 23 elements and release the parameter sets, showing that the transfer ratio provides a cheap pre-test before any parameterization campaign.

cond-mat.mtrl-sci↗

arXiv2026

Grounded verification of chemical and materials reasoning: detection is the bottleneck

Language models are moving into chemistry and materials discovery workflows, where a wrong molecular formula, space group, or formation energy can silently propagate into downstream decisions. These confabulations hide inside fluent reasoning traces and concentrate on rare, long-tail entities, where model confidence is least trustworthy. Retrieving reference data for every prompt would catch them, but at a heavy coverage and abstention cost. We show that deterministic, database-grounded verification catches and repairs these errors selectively, and that the binding constraint is detection rather than repair. Our tiered verifier extracts each checkable claim, tests it against authoritative databases and physical law, and retrieves a reference value only when a check fails. Across four models and over five hundred prompts with pinned conditions, gated correction cuts the error rate of committed formulas from 22% to 4% with 3.2 times fewer retrievals than blanket augmentation, and it outperforms a conversational retrieval oracle when every answer, corrected or not, is scored. When a flag fires, repair almost always succeeds; the benefit reaches the final answer only where the verifier's scope covers it and where long-tail error exists. Checkable claims, checked cheaply, are a practical lever for trustworthy machine reasoning in chemistry.

cs.LG↗

arXiv2026

Geometric Algebra Meets Cartesian Tensors: Higher-Order Equivariance for Interatomic Potentials

$\mathrm{Cl}(3,0)$ interatomic potentials, despite their algebraic elegance, predict force magnitudes accurately but force directions poorly. Across ten rMD17 molecules, every $L \leq 1$ baseline in our twelve-model study attains aggregate force-cosine similarity below $0.25$. The cause is structural. The geometric product of two vectors in $\mathbb{R}^3$ realises only the $L=0$ and $L=1$ components of its irreducible representation content, leaving the symmetric-traceless rank-2 component absent from the per-edge bilinear that drives each message-passing layer. We address this with CliffordSTF, which couples the Clifford multivector to closed-form symmetric-traceless tensor tracks at ranks two and three through bilinear cross-track contractions, using a single learned bilinear and no Clebsch--Gordan tables, Wigner-$D$ matrices, or e3nn calls. On rMD17, CliffordSTF raises aggregate force-cosine similarity from $0.055$ (base Clifford) to $0.551$, an order-of-magnitude relative directional gain, alongside improved magnitude accuracy (force MAE $15.8\%$ lower; energy MAE $10.9\%$ lower). It outperforms all CG-free or body-ordered baselines in our study (all $\leq 0.17$). On catalysis benchmarks, CliffordSTF achieves the best out-of-distribution S2EF energy MAE on OC22 in our experiments, and the best in-distribution energy MAE among $L \geq 2$ methods on OC22 IS2RE. An eleven-variant ablation shows the two tracks are complementary: neither alone matches the combined model.

physics.chem-ph↗

arXiv2026

STEMGym: Benchmarking Sequential Decision-Making under Dose Budgets in Autonomous Electron Microscopy

A central premise of autonomous scientific imaging is that smarter navigation, whether Bayesian, RL-based, or otherwise adaptive, is the principal lever for sample-efficient acquisition. We present evidence to the contrary in scanning transmission electron microscopy (STEM), an atomic-resolution imaging modality whose every measurement deposits damaging electron dose. We introduce STEMGym, an open-source Gymnasium benchmark of 15 physics-simulated STEM worlds spanning five materials, three difficulty levels, and four characterisation tasks, scored by the Dose-Efficiency Curve area (DEC-AUC), a single scalar capturing the information-vs-dose Pareto frontier. Across 33 agent configurations under realistic dose budgets, the dominant determinant of dose efficiency is the analyst (perception) pipeline, not the navigator: pairing a trained CNN analyst with na\"ive raster scanning raises DEC-AUC by 5.5x over a CNN-free raster baseline (0.287 vs.\ 0.052), while substituting Bayesian or adaptive finite-state-machine navigation for raster yields no statistically significant further gain. Production-tier vision-language models further underperform task-specific CNNs by {\sim}13x on crystallographic defect analysis. By decoupling perception, navigation, and planning under a unified dose budget, STEMGym reframes where ML effort should be invested in autonomous electron microscopy and provides the measurement infrastructure to test it.

cs.LG↗

arXiv2026

How Far Can You Grow? Characterizing the Extrapolation Frontier of Graph Generative Models for Materials Science

Every generative model for crystalline materials harbors a critical structure size beyond which its outputs become unreliable; we call this the extrapolation frontier. Despite its consequences for nanomaterial design, this frontier has never been systematically measured. We introduce RADII, a radius-resolved benchmark of ~75,000 crystal-derived nanoparticle structures (33-11,298 atoms) that treats radius as a continuous scaling knob, tracing generation quality from in- to out-of-distribution under leakage-free splits. Each model is conditioned on target composition and atom count, isolating geometric extrapolation as the evaluation variable. RADII provides frontier-specific diagnostics: per-radius error profiles pinpoint each architecture's scaling ceiling, surface-interior decomposition separates boundary from bulk failures, and cross-metric sequencing reveals which aspect of structural fidelity breaks first. Benchmarking five state-of-the-art architectures, we find that: (i) well-behaved models degrade by ~13% in global positional error beyond training radii, while divergent models show poor fidelity across scales, with local bond fidelity ranging from negligible degradation to over 2x error growth; (ii) no two architectures share a failure sequence, revealing the frontier as a multi-dimensional surface shaped by model family; and (iii) well-behaved models follow the expected geometric scaling exponent alpha ~ 1/3, whose in-distribution fit predicts out-of-distribution error, making frontiers forecastable. Scaling MatterGen to its published parameter count stabilizes sampling but does not close the frontier, while DiffCSP remains unstable at published scale. These findings establish output scale as a first-class evaluation axis for geometric generative models. Code and data: https://github.com/KurbanIntelligenceLab/RADII.

cond-mat.mtrl-sci↗

arXiv2026

SCALAR: Quantifying Structural Hallucination, Consistency, and Reasoning Gaps in Materials Foundation Models

Large language models are increasingly applied to materials science reasoning, yet their behavior under physically structured distribution shifts remains poorly understood. We introduce SCALAR (Structural Consistency And Logic Across Regimes), a benchmark for evaluating geometric scale generalization and its connection to structural hallucination, consistency, and reasoning in materials foundation models. Given canonical crystal representations, models must reason about derived nanoparticle structures obtained through supercell expansion and geometric truncation across length scales spanning a few atoms to over 18,000 atoms, totaling $\approx$100,000 structures from DFT-validated unit cells. SCALAR defines three tasks. (i) CIF to property prediction. (ii) A Chain-of-Thought variant with explicit physics-grounded reasoning. (iii) Inverse retrieval identifying crystals from candidates given target properties. Outputs are evaluated via structured metrics capturing numeric error, hallucination, cross-prompt consistency, monotonic reasoning, output validity, and retrieval regret. Experiments across diverse foundation models reveal large, model-dependent shifts under explicit reasoning, often reducing hallucination and error, but frequently destabilizing consistency or validity. These results demonstrate that geometric scale generalization cannot be inferred from accuracy alone. Supplementary materials are available at https://github.com/KurbanIntelligenceLab/SCALAR.

cs.LG↗

arXiv2026

C2NP: A Benchmark for Learning Scale-Dependent Geometric Invariances in 3D Materials Generation

Generative models for materials have achieved strong performance on periodic bulk crystals, yet their ability to generalize across scale transitions to finite nanostructures remains largely untested. We introduce Crystal-to-Nanoparticle (C2NP), a systematic benchmark for evaluating generative models when moving between infinite crystalline unit cells and finite nanoparticles, where surface effects and size-dependent distortions dominate. C2NP defines two complementary tasks: (i) generating nanoparticles of specified radii from periodic unit cells, testing whether models capture surface truncation and geometric constraints; and (ii) recovering bulk lattice parameters and space-group symmetry from finite particle configurations, assessing whether models can infer underlying crystallographic order despite surface perturbations. Using diverse materials as a structurally consistent testbed, we construct over 170,000 nanoparticle configurations by carving particles from supercells derived from DFT-relaxed crystal unit cells, and introduce size-based splits that separate interpolation from extrapolation regimes. Experiments with state-of-the-art approaches, including diffusion, flow-matching, and variational models, show that even when losses are low, models often fail geometrically under distribution shift, yielding large lattice-recovery errors and near-zero joint accuracy on structure and symmetry. Overall, our results suggest that current methods rely on template memorization rather than scalable physical generalization. C2NP offers a controlled, reproducible framework for diagnosing these failures, with immediate applications to nanoparticle catalyst design, nanostructured hydrides for hydrogen storage, and materials discovery. Dataset and code are available at https://github.com/KurbanIntelligenceLab/C2NP.

cond-mat.mtrl-sci↗

arXiv2025

QuantumCanvas: A Multimodal Benchmark for Visual Learning of Atomic Interactions

Despite rapid advances in molecular and materials machine learning, most models still lack physical transferability: they fit correlations across whole molecules or crystals rather than learning the quantum interactions between atomic pairs. Yet bonding, charge redistribution, orbital hybridization, and electronic coupling all emerge from these two-body interactions that define local quantum fields in many-body systems. We introduce QuantumCanvas, a large-scale multimodal benchmark that treats two-body quantum systems as foundational units of matter. The dataset spans 2,850 element-element pairs, each annotated with 18 electronic, thermodynamic, and geometric properties and paired with ten-channel image representations derived from l- and m-resolved orbital densities, angular field transforms, co-occupancy maps, and charge-density projections. These physically grounded images encode spatial, angular, and electrostatic symmetries without explicit coordinates, providing an interpretable visual modality for quantum learning. Benchmarking eight architectures across 18 targets, we report mean absolute errors of 0.201 eV on energy gap using GATv2, 0.265 eV on HOMO and 0.274 eV on LUMO using EGNN. For energy-related quantities, DimeNet attains 2.27 eV total-energy MAE and 0.132 eV repulsive-energy MAE, while a multimodal fusion model achieves a 2.15 eV Mermin free-energy MAE. Pretraining on QuantumCanvas further improves convergence stability and generalization when fine-tuned on larger datasets such as QM9, MD17, and CrysMTM. By unifying orbital physics with vision-based representation learning, QuantumCanvas provides a principled and interpretable basis for learning transferable quantum interactions through coupled visual and numerical modalities. Dataset and model implementations are available at https://github.com/KurbanIntelligenceLab/QuantumCanvas.

cs.CV↗

arXiv2025

Stress-Testing Multimodal Foundation Models for Crystallographic Reasoning

Evaluating foundation models for crystallographic reasoning requires benchmarks that isolate generalization behavior while enforcing physical constraints. This work introduces a multiscale multicrystal dataset with two physically grounded evaluation protocols to stress-test multimodal generative models. The Spatial-Exclusion benchmark withholds all supercells of a given radius from a diverse dataset, enabling controlled assessments of spatial interpolation and extrapolation. The Compositional-Exclusion benchmark omits all samples of a specific chemical composition, probing generalization across stoichiometries. Nine vision--language foundation models are prompted with crystallographic images and textual context to generate structural annotations. Responses are evaluated via (i) relative errors in lattice parameters and density, (ii) a physics-consistency index penalizing volumetric violations, and (iii) a hallucination score capturing geometric outliers and invalid space-group predictions. These benchmarks establish a reproducible, physically informed framework for assessing generalization, consistency, and reliability in large-scale multimodal models. Dataset and code are available at https://github.com/KurbanIntelligenceLab/StressTestingMMFMinCR.

cs.CV↗

arXiv2025

Beyond Atomic Geometry Representations in Materials Science: A Human-in-the-Loop Multimodal Framework

Most materials science datasets are limited to atomic geometries (e.g., XYZ files), restricting their utility for multimodal learning and comprehensive data-centric analysis. These constraints have historically impeded the adoption of advanced machine learning techniques in the field. This work introduces MultiCrystalSpectrumSet (MCS-Set), a curated framework that expands materials datasets by integrating atomic structures with 2D projections and structured textual annotations, including lattice parameters and coordination metrics. MCS-Set enables two key tasks: (1) multimodal property and summary prediction, and (2) constrained crystal generation with partial cluster supervision. Leveraging a human-in-the-loop pipeline, MCS-Set combines domain expertise with standardized descriptors for high-quality annotation. Evaluations using state-of-the-art language and vision-language models reveal substantial modality-specific performance gaps and highlight the importance of annotation quality for generalization. MCS-Set offers a foundation for benchmarking multimodal models, advancing annotation practices, and promoting accessible, versatile materials science datasets. The dataset and implementations are available at https://github.com/KurbanIntelligenceLab/MultiCrystalSpectrumSet.

cs.LG↗

arXiv2025

xChemAgents: Agentic AI for Explainable Quantum Chemistry

Recent progress in multimodal graph neural networks has demonstrated that augmenting atomic XYZ geometries with textual chemical descriptors can enhance predictive accuracy across a range of electronic and thermodynamic properties. However, naively appending large sets of heterogeneous descriptors often degrades performance on tasks sensitive to molecular shape or symmetry, and undermines interpretability. xChemAgents proposes a cooperative agent framework that injects physics-aware reasoning into multimodal property prediction. xChemAgents comprises two language-model-based agents: a Selector, which adaptively identifies a sparse, weighted subset of descriptors relevant to each target, and provides a natural language rationale; and a Validator, which enforces physical constraints such as unit consistency and scaling laws through iterative dialogue. On standard benchmark datasets, xChemAgents achieves up to a 22% reduction in mean absolute error over the state-of-the-art baselines, while producing faithful, human-interpretable explanations. Experiment results highlight the potential of cooperative, self-verifying agents to enhance both accuracy and transparency in foundation-model-driven materials science. The implementation and accompanying dataset are available at https://github.com/KurbanIntelligenceLab/xChemAgents.

cs.MA↗

arXiv2025

Understanding the Capabilities of Molecular Graph Neural Networks in Materials Science Through Multimodal Learning and Physical Context Encoding

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that integrates textual descriptors, such as IUPAC names, molecular formulas, physicochemical properties, and synonyms, alongside molecular graphs. A gated fusion mechanism balances geometric and textual features, allowing models to exploit complementary information. Experiments on benchmark datasets indicate that adding textual data yields notable improvements for certain electronic properties, while gains remain limited for others. Furthermore, the GNN architectures display similar performance patterns (improving and deteriorating on analogous targets), suggesting they learn comparable representations rather than distinctly different physical insights.

cs.LG↗