arXiv subjects

N. M. Anoop Krishnan

Publications and source records attributed to N. M. Anoop Krishnan.

At least 19 recordsLinked to original sources

arXiv2026

MatSKRAFT: A framework for large-scale materials knowledge extraction from scientific tables

Scientific progress increasingly depends on synthesizing knowledge across vast literature, yet most experimental data remains trapped in semi-structured formats that resist systematic extraction and analysis. Here, we present MatSKRAFT, a computational framework that automatically extracts and integrates materials science knowledge from tabular data at unprecedented scale. Our approach transforms tables into graph-based representations processed by constraint-driven GNNs that encode scientific principles directly into model architecture. MatSKRAFT significantly outperforms contemporary frontier large language models, achieving F1 scores of 89.33 for property extraction and 71.35 for composition extraction, while processing data 6-496 times faster compared to the fastest and the slowest models respectively, with modest hardware requirements. Applied to 66,267 tables from more than 45,500 research publications, we construct a comprehensive database containing 509,281 entries, including 104,000 compositions that expand coverage beyond major existing databases. This systematic approach reveals previously overlooked materials with distinct property combinations and enables data-driven discovery of composition-property relationships forming the cornerstone of materials and scientific discovery.

cs.IR↗

arXiv2026

Sustainable Materials Discovery in the Era of Artificial Intelligence

Artificial intelligence (AI) has transformed materials discovery, enabling rapid exploration of chemical space through generative models and surrogate screening. Yet current generative AI models for materials discovery, which now drive exploration of vast chemical and structural spaces, optimize candidates exclusively for structural stability and functional properties, with no integration of environmental assessment at any stage of the design loop. Prospective and ex-ante life cycle assessment methods exist and have been applied to emerging technologies, but they operate as standalone downstream analyses, not as active constraints within generative or active-learning pipelines. The result is that environmental feedback, even when produced, arrives after design decisions have been made rather than informing them. The disconnect between atomic-scale design and lifecycle assessment (LCA) reflects fundamental challenges: (i) data scarcity across heterogeneous sources, (ii) scale gaps from atoms to industrial systems, (iii) uncertainty in synthesis pathways, and (iv) the absence of frameworks that co-optimize performance with environmental impact. In this Perspective, we propose integrating upstream ML-assisted materials discovery with downstream LCA into the ML-LCA framework, comprising five components: information extraction for building materials-environment knowledge bases, harmonized databases linking properties to sustainability metrics, multi-scale models bridging atomic properties to lifecycle impacts, ensemble prediction of manufacturing pathways with uncertainty quantification, and uncertainty-aware optimization enabling simultaneous performance-sustainability navigation. Case studies spanning polymers, glass, photoresists, and cement demonstrate both necessity and feasibility while identifying material-specific integration challenges.

cond-mat.mtrl-sci↗

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

Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows

Predictive models in biomedicine depend on structured assay data locked in the text, tables, and supplements of primary publications. This bottleneck is especially acute in targeted protein degradation (TPD), where each assay record must combine compound identity, degradation target, recruiter, assay context, and endpoint values reported across sections, tables, and supplementary files. Inconsistent compound identifiers and incomplete or implicit assay context further demand domain-specific logic that generic LLM pipelines do not provide. Existing molecular glue and PROTAC databases are manually curated and often lack the experimental context required for downstream modeling. We formulate TPD database extraction as a domain-specific curation task and present an expert-in-the-loop LLM workflow, evaluated through a triangular comparison among LLM predictions, standardized baseline records, and expert-annotated ground truth. A lightweight cross-validated prompt-refinement module adapts extraction instructions from scarce expert annotations. With only seven annotated molecular glue publications, the workflow achieved record-level $F_1 = 0.98$ and transferred to PROTACs by terminology substitution alone, maintaining record-level $F_1 > 0.93$. Applied at scale, it expanded molecular glue and PROTAC databases by 81% and 92% records, respectively, with 92% and 82.5% of newly recovered records validated as correct upon expert review. The workflow also recovered kinetic and assay-context information essential for cross-study potency comparison and condition-aware degradation modeling. We release the workflow, prompts, evaluation code, and extracted datasets as resources for TPD data curation and AI-assisted scientific curation more broadly.

q-bio.QM↗

arXiv2026

MDGYM: Benchmarking AI Agents on Molecular Simulations

The promise of AI-driven scientific discovery hinges on whether AI agents can autonomously design and execute the computational workflows that underpin modern science. Molecular dynamics (MD) simulation presents a natural test bed to stress-test this claim; it requires translating physical intuition into syntactically and semantically correct input scripts, reasoning about initial and boundary conditions, diagnosing numerically unstable trajectories, and interpreting outputs against known physical behavior and laws. We introduce MDGYM, a benchmark of 169 expert-curated MD simulations spanning LAMMPS and GROMACS, two widely used MD packages, across three increasing difficulty levels. We evaluate three agentic frameworks -- Claude Code, Codex, and OpenHands -- with four LLMs, and find that all perform poorly: even the strongest agent solves only 21\% of easy-level tasks, with less than 10\% at higher difficulties. Trajectory analysis reveals a characteristic pattern of failure -- agents successfully invoke simulation machinery but produce physically unstable configurations, fabricate numerical outputs without executing the underlying computation, or abandon tasks prematurely rather than iterating through simulation-specific errors. These failure modes are qualitatively distinct from those observed in general software engineering benchmarks, indicating that fluent code generation does not transfer to grounded physical reasoning.

cs.AI↗

arXiv2026

Agentic AI Scientists Are Not Built For Autonomous Scientific Discovery

A growing body of work pursues AI scientists capable of end-to-end autonomous scientific discovery. This position paper argues that although they already function as co-scientists, agentic AI scientists are not built for autonomous scientific discovery. We identify the following challenges in building and deploying autonomous AI scientists: (1) Problem selection is influenced by the McNamara fallacy; (2) Agents are built on large language models (LLMs) whose training corpora omit tacit procedural and failure knowledge of laboratory practice; (3) Preference optimisation during post-training compresses output diversity toward consensus; and (4) Most scientific benchmarks measure single-turn prediction accuracy and lack feedback from physical experiments back to the computational model. These challenges are not just questions of scale and scaffolding; they require revisiting fundamental design choices. To build truly autonomous AI scientists, we recommend the use of scientific simulations as verifiers for training, the design of persistent world models that represent the shifting objectives governing real investigations, the establishment of a centralized preregistration repository for all AI-generated hypotheses, and application driven by scientific need rather than tool affordance.

cs.AI↗

arXiv2026

AMGenC: Generating Charge Balanced Amorphous Materials

Amorphous (disordered) materials are solids that have shown great potential in various domains, including energy storage, thermal management, and advanced materials. Unlike crystalline materials that can be described by unit cells containing a few to hundreds of atoms, amorphous materials require larger simulation cells with at least hundreds to thousands of atoms. To advance the design of amorphous materials with desired properties and facilitate the exploration of their vast design space, generative inverse design has emerged as a promising approach. It aims to directly output materials with properties closely aligned with the desired ones using probabilistic generative models conditioned on desired properties, which can be more resource efficient than the traditional trial-and-error approach. However, due to the inherent stochasticity of probabilistic generative models, when element assignments are unconstrained, a large portion of generated materials may be charge unbalanced, and no existing methods can effectively mitigate this limitation. In this work, we propose AMGenC, a new generative inverse design method for amorphous materials that can guarantee the generation of charge balanced samples, with minimal additional computational overhead and without sacrificing inverse design accuracy. AMGenC achieves this through an element noise that gives the generation process a starting point centered around charge balance, and the combination of a per-step soft projection and a final discrete projection for steering the elements toward exact charge balance throughout the generation. We perform extensive experiments on two amorphous materials datasets. Experimental results provide evidence that AMGenC achieves its design goal.

cs.LG↗

arXiv2026

A Multi-Plant Machine Learning Framework for Emission Prediction, Forecasting, and Control in Cement Manufacturing

Cement production is among the largest contributors to industrial air pollution, emitting ~3 Mt NOx/year. The industry-standard mitigation approach, selective non-catalytic reduction (SNCR), exhibits low NH3 utilization efficiency, resulting in operational inefficiencies and increased reagent costs. Here, we develop a data-driven framework for emission control using large-scale operational data from four cement plants worldwide. Benchmarking nine machine learning architectures, we observe that prediction error varies ~3-5x across plants due to variation in data richness. Incorporating short-term process history nearly triples NOx prediction accuracy, revealing that NOx formation carries substantial process memory, a timescale dependence that is absent in CO and CO2. Further, we develop models that forecast NOx overshoots as early as nine minutes, providing a buffer for operational adjustments. The developed framework controls NOx formation at the source, reducing NH3 consumption in downstream SNCR. Surrogate model projections estimate a ~34-64% reduction in NOx while preserving clinker quality, corresponding to a reduction of ~290 t NOx/year and ~58,000 USD/year in NH3 savings. This work establishes a generalizable framework for data-driven emission control, offering a pathway toward low-emission operation without structural modifications or additional hardware, with potential applicability to other hard-to-abate industries such as steel, glass, and lime.

cs.LG↗

arXiv2026

AI scientists produce results without reasoning scientifically

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

cs.AI↗

arXiv2026

Natural Language Embeddings of Synthesis and Testing conditions Enhance Glass Dissolution Prediction

Long-term chemical durability of glass, crucial for immobilizing nuclear waste, is governed by glass properties such as composition, surface geometry, as well as external factors like thermodynamic conditions and surrounding medium. Despite decades of research, there are no models that account for these intrinsic and extrinsic factors to predict the dissolution rates of glass compositions. To address this challenge, we evaluate the role of natural language embeddings capturing the synthesis and testing conditions in enhancing the predictability of glass dissolution. Evaluating the approach on hand-curated ~700 datapoints extracted from the literature, we reveal that the machine learning (ML) model including natural language embeddings (NLP-ML) outperforms classical ML model in predicting glass dissolution rate. Furthermore, we developed a generalizable ML model by transforming the compositional features to structural descriptors of glass alongside NLP-derived features, enabling extrapolation capability to glass compositions with completely new elements absent in the training data. Evaluating this model on a completely new dataset of glass compositions 34 chemical components in contrast to the training dataset that had only 28 components, we demonstrate that the model indeed exhibits generalizability to glass compositions that are out-of-distribution. Altogether, this integrated approach offers a pathway towards high-fidelity glass dissolution prediction and accelerate the discovery of novel glass compositions with tailored durability for sustainable nuclear waste management.

cond-mat.mtrl-sci↗

arXiv2026

LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models

Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical space. Yet, the lack of standardized evaluation frameworks makes it challenging to evaluate, compare, and further develop these ML models meaningfully. In this work, we introduce LeMat-GenBench, a unified benchmark for generative models of crystalline materials, supported by a set of evaluation metrics designed to better inform model development and downstream applications. We release both an open-source evaluation suite and a public leaderboard on Hugging Face, and benchmark 12 recent generative models. Results reveal that an increase in stability leads to a decrease in novelty and diversity on average, with no model excelling across all dimensions. Altogether, LeMat-GenBench establishes a reproducible and extensible foundation for fair model comparison and aims to guide the development of more reliable, discovery-oriented generative models for crystalline materials.

cs.LG↗

arXiv2025

Transferable potential for molecular dynamics simulations of borosilicate glasses and structural comparison of machine learning optimized parameters

The simulation of borosilicate glasses is challenging due to the composition and temperature dependent coordination state of boron atoms. Here, we present a newly developed machine learning optimized classical potential for molecular dynamics simulations that achieves transferability across diverse borosilicate glass compositions. Our potential accurately predicts the glass structural variations in short- and medium-range order in different glass compositions, including validating our potential against experimental X-ray structure factor data. Notably, these data are not included in the optimization framework, which focuses exclusively on density and four-fold coordinated boron fraction. We further investigate the impact of empirical parameters in the force field formulation on the microscopic bond lengths, bond angles and the macroscopic densities, providing new insights into the relationship between interatomic potentials and bulk glass behaviors.

cond-mat.dis-nn↗

arXiv2025

On the Equivalence of Regression and Classification

A formal link between regression and classification has been tenuous. Even though the margin maximization term $\|w\|$ is used in support vector regression, it has at best been justified as a regularizer. We show that a regression problem with $M$ samples lying on a hyperplane has a one-to-one equivalence with a linearly separable classification task with $2M$ samples. We show that margin maximization on the equivalent classification task leads to a different regression formulation than traditionally used. Using the equivalence, we demonstrate a ``regressability'' measure, that can be used to estimate the difficulty of regressing a dataset, without needing to first learn a model for it. We use the equivalence to train neural networks to learn a linearizing map, that transforms input variables into a space where a linear regressor is adequate.

cs.LG↗

arXiv2025

Optimization of Transferable Interatomic Potentials for Glasses toward Experimental Properties

The accuracy of molecular simulations is fundamentally limited by the interatomic potentials that govern atomic interactions. Traditional potential development, which relies heavily on ab initio calculations, frequently struggles to reproduce the experimentally observed properties that govern real material behavior. To address this challenge, we present a machine learning-driven, active-learning optimization framework for optimizing classical interatomic potentials to reproduce experimental properties. Our method, here showcased on soda-lime borosilicate glasses, targets both global (density) and local (boron coordination) structural features across a wide range of compositions. By combining a surrogate model with iterative active learning, the framework efficiently explores a five-dimensional parameter space using only 400 molecular dynamics simulations over 17 iterations, making it highly data-efficient and eliminating the need for extensive simulation campaigns. Two transferable parameter sets are identified, each demonstrating good agreement with experimental measurements, including glass density, fraction of four-fold boron, and X-ray structure factor. The framework effectively captures and manages inherent trade-offs between structural objectives and compositional regimes, providing insights into the coordination behavior of boron in complex glass networks. The resulting classical force fields are generalizable and do not require reparameterization for individual compositions. Altogether, this work offers a scalable and experimentally grounded approach for developing transferable interatomic potentials suitable for a broad range of materials, including multi-component glass systems, and beyond.

cond-mat.dis-nn↗

arXiv2025

Autonomous Microscopy Experiments through Large Language Model Agents

Large language models (LLMs) are revolutionizing self driving laboratories (SDLs) for materials research, promising unprecedented acceleration of scientific discovery. However, current SDL implementations rely on rigid protocols that fail to capture the adaptability and intuition of expert scientists in dynamic experimental settings. We introduce Artificially Intelligent Lab Assistant (AILA), a framework automating atomic force microscopy through LLM driven agents. Further, we develop AFMBench a comprehensive evaluation suite challenging AI agents across the complete scientific workflow from experimental design to results analysis. We find that state of the art models struggle with basic tasks and coordination scenarios. Notably, Claude 3.5 sonnet performs unexpectedly poorly despite excelling in materials domain question answering (QA) benchmarks, revealing that domain specific QA proficiency does not necessarily translate to effective agentic capabilities. Additionally, we observe that LLMs can deviate from instructions, raising safety alignment concerns for SDL applications. Our ablations reveal that multi agent frameworks outperform single-agent architectures. We also observe significant prompt fragility, where slight modifications in prompt structure cause substantial performance variations in capable models like GPT 4o. Finally, we evaluate AILA's effectiveness in increasingly advanced experiments AFM calibration, feature detection, mechanical property measurement, graphene layer counting, and indenter detection. Our findings underscore the necessity for rigorous benchmarking protocols and prompt engineering strategies before deploying AI laboratory assistants in scientific research environments.

cs.CY↗

arXiv2025

Reactive Glass Metal Interaction under Ambient Conditions Enables Surface Modification of Gold Nanoislands

Stabilizing gold nanoparticles with tunable surface composition via reactive metal support interactions under ambient conditions remains a significant challenge. We discovered that a reactive glass metal interaction (RGMI) under ambient conditions, driven by the intrinsic catalytic activity of gold nanoislands (GNIs) and the unique properties of sodium aluminophosphosilicate glass, including its chemical composition, molar volume, and high Na ion mobility, enables the formation of robustly anchored GNIs with altered surface compositions. Comprehensive characterization reveals that the adsorption of Na and P at the GNI surfaces induces lattice distortions in the Au(111) planes. Additionally, a smooth GNI glass interface significantly influences the hot carrier dynamics of the GNIs. Altogether, RGMI presents a versatile strategy for engineering stable, multi element nanostructures with potential applications in heterogeneous catalysis, sensing, and optoelectronics.

cond-mat.mtrl-sci↗

arXiv2025

Probing the limitations of multimodal language models for chemistry and materials research

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

cs.LG↗

arXiv2025

Energy & Force Regression on DFT Trajectories is Not Enough for Universal Machine Learning Interatomic Potentials

Universal Machine Learning Interactomic Potentials (MLIPs) enable accelerated simulations for materials discovery. However, current research efforts fail to impactfully utilize MLIPs due to: 1. Overreliance on Density Functional Theory (DFT) for MLIP training data creation; 2. MLIPs' inability to reliably and accurately perform large-scale molecular dynamics (MD) simulations for diverse materials; 3. Limited understanding of MLIPs' underlying capabilities. To address these shortcomings, we aargue that MLIP research efforts should prioritize: 1. Employing more accurate simulation methods for large-scale MLIP training data creation (e.g. Coupled Cluster Theory) that cover a wide range of materials design spaces; 2. Creating MLIP metrology tools that leverage large-scale benchmarking, visualization, and interpretability analyses to provide a deeper understanding of MLIPs' inner workings; 3. Developing computationally efficient MLIPs to execute MD simulations that accurately model a broad set of materials properties. Together, these interdisciplinary research directions can help further the real-world application of MLIPs to accurately model complex materials at device scale.

cond-mat.mtrl-sci↗