Adib Bazgir

Yoel Zimmermann, Adib Bazgir, Alexander Al-Feghali et al.

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Seyed Mohamad Ali Tousi, Adib Bazgir, Yuwen Zhang et al.

We present a hybrid quantum-classical framework augmented with learned error mitigation for solving the viscous Burgers equation on noisy intermediate-scale quantum (NISQ) hardware. Using the Cole-Hopf transformation, the nonlinear Burgers equation is mapped to a diffusion equation, discretized on uniform grids, and encoded into a quantum state whose time evolution is approximated via Trotterized nearest-neighbor circuits implemented in Qiskit. Quantum simulations are executed on noisy Aer backends and IBM superconducting quantum devices and are benchmarked against high-accuracy classical solutions obtained using a Krylov-based solver applied to the corresponding discretized Hamiltonian. From measured quantum amplitudes, we reconstruct the velocity field and evaluate physical and numerical diagnostics, including the L2 error, shock location, and dissipation rate, both with and without zero-noise extrapolation (ZNE). To enable data-driven error mitigation, we construct a large parametric dataset by sweeping viscosity, time step, grid resolution, and boundary conditions, producing matched tuples of noisy, ZNE-corrected, hardware, and classical solutions together with detailed circuit metadata. Leveraging this dataset, we train an attention-based graph neural network that incorporates circuit structure, light-cone information, global circuit parameters, and noisy quantum outputs to predict error-mitigated solutions. Across a wide range of parameters, the learned model consistently reduces the discrepancy between quantum and classical solutions beyond what is achieved by ZNE alone. We discuss extensions of this approach to higher-dimensional Burgers systems and more general quantum partial differential equation solvers, highlighting learned error mitigation as a promising complement to physics-based noise reduction techniques on NISQ devices.

Utkarsh Pratiush, Austin Houston, Kamyar Barakati et al.

Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1

Aritra Roy, Kevin Shen, Andrew MacBride et al.

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.

Yoel Zimmermann, Adib Bazgir, Zartashia Afzal et al.

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

Adib Bazgir, Amir Habibdoust, Xing Song et al.

Alzheimer's disease (AD) presents a complex, multifaceted challenge to patients, caregivers, and the healthcare system, necessitating integrated and dynamic support solutions. While artificial intelligence (AI) offers promising avenues for intervention, current applications are often siloed, addressing singular aspects of the disease such as diagnostics or caregiver support without systemic integration. This paper proposes a novel methodological framework for a comprehensive, multi-agent system (MAS) designed for holistic Alzheimer's disease management. The objective is to detail the architecture of a collaborative ecosystem of specialized AI agents, each engineered to address a distinct challenge in the AD care continuum, from caregiver support and multimodal data analysis to automated research and clinical data interpretation. The proposed framework is composed of eight specialized, interoperable agents. These agents are categorized by function: (1) Caregiver and Patient Support, (2) Data Analysis and Research, and (3) Advanced Multimodal Workflows. The methodology details the technical architecture of each agent, leveraging a suite of advanced technologies including large language models (LLMs) such as GPT-4o and Gemini, multi-agent orchestration frameworks, Retrieval-Augmented Generation (RAG) for evidence-grounded responses, and specialized tools for web scraping, multimodal data processing, and in-memory database querying. This paper presents a detailed architectural blueprint for an integrated AI ecosystem for AD care. By moving beyond single-purpose tools to a collaborative, multi-agent paradigm, this framework establishes a foundation for developing more adaptive, personalized, and proactive solutions. This methodological approach aims to pave the way for future systems capable of synthesizing diverse data streams to improve patient outcomes and reduce caregiver burden.

Adib Bazgir, Amir Habibdoust, Yuwen Zhang et al.

Large Language Models (LLMs) have demonstrated remarkable capabilities in various reasoning and generation tasks. However, their proficiency in complex causal reasoning, discovery, and estimation remains an area of active development, often hindered by issues like hallucination, reliance on spurious correlations, and difficulties in handling nuanced, domain-specific, or personalized causal relationships. Multi-agent systems, leveraging the collaborative or specialized abilities of multiple LLM-based agents, are emerging as a powerful paradigm to address these limitations. This review paper explores the burgeoning field of causal multi-agent LLMs. We examine how these systems are designed to tackle different facets of causality, including causal reasoning and counterfactual analysis, causal discovery from data, and the estimation of causal effects. We delve into the diverse architectural patterns and interaction protocols employed, from pipeline-based processing and debate frameworks to simulation environments and iterative refinement loops. Furthermore, we discuss the evaluation methodologies, benchmarks, and diverse application domains where causal multi-agent LLMs are making an impact, including scientific discovery, healthcare, fact-checking, and personalized systems. Finally, we highlight the persistent challenges, open research questions, and promising future directions in this synergistic field, aiming to provide a comprehensive overview of its current state and potential trajectory.

Adib Bazgir, Amir Habibdoust Lafmajani, Yuwen Zhang

Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform intervention-based reasoning to infer cause-and-effect. Addressing this requires overcoming key challenges: designing safe, controllable agentic frameworks; developing rigorous benchmarks for causal evaluation; integrating heterogeneous data sources; and synergistically combining LLMs with structured knowledge (KGs) and formal causal inference tools. Such agents could unlock transformative opportunities, including accelerating drug discovery through automated hypothesis generation and simulation, enabling personalized medicine through patient-specific causal models. This research agenda aims to foster interdisciplinary efforts, bridging causal concepts and foundation models to develop reliable AI partners for biomedical progress.