Showing 1–10 of 10 results for author: Bernales, V

QCalEval: Benchmarking Vision-Language Models for Quantum Calibration Plot Understanding

Authors: Shuxiang Cao, Zijian Zhang, Abhishek Agarwal, Grace Bratrud, Niyaz R. Beysengulov, Daniel C. Cole, Alejandro Gómez Frieiro, Elena O. Glen, Hao Hsu, Gang Huang, Raymond Jow, Greshma Shaji, Tom Lubowe, Ligeng Zhu, Luis Mantilla Calderón, Nicola Pancotti, Joel Pendleton, Brandon Severin, Charles Etienne Staub, Sara Sussman, Antti Vepsäläinen, Neel Rajeshbhai Vora, Yilun Xu, Varinia Bernales, Daniel Bowring , et al. (7 additional authors not shown)

Abstract: Quantum computing calibration depends on interpreting experimental data, and calibration plots provide the most universal human-readable representation for this task, yet no systematic evaluation exists of how well vision-language models (VLMs) interpret them. We introduce QCalEval, the first VLM benchmark for quantum calibration plots: 243 samples across 87 scenario types from 22 experiment famil… ▽ More Quantum computing calibration depends on interpreting experimental data, and calibration plots provide the most universal human-readable representation for this task, yet no systematic evaluation exists of how well vision-language models (VLMs) interpret them. We introduce QCalEval, the first VLM benchmark for quantum calibration plots: 243 samples across 87 scenario types from 22 experiment families, spanning superconducting qubits and neutral atoms, evaluated on six question types in both zero-shot and in-context learning settings. The best general-purpose zero-shot model reaches a mean score of 72.3, and many open-weight models degrade under multi-image in-context learning, whereas frontier closed models improve substantially. A supervised fine-tuning ablation at the 9-billion-parameter scale shows that SFT improves zero-shot performance but cannot close the multimodal in-context learning gap. As a reference case study, we release NVIDIA Ising Calibration 1, an open-weight model based on Qwen3.5-35B-A3B that reaches 74.7 zero-shot average score. △ Less

Submitted 28 April, 2026; originally announced April 2026.

Report number: FERMILAB-PUB-26-0235-ETD

El Agente Forjador: Task-Driven Agent Generation for Quantum Simulation

Authors: Zijian Zhang, Aiwei Yin, Amaan Baweja, Jiaru Bai, Ignacio Gustin, Varinia Bernales, Alán Aspuru-Guzik

Abstract: AI for science promises to accelerate the discovery process. The advent of large language models (LLMs) and agentic workflows enables the expediting of a growing range of scientific tasks. However, most of the current generation of agentic systems depend on static, hand-curated toolsets that hinder adaptation to new domains and evolving libraries. We present El Agente Forjador, a multi-agent frame… ▽ More AI for science promises to accelerate the discovery process. The advent of large language models (LLMs) and agentic workflows enables the expediting of a growing range of scientific tasks. However, most of the current generation of agentic systems depend on static, hand-curated toolsets that hinder adaptation to new domains and evolving libraries. We present El Agente Forjador, a multi-agent framework in which universal coding agents autonomously forge, validate, and reuse computational tools through a four-stage workflow of tool analysis, tool generation, task execution, and iterative solution evaluation. Evaluated across 24 tasks spanning quantum chemistry and quantum dynamics on five coding agent setups, we compare three operating modes: zero-shot generation of tools per task, reuse of a curriculum-built toolset, and direct problem-solving with the coding agents as the baseline. We find that our tool generation and reuse framework consistently improves accuracy over the baseline. We also show that reusing a toolset built by a stronger coding agent can reduce API cost and substantially raises the solution quality for weaker coding agents. Case studies further demonstrate that tools forged for different domains can be combined to solve hybrid tasks. Taken together, these results show that LLM-based agents can use their scientific knowledge and coding capabilities to autonomously build reusable scientific tools, pointing toward a paradigm in which agent capabilities are defined by the tasks they are designed to solve rather than by explicitly engineered implementations. △ Less

Submitted 16 April, 2026; originally announced April 2026.

El Agente Gráfico: A Semantic Execution Runtime for Scientific Agents

Authors: Jiaru Bai, Abdulrahman Aldossary, Thomas Swanick, Marcel Müller, Yeonghun Kang, Changhyeok Choi, Naruki Yoshikawa, Zijian Zhang, Jin Won Lee, Tsz Wai Ko, Aiwei Yin, Mohammad Ghazi Vakili, Chris Crebolder, Varinia Bernales, Alán Aspuru-Guzik

Abstract: Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gráfico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state tr… ▽ More Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gráfico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state transitions, record provenance and confine model judgement to explicit decision points. Using the same top-level LLM and task-specific rubrics on six university-level quantum chemistry exercises, El Agente Gráfico improved performance while reducing model cost by approximately 80% and wall-clock time by more than fourfold relative to our previous multi-agent architecture. Across ensemble spectroscopy and metal-organic framework (MOF) design, the runtime supported typed-state transfer, parallel execution and cross-session persistence. Open-ended studies of a disulfide redox mechanism and the vibrational hypothesis of olfaction required the agent to define the chemical scope and computational pathway of each investigation. A graph-construction skill distilled from these studies then enabled coding agents to author typed execution graphs for MOF literature mining. Together, these results show how typed execution graphs turn reusable procedural knowledge into scientific protocols that can be inspected, revised and transferred across computational and physical systems. △ Less

Submitted 7 August, 2026; v1 submitted 19 February, 2026; originally announced February 2026.

El Agente Quntur: A research collaborator agent for quantum chemistry

Authors: Juan B. Pérez-Sánchez, Yunheng Zou, Jorge A. Campos-Gonzalez-Angulo, Marcel Müller, Ignacio Gustin, Andrew Wang, Han Hao, Tsz Wai Ko, Changhyeok Choi, Eric S. Isbrandt, Mohammad Ghazi Vakili, Hanyong Xu, Chris Crebolder, Varinia Bernales, Alán Aspuru-Guzik

Abstract: Quantum chemistry is a foundational enabling tool for the fields of chemistry, materials science, computational biology and others. Despite of its power, the practical application of quantum chemistry simulations remains in the hands of qualified experts due to methodological complexity, software heterogeneity, and the need for informed interpretation of results. To bridge the accessibility gap fo… ▽ More Quantum chemistry is a foundational enabling tool for the fields of chemistry, materials science, computational biology and others. Despite of its power, the practical application of quantum chemistry simulations remains in the hands of qualified experts due to methodological complexity, software heterogeneity, and the need for informed interpretation of results. To bridge the accessibility gap for these tools and expand their reach to chemists with broader backgrounds, we introduce El Agente Quntur, a hierarchical, multi-agent AI system designed to operate not merely as an automation tool but as a research collaborator for computational quantum chemistry. Quntur was designed following three main strategies: i) elimination of hard-coded procedural policies in favour of reasoning-driven decisions, ii) construction of general and composable actions that facilitate generalization and efficiency, and iii) implementation of guided deep research to integrate abstract quantum-chemical reasoning across subdisciplines and a detailed understanding of the software's internal logic and syntax. Although instantiated in ORCA, these design principles are applicable to research agents more generally and easily expandable to additional quantum chemistry packages and beyond. Quntur supports the full range of calculations available in ORCA 6.0 and reasons over software documentation and scientific literature to plan, execute, adapt, and analyze in silico chemistry experiments following best practices. We discuss the advances and current bottlenecks in agentic systems operating at the research level in computational chemistry, and outline a roadmap toward a fully autonomous end-to-end computational chemistry research agent. △ Less

Submitted 13 April, 2026; v1 submitted 4 February, 2026; originally announced February 2026.

El Agente Estructural: An Artificially Intelligent Molecular Editor

Authors: Changhyeok Choi, Yunheng Zou, Marcel Müller, Han Hao, Yeonghun Kang, Juan B. Pérez-Sánchez, Ignacio Gustin, Hanyong Xu, Andrew Wang, Mohammad Ghazi Vakili, Chris Crebolder, Alán Aspuru-Guzik, Varinia Bernales

Abstract: We present El Agente Estructural, a multimodal, natural-language-driven geometry-generation and manipulation agent for autonomous chemistry and molecular modelling. Unlike molecular generation or editing via generative models, Estructural mimics how human experts directly manipulate molecular systems in three dimensions by integrating a comprehensive set of domain-informed tools and vision-languag… ▽ More We present El Agente Estructural, a multimodal, natural-language-driven geometry-generation and manipulation agent for autonomous chemistry and molecular modelling. Unlike molecular generation or editing via generative models, Estructural mimics how human experts directly manipulate molecular systems in three dimensions by integrating a comprehensive set of domain-informed tools and vision-language models. This design enables precise control over atomic or functional group replacements, atomic connectivity, and stereochemistry without the need to rebuild extensive core molecular frameworks. Through a series of representative case studies, we demonstrate that Estructural enables chemically meaningful geometry manipulation across a wide range of real-world scenarios. These include site-selective functionalization, ligand binding, ligand exchange, stereochemically controlled structure construction, isomer interconversion, fragment-level structural analysis, image-guided generation of structures from schematic reaction mechanisms, and mechanism-driven geometry generation and modification. These examples illustrate how multimodal reasoning, when combined with specialized geometry-aware tools, supports interactive and context-aware molecular modelling beyond structure generation. Looking forward, the integration of Estructural into El Agente Quntur, an autonomous multi-agent quantum chemistry platform, enhances its capabilities by adding sophisticated tools for the generation and editing of three-dimensional structures. △ Less

Submitted 13 April, 2026; v1 submitted 4 February, 2026; originally announced February 2026.

EGMOF: Efficient Generation of Metal-Organic Frameworks Using a Hybrid Diffusion-Transformer Architecture

Authors: Seunghee Han, Yeonghun Kang, Taeun Bae, Junho Kim, Younghun Kim, Varinia Bernales, Alan Aspuru-Guzik, Jihan Kim

Abstract: Designing materials with targeted properties remains challenging due to the vastness of chemical space and the scarcity of property-labeled data. While recent advances in generative models offer a promising way for inverse design, most approaches require large datasets and must be retrained for every new target property. Here, we introduce the EGMOF (Efficient Generation of MOFs), a hybrid diffusi… ▽ More Designing materials with targeted properties remains challenging due to the vastness of chemical space and the scarcity of property-labeled data. While recent advances in generative models offer a promising way for inverse design, most approaches require large datasets and must be retrained for every new target property. Here, we introduce the EGMOF (Efficient Generation of MOFs), a hybrid diffusion-transformer framework that overcomes these limitations through a modular, descriptor-mediated workflow. EGMOF decomposes inverse design into two steps: (1) a one-dimensional diffusion model (Prop2Desc) that maps desired properties to chemically meaningful descriptors followed by (2) a transformer model (Desc2MOF) that generates structures from these descriptors. This modular hybrid design enables minimal retraining and maintains high accuracy even under small-data conditions. On a hydrogen uptake dataset, EGMOF achieved over 94% validity and 91% hit rate, representing significant improvements of up to 39% in validity and 29% in hit rate compared to existing methods, while remaining effective with only 1,000 training samples. Moreover, our model successfully performed conditional generation across 29 diverse property datasets, including CoREMOF, QMOF, and text-mined experimental datasets, whereas previous models have not. This work presents a data-efficient, generalizable approach to the inverse design of diverse MOFs and highlights the potential of modular inverse design workflows for broader materials discovery. △ Less

Submitted 19 April, 2026; v1 submitted 4 November, 2025; originally announced November 2025.

Schema for In-Context Learning

Authors: Pan Chen, Shaohong Chen, Mark Wang, Shi Xuan Leong, Priscilla Fung, Varinia Bernales, Alan Aspuru-Guzik

Abstract: In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pr… ▽ More In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce Schema-Activated In-Context Learning (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. Schema-Activated In-Context Learning not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs. △ Less

Submitted 28 March, 2026; v1 submitted 14 October, 2025; originally announced October 2025.

Shoot from the HIP: Hessian Interatomic Potentials without derivatives

Authors: Andreas Burger, Luca Thiede, Nikolaj Rønne, Varinia Bernales, Nandita Vijaykumar, Tejs Vegge, Arghya Bhowmik, Alan Aspuru-Guzik

Abstract: Fundamental tasks in computational chemistry, from transition state search to vibrational analysis, rely on molecular Hessians, which are the second derivatives of the potential energy. Yet, Hessians are computationally expensive to calculate and scale poorly with system size, with both quantum mechanical methods and neural networks. In this work, we demonstrate that Hessians can be predicted dire… ▽ More Fundamental tasks in computational chemistry, from transition state search to vibrational analysis, rely on molecular Hessians, which are the second derivatives of the potential energy. Yet, Hessians are computationally expensive to calculate and scale poorly with system size, with both quantum mechanical methods and neural networks. In this work, we demonstrate that Hessians can be predicted directly from a deep learning model, without relying on automatic differentiation or finite differences. We observe that one can construct SE(3)-equivariant, symmetric Hessians from irreducible representations (irrep) features up to degree $l$=2 computed during message passing in graph neural networks. This makes HIP Hessians one to two orders of magnitude faster, more accurate, more memory efficient, easier to train, and enables more favorable scaling with system size. We validate our predictions across a wide range of downstream tasks, demonstrating consistently superior performance for transition state search, accelerated geometry optimization, zero-point energy corrections, and vibrational analysis benchmarks. We open-source the HIP codebase and model weights to enable further development of the direct prediction of Hessians at https://github.com/BurgerAndreas/hip △ Less

Submitted 27 June, 2026; v1 submitted 25 September, 2025; originally announced September 2025.

Comments: https://github.com/BurgerAndreas/hip

The Rise of Generative AI for Metal-Organic Framework Design and Synthesis

Authors: Chenru Duan, Aditya Nandy, Shyam Chand Pal, Xin Yang, Wenhao Gao, Yuanqi Du, Hendrik Kraß, Yeonghun Kang, Varinia Bernales, Zuyang Ye, Tristan Pyle, Ray Yang, Zeqi Gu, Philippe Schwaller, Shengqian Ma, Shijing Sun, Alán Aspuru-Guzik, Seyed Mohamad Moosavi, Robert Wexler, Zhiling Zheng

Abstract: Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches that can autonomously propose and synthesize in the laboratory new porous reticular structures on demand. We outline the progress of employing deep learning models… ▽ More Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches that can autonomously propose and synthesize in the laboratory new porous reticular structures on demand. We outline the progress of employing deep learning models, such as variational autoencoders, diffusion models, and large language model-based agents, that are fueled by the growing amount of available data from the MOF community and suggest novel crystalline materials designs. These generative tools can be combined with high-throughput computational screening and even automated experiments to form accelerated, closed-loop discovery pipelines. The result is a new paradigm for reticular chemistry in which AI algorithms more efficiently direct the search for high-performance MOF materials for clean air and energy applications. Finally, we highlight remaining challenges such as synthetic feasibility, dataset diversity, and the need for further integration of domain knowledge. △ Less

Submitted 15 August, 2025; originally announced August 2025.

Comments: 10 pages, 5 figures

Journal ref: Matter (2026)

El Agente: An Autonomous Agent for Quantum Chemistry

Authors: Yunheng Zou, Austin H. Cheng, Abdulrahman Aldossary, Jiaru Bai, Shi Xuan Leong, Jorge Arturo Campos-Gonzalez-Angulo, Changhyeok Choi, Cher Tian Ser, Gary Tom, Andrew Wang, Zijian Zhang, Ilya Yakavets, Han Hao, Chris Crebolder, Varinia Bernales, Alán Aspuru-Guzik

Abstract: Computational chemistry tools are widely used to study the behaviour of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El Agente Q, an LLM-based multi-agent system that dynamically generates and executes quantum chemistry workflows from natural language user prompts. The system is bui… ▽ More Computational chemistry tools are widely used to study the behaviour of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El Agente Q, an LLM-based multi-agent system that dynamically generates and executes quantum chemistry workflows from natural language user prompts. The system is built on a novel cognitive architecture featuring a hierarchical memory framework that enables flexible task decomposition, adaptive tool selection, post-analysis, and autonomous file handling and submission. El Agente Q is benchmarked on six university-level course exercises and two case studies, demonstrating robust problem-solving performance (averaging >87% task success) and adaptive error handling through in situ debugging. It also supports longer-term, multi-step task execution for more complex workflows, while maintaining transparency through detailed action trace logs. Together, these capabilities lay the foundation for increasingly autonomous and accessible quantum chemistry. △ Less

Submitted 8 August, 2025; v1 submitted 5 May, 2025; originally announced May 2025.