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Researcher profile

Mohd Zaki

Mohd Zaki contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
cond-mat.mtrl-sciArtificial Intelligencephysics.data-anComputation and LanguageDigital Librariesphysics.comp-phphysics.opticsSoftware Engineering

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Published work

5 published item(s)

preprint2026arXiv

Can Coding Agents Reproduce Findings in Computational Materials Science?

Large language models are increasingly deployed as autonomous coding agents and have achieved remarkably strong performance on software engineering benchmarks. However, it is unclear whether such success transfers to computational scientific workflows, where tasks require not only strong coding ability, but also the ability to navigate complex, domain-specific procedures and to interpret results in the context of scientific claims. To address this question, we present AutoMat, a benchmark for evaluating LLM-based agents' ability to reproduce claims from computational materials science. AutoMat poses three interrelated challenges: recovering underspecified computational procedures, navigating specialized toolchains, and determining whether the resulting evidence supports a claim. By working closely with subject matter experts, we curate a set of claims from real materials science papers to test whether coding agents can recover and execute the end-to-end workflow needed to support (or undermine) such claims. We then evaluate multiple representative coding agent settings across several foundation models. Our results show that current LLM-based agents obtain low overall success rates on AutoMat, with the best-performing setting achieving a success rate of only 54.1%. Error analysis further reveals that agents perform worst when workflows must be reconstructed from paper text alone and that they fail primarily due to incomplete procedures, methodological deviations, and execution fragility. Taken together, these findings position AutoMat as both a benchmark for computational scientific reproducibility and a tool for diagnosing the current limitations of agentic systems in AI-for-science settings.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Glass Hardness: Predicting Composition and Load Effects via Symbolic Reasoning-Informed Machine Learning

Glass hardness varies in a non-linear fashion with the chemical composition and applied load, a phenomenon known as the indentation size effect (ISE), which is challenging to predict quantitatively. Here, using a curated dataset of over approx. 3000 inorganic glasses from the literature comprising the composition, indentation load, and hardness, we develop machine learning (ML) models to predict the composition and load dependence of Vickers hardness. Interestingly, when tested on new glass compositions unseen during the training, the standard data-driven ML model failed to capture the ISE. To address this gap, we combined an empirical expression (Bernhardt law) to describe the ISE with ML to develop a framework that incorporates the symbolic law representing the domain reasoning in ML, namely Symbolic Reasoning-Informed ML Procedure (SRIMP). We show that the resulting SRIMP outperforms the data-driven ML model in predicting the ISE. Finally, we interpret the SRIMP model to understand the contribution of the glass network formers and modifiers toward composition and load-dependent (ISE) and load-independent hardness. The deconvolution of the hardness into load-dependent and load-independent terms paves the way toward a holistic understanding of composition and ISE in glasses, enabling the accelerated discovery of new glass compositions with targeted hardness.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Looking Through Glass: Knowledge Discovery from Materials Science Literature using Natural Language Processing

Most of the knowledge in materials science literature is in the form of unstructured data such as text and images. Here, we present a framework employing natural language processing, which automates text and image comprehension and precision knowledge extraction from inorganic glasses' literature. The abstracts are automatically categorized using latent Dirichlet allocation (LDA), providing a way to classify and search semantically linked publications. Similarly, a comprehensive summary of images and plots are presented using the 'Caption Cluster Plot' (CCP), which provides direct access to the images buried in the papers. Finally, we combine the LDA and CCP with the chemical elements occurring in the manuscript to present an 'Elemental map', a topical and image-wise distribution of chemical elements in the literature. Overall, the framework presented here can be a generic and powerful tool to extract and disseminate material-specific information on composition-structure-processing-property dataspaces, allowing insights into fundamental problems relevant to the materials science community and accelerated materials discovery.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Unveiling the Glass Veil: Elucidating the Optical Properties in Glasses with Interpretable Machine Learning

Due to their excellent optical properties, glasses are used for various applications ranging from smartphone screens to telescopes. Developing compositions with tailored Abbe number (Vd) and refractive index (nd), two crucial optical properties, is a major challenge. To this extent, machine learning (ML) approaches have been successfully used to develop composition-property models. However, these models are essentially black-box in nature and suffer from the lack of interpretability. In this paper, we demonstrate the use of ML models to predict the composition-dependent variations of Vd and n at 587.6 nm (nd). Further, using Shapely Additive exPlanations (SHAP), we interpret the ML models to identify the contribution of each of the input components toward a target prediction. We observe that the glass formers such as SiO2, B2O3, and P2O5, and intermediates like TiO2, PbO, and Bi2O3 play a significant role in controlling the optical properties. Interestingly, components that contribute toward increasing the nd are found to decrease the Vd and vice-versa. Finally, we develop the Abbe diagram, also known as the "glass veil", using the ML models, allowing accelerated discovery of new glasses for optical properties beyond the experimental pareto front. Overall, employing explainable ML, we discover the hidden compositional control on the optical properties of oxide glasses.

0 citations0 reviewsNo code linkedOpen access