arXiv subjects

Tonio Buonassisi

Publications and source records attributed to Tonio Buonassisi.

At least 19 recordsLinked to original sources

arXiv2026

Synthesizing like a chemist: an iterative, feedback-driven loop for materials discovery

Most computationally predicted materials are never synthesized because conventional synthesis optimization is slow, expertise-dependent, and iterative. Here we present a closed-loop framework that automates this expert workflow by placing human tacit knowledge in the loop through a large language model (LLM) that distills synthesis knowledge from the literature, high-throughput hyperspectral imaging for rapid film evaluation, and multi-objective Bayesian optimization guided by experimental feedback. In a paired optimization campaign, LLM-assisted initialization produced more Pareto-optimal samples and higher hypervolume than a Latin hypercube sampling baseline at matched trial counts, and this advantage persisted throughout iterative optimization. We demonstrate the framework by synthesizing the previously unreported perovskite-inspired compound Rb3BiI6 as thin films and validating the optimized films by optical bandgap analysis and X-ray diffraction. The framework transforms synthesis prediction from single-shot recommendation to iterative learning, providing a generalizable strategy to accelerate automated and fully autonomous experimental materials discovery.

cond-mat.mtrl-sci↗

arXiv2026

How Molecular Generative Models Organize Molecular Identity

Generative models for matter are often evaluated as samplers over output representations, and their latent spaces are commonly used as proxies for navigating chemical space. Much less is known about how these models internally arrange discrete chemical identities within those representations. We study this arrangement by making molecular identity explicit and pulling it back through the generative process. Through these pullbacks we probe the regions that generate the same object, exposing the trained model's internal repertoire: a fixed partition that determines which objects (novel or not) the model can produce. Across three molecular generative architectures, we find that this repertoire is arranged into piecewise-constant regions separated by recurring coarse-to-fine boundaries. Its organization depends on the representation probed, the identity convention, decoder stochasticity, and the metric used to compare coordinates. During training, local chemical organization stabilizes while the number of distinct molecular identities represented within each neighborhood continues to change. Internal organization must therefore be characterized, rather than assumed, before a generative space can be treated as chemically navigable.

cs.LG↗

arXiv2025

Closed-Loop Robotic Manipulation of Transparent Substrates for Self-Driving Laboratories using Deep Learning Micro-Error Correction

Self-driving laboratories (SDLs) have accelerated the throughput and automation capabilities for discovering and improving chemistries and materials. Although these SDLs have automated many of the steps required to conduct chemical and materials experiments, a commonly overlooked step in the automation pipeline is the handling and reloading of substrates used to transfer or deposit materials onto for downstream characterization. Here, we develop a closed-loop method of Automated Substrate Handling and Exchange (ASHE) using robotics, dual-actuated dispensers, and deep learning-driven computer vision to detect and correct errors in the manipulation of fragile and transparent substrates for SDLs. Using ASHE, we demonstrate a 98.5% first-time placement accuracy across 130 independent trials of reloading transparent glass substrates into an SDL, where only two substrate misplacements occurred and were successfully detected as errors and automatically corrected. Through the development of more accurate and reliable methods for handling various types of substrates, we move toward an improvement in the automation capabilities of self-driving laboratories, furthering the acceleration of novel chemical and materials discoveries.

cs.RO↗

arXiv2025

Kosmos: An AI Scientist for Autonomous Discovery

Data-driven scientific discovery requires iterative cycles of literature search, hypothesis generation, and data analysis. Substantial progress has been made towards AI agents that can automate scientific research, but all such agents remain limited in the number of actions they can take before losing coherence, thus limiting the depth of their findings. Here we present Kosmos, an AI scientist that automates data-driven discovery. Given an open-ended objective and a dataset, Kosmos runs for up to 12 hours performing cycles of parallel data analysis, literature search, and hypothesis generation before synthesizing discoveries into scientific reports. Unlike prior systems, Kosmos uses a structured world model to share information between a data analysis agent and a literature search agent. The world model enables Kosmos to coherently pursue the specified objective over 200 agent rollouts, collectively executing an average of 42,000 lines of code and reading 1,500 papers per run. Kosmos cites all statements in its reports with code or primary literature, ensuring its reasoning is traceable. Independent scientists found 79.4% of statements in Kosmos reports to be accurate, and collaborators reported that a single 20-cycle Kosmos run performed the equivalent of 6 months of their own research time on average. Furthermore, collaborators reported that the number of valuable scientific findings generated scales linearly with Kosmos cycles (tested up to 20 cycles). We highlight seven discoveries made by Kosmos that span metabolomics, materials science, neuroscience, and statistical genetics. Three discoveries independently reproduce findings from preprinted or unpublished manuscripts that were not accessed by Kosmos at runtime, while four make novel contributions to the scientific literature.

cs.AI↗

arXiv2025

Multi-Variable Batch Bayesian Optimization in Materials Research: Synthetic Data Analysis of Noise Sensitivity and Problem Landscape Effects

Bayesian Optimization (BO) machine learning method is increasingly used to guide experimental optimization tasks in materials science. To emulate the large number of input variables and noise-containing results in experimental materials research, we perform batch BO simulation of six design variables with a range of noise levels. Two test cases relevant for materials science problems are examined: a needle-in-a-haystack case (Ackley function) that may be encountered in, e.g., molecule optimizations, and a smooth landscape with a local optimum in addition to the global optimum (Hartmann function) that may be encountered in, e.g., material composition optimization. We show learning curves, performance metrics, and visualization to effectively track the optimization progression and evaluate how the optimization outcomes are affected by noise, batch-picking method, choice of acquisition function, and exploration hyperparameter values. We find that the effects of noise depend on the problem landscape: noise degrades the optimization results of a needle-in-a-haystack search (Ackley) dramatically more. However, with increasing noise, we observe an increasing probability of landing on the local optimum in Hartmann. Therefore, prior knowledge of the problem domain structure and noise level is essential when designing BO for materials research experiments. Synthetic data studies -- with known ground truth and controlled noise levels -- enable us to isolate and evaluate the impact of different batch BO components, {\it e.g.}, acquisition policy, objective metrics, and hyperparameter values, before transitioning to the inherent uncertainties of real experimental systems. The results and methodology of this study will facilitate a greater utilization of BO in guiding experimental materials research, specifically in settings with a large number of design variables to optimize.

stat.ML↗

arXiv2025

A closed-loop AI framework for hypothesis-driven and interpretable materials design

Scientific hypothesis generation is central to materials discovery, yet current approaches often emphasize either conceptual (idea-to-data) reasoning or data-driven (data-to-idea) analysis, rarely achieving an effective integration of both. Here, we present a generalizable active learning workflow that integrates top-down, theory-driven hypothesis generation, guided by a large language model. This is complemented by bottom-up, data-driven hypothesis testing through a root-cause association study. We demonstrate this approach through the design of equimolar quinary-cation two-dimensional perovskite, a chemically complex system with over 850,000 possible cation combinations. In the top-down component, the large language model drives closed-loop optimization by proposing candidates that are likely to achieve phase purity, leveraging domain knowledge and chain-of-thought reasoning. With each iteration, the model identifies an increasing number of near phase-pure compositions, sampling less than 0.004% of the design space. In parallel, the bottom-up association study identifies molecular features with statistically significant influences on phase purity. The integration of these approaches enables the convergence of conceptual and statistical hypotheses, leading to generalizable and rational design rules for phase-pure quinary-cation two-dimensional perovskites. As a proof of concept, we applied the optimized phase-pure quinary-cation two-dimensional perovskite film as a surface capping layer in perovskite solar cells, achieving good performance and stability. Our framework enables the development of interpretable and generalizable design rules that are applicable to a wide range of optimization processes within complex design spaces, providing a foundational strategy for rational, scalable, and efficient materials discovery.

cond-mat.mtrl-sci↗

arXiv2025

Disentangling the Effects of Simultaneous Environmental Variables on Perovskite Synthesis and Device Performance via Interpretable Machine Learning

Despite the rapid rise in perovskite solar cell efficiency, poor reproducibility remains a major barrier to commercialization. Film crystallization and device performance are highly sensitive to environmental factors during fabrication, yet their complex interactions are not well understood. In this work, we present a systematic framework to investigate the influence of both individual and coupled environmental variables on device efficiency and crystallization kinetics. We developed an integrated fabrication platform with precise, independent control over ambient solvent partial pressure, absolute humidity, and temperature during spin-coating and thermal-annealing processes, respectively. Using the platform, we implemented a closed-loop Bayesian optimization framework to efficiently explore the multi-dimensional processing space. We mapped the impact of these environmental variables on device performance and identified coupled effects among them. In-situ grazing-incidence wide-angle X-ray scattering measurements further validated these findings by revealing a nonlinear interaction between absolute humidity and solvent partial pressure during spin-coating, which affects crystallization dynamics. To isolate and quantify these interactions, we developed an interpretable machine learning approach that combines knowledge distillation with Shapley interaction analysis. The model revealed the contribution of each interaction varies across different processing conditions. Our study highlights the importance of integrated ambient sensing and control to achieve repeatable perovskite solar cells, and demonstrates the utility of combining active learning with interpretable machine learning to navigate complex, high-dimensional processing landscapes.

cond-mat.mtrl-sci↗

arXiv2025

Multimodal transformers with elemental priors for phase classification of X-ray diffraction spectra

Classifying a crystalline solid's phase using X-ray diffraction (XRD) is a challenging endeavor, first because this is a poorly constrained problem as there are nearly limitless candidate phases to compare against a given experimental spectrum, and second because experimental signals are confounded by overlapping peaks, preferred orientations, and phase mixtures. To address this challenge, we develop Chem-XRD, a multimodal framework based on vision transformer (ViT) architecture with two defining features: (i) crystallographic data is constrained by elemental priors and (ii) phase is classified according to probabilities (not absolutes). Elemental information can be extracted from pre-synthesis precursors or post-synthesis elemental analysis. By combining structural and elemental modalities, Chem-XRD simultaneously predicts both the number and identity of phases of lead-halide perovskite materials and their decomposition products. Through integrated gradient calculations, we show that the model can adeptly adjust the contributions of structural and elemental modalities toward the final prediction of phase identification, achieving a level of interpretability beyond what self-attention mechanisms can achieve.

physics.app-ph↗

arXiv2025

A tomographic interpretation of structure-property relations for materials discovery

Recent advancements in machine learning (ML) for materials have demonstrated that "simple" materials representations (e.g., the chemical formula alone without structural information) can sometimes achieve competitive property prediction performance in common-tasks. Our physics-based intuition would suggest that such representations are "incomplete", which indicates a gap in our understanding. This work proposes a tomographic interpretation of structure-property relations of materials to bridge that gap by defining what is a material representation, material properties, the material and the relationships between these three concepts using ideas from information theory. We verify this framework performing an exhaustive comparison of property-augmented representations on a range of material's property prediction objectives, providing insight into how different properties can encode complementary information.

cond-mat.mtrl-sci↗

arXiv2024

A Self-Supervised Robotic System for Autonomous Contact-Based Spatial Mapping of Semiconductor Properties

Integrating robotically driven contact-based material characterization techniques into self-driving laboratories can enhance measurement quality, reliability, and throughput. While deep learning models support robust autonomy, current methods lack reliable pixel-precision positioning and require extensive labeled data. To overcome these challenges, we propose an approach for building self-supervised autonomy into contact-based robotic systems that teach the robot to follow domain expert measurement principles at high-throughputs. Firstly, we design a vision-based, self-supervised convolutional neural network (CNN) architecture that uses differentiable image priors to optimize domain-specific objectives, refining the pixel precision of predicted robot contact poses by 20.0% relative to existing approaches. Secondly, we design a reliable graph-based planner for generating distance-minimizing paths to accelerate the robot measurement throughput and decrease planning variance by 6x. We demonstrate the performance of this approach by autonomously driving a 4-degree-of-freedom robotic probe for 24 hours to characterize semiconductor photoconductivity at 3,025 uniquely predicted poses across a gradient of drop-casted perovskite film compositions, achieving throughputs over 125 measurements per hour. Spatially mapping photoconductivity onto each drop-casted film reveals compositional trends and regions of inhomogeneity, valuable for identifying manufacturing process defects. With this self-supervised CNN-driven robotic system, we enable high-precision and reliable automation of contact-based characterization techniques at high throughputs, thereby allowing the measurement of previously inaccessible yet important semiconductor properties for self-driving laboratories.

cs.RO↗

arXiv2024

Long-Term Research & Design Strategies for Fusion Energy Materials

Fusion energy is at an important inflection point in its development: multiple government agencies and private companies are now planning fusion pilot plants to deliver electricity to the grid in the next decade. However, realizing fusion as a technically and economically viable energy source depends on developing and qualifying materials that can withstand the extreme environment inside a fusion power plant. This Perspective seeks to engage the broader materials science community in this long-term effort. We first outline the principal materials challenges and research opportunities for fusion. Next, we argue that fusion is distinct from other energy applications with respect to materials, not just in the magnitude and complexity of the technical challenges but also in the present level of uncertainty in materials design requirements. To address this, we finally propose a research framework based on an iterative co-evolution of materials science and fusion power plant design requirements.

cond-mat.mtrl-sci↗

arXiv2024

Exploring material compositions for synthesis using oxidation states

Recent advances in machine learning techniques have made it possible to use high-throughput screening to identify novel materials with specific properties. However, the large number of potential candidates produced by these techniques can make it difficult to select the most promising ones. In this study, we develop the oxidation state probability (OSP) method which evaluates ternary compounds based on the probability (the OSP metric) of each element to adopt the required oxidation states for fulfilling charge neutrality. We compare this model with Roost and the Fourier-transformed crystal properties (FTCP)-based synthesizability score. Among the top 1000 systems with the most database entries in Materials Project (MP), more than 500 systems exhibit an attested compound among the top 3 compositions when ranked by the OSP metric. We find that the OSP method shows promising results for certain classes of ternary systems, especially those containing nonmetals, s-block, or transition metals. When applied to the Cu-In-Te ternary system, an interesting system for thermoelectric applications, the OSP method predicted the synthesizability of CuIn$_3$Te$_5$ without prior knowledge, and we have successfully synthesized CuIn$_3$Te$_5$ in experiment. Our method has the potential to accelerate the discovery of novel compounds by providing a guide for experimentalists to easily select the most synthesizable candidates from an arbitrarily large set of possible chemical compositions.

cond-mat.mtrl-sci↗

arXiv2023

Using Scalable Computer Vision to Automate High-throughput Semiconductor Characterization

High-throughput materials synthesis methods have risen in popularity due to their potential to accelerate the design and discovery of novel functional materials, such as solution-processed semiconductors. After synthesis, key material properties must be measured and characterized to validate discovery and provide feedback to optimization cycles. However, with the boom in development of high-throughput synthesis tools that champion production rates up to $10^4$ samples per hour with flexible form factors, most sample characterization methods are either slow (conventional rates of $10^1$ samples per hour, approximately 1000x slower) or rigid (e.g., designed for standard-size microplates), resulting in a bottleneck that impedes the materials-design process. To overcome this challenge, we propose a set of automated material property characterization (autocharacterization) tools that leverage the adaptive, parallelizable, and scalable nature of computer vision to accelerate the throughput of characterization by 85x compared to the non-automated workflow. We demonstrate a generalizable composition mapping tool for high-throughput synthesized binary material systems as well as two scalable autocharacterization algorithms that (1) autonomously compute the band gap of 200 unique compositions in 6 minutes and (2) autonomously compute the degree of degradation in 200 unique compositions in 20 minutes, generating ultra-high compositional resolution trends of band gap and stability. We demonstrate that the developed band gap and degradation detection autocharacterization methods achieve 98.5% accuracy and 96.9% accuracy, respectively, on the FA$_{1-x}$MA$_{x}$PbI$_3$, $0\leq x \leq 1$ perovskite semiconductor system.

eess.IV↗

arXiv2023

Decreasing the Computing Time of Bayesian Optimization using Generalizable Memory Pruning

Bayesian optimization (BO) suffers from long computing times when processing highly-dimensional or large data sets. These long computing times are a result of the Gaussian process surrogate model having a polynomial time complexity with the number of experiments. Running BO on high-dimensional or massive data sets becomes intractable due to this time complexity scaling, in turn, hindering experimentation. Alternative surrogate models have been developed to reduce the computing utilization of the BO procedure, however, these methods require mathematical alteration of the inherit surrogate function, pigeonholing use into only that function. In this paper, we demonstrate a generalizable BO wrapper of memory pruning and bounded optimization, capable of being used with any surrogate model and acquisition function. Using this memory pruning approach, we show a decrease in wall-clock computing times per experiment of BO from a polynomially increasing pattern to a sawtooth pattern that has a non-increasing trend without sacrificing convergence performance. Furthermore, we illustrate the generalizability of the approach across two unique data sets, two unique surrogate models, and four unique acquisition functions. All model implementations are run on the MIT Supercloud state-of-the-art computing hardware.

cs.LG↗

arXiv2023

Exploring the MIT Mathematics and EECS Curriculum Using Large Language Models

We curate a comprehensive dataset of 4,550 questions and solutions from problem sets, midterm exams, and final exams across all MIT Mathematics and Electrical Engineering and Computer Science (EECS) courses required for obtaining a degree. We evaluate the ability of large language models to fulfill the graduation requirements for any MIT major in Mathematics and EECS. Our results demonstrate that GPT-3.5 successfully solves a third of the entire MIT curriculum, while GPT-4, with prompt engineering, achieves a perfect solve rate on a test set excluding questions based on images. We fine-tune an open-source large language model on this dataset. We employ GPT-4 to automatically grade model responses, providing a detailed performance breakdown by course, question, and answer type. By embedding questions in a low-dimensional space, we explore the relationships between questions, topics, and classes and discover which questions and classes are required for solving other questions and classes through few-shot learning. Our analysis offers valuable insights into course prerequisites and curriculum design, highlighting language models' potential for learning and improving Mathematics and EECS education.

cs.CL↗

arXiv2023

Fast Bayesian Optimization of Needle-in-a-Haystack Problems using Zooming Memory-Based Initialization (ZoMBI)

Needle-in-a-Haystack problems exist across a wide range of applications including rare disease prediction, ecological resource management, fraud detection, and material property optimization. A Needle-in-a-Haystack problem arises when there is an extreme imbalance of optimum conditions relative to the size of the dataset. For example, only $0.82\%$ out of $146$k total materials in the open-access Materials Project database have a negative Poisson's ratio. However, current state-of-the-art optimization algorithms are not designed with the capabilities to find solutions to these challenging multidimensional Needle-in-a-Haystack problems, resulting in slow convergence to a global optimum or pigeonholing into a local minimum. In this paper, we present a Zooming Memory-Based Initialization algorithm, entitled ZoMBI. ZoMBI actively extracts knowledge from the previously best-performing evaluated experiments to iteratively zoom in the sampling search bounds towards the global optimum "needle" and then prunes the memory of low-performing historical experiments to accelerate compute times by reducing the algorithm time complexity from $O(n^3)$ to $O(ϕ^3)$ for $ϕ$ forward experiments per activation, which trends to a constant $O(1)$ over several activations. Additionally, ZoMBI implements two custom adaptive acquisition functions to further guide the sampling of new experiments toward the global optimum. We validate the algorithm's optimization performance on three real-world datasets exhibiting Needle-in-a-Haystack and further stress-test the algorithm's performance on an additional 174 analytical datasets. The ZoMBI algorithm demonstrates compute time speed-ups of 400x compared to traditional Bayesian optimization as well as efficiently discovering optima in under 100 experiments that are up to 3x more highly optimized than those discovered by similar methods MiP-EGO, TuRBO, and HEBO.

cs.LG↗

arXiv2022

Tackling Data Scarcity with Transfer Learning: A Case Study of Thickness Characterization from Optical Spectra of Perovskite Thin Films

Transfer learning increasingly becomes an important tool in handling data scarcity often encountered in machine learning. In the application of high-throughput thickness as a downstream process of the high-throughput optimization of optoelectronic thin films with autonomous workflows, data scarcity occurs especially for new materials. To achieve high-throughput thickness characterization, we propose a machine learning model called thicknessML that predicts thickness from UV-Vis spectrophotometry input and an overarching transfer learning workflow. We demonstrate the transfer learning workflow from generic source domain of generic band-gapped materials to specific target domain of perovskite materials, where the target domain data only come from limited number (18) of refractive indices from literature. The target domain can be easily extended to other material classes with a few literature data. Defining thickness prediction accuracy to be within-10% deviation, thicknessML achieves 92.2% (with a deviation of 3.6%) accuracy with transfer learning compared to 81.8% (with a deviation of 3.6%) 11.7% without (lower mean and larger standard deviation). Experimental validation on six deposited perovskite films also corroborates the efficacy of the proposed workflow by yielding a 10.5% mean absolute percentage error (MAPE).

cs.LG↗

arXiv2022

Human Evaluation of Text-to-Image Models on a Multi-Task Benchmark

We provide a new multi-task benchmark for evaluating text-to-image models. We perform a human evaluation comparing the most common open-source (Stable Diffusion) and commercial (DALL-E 2) models. Twenty computer science AI graduate students evaluated the two models, on three tasks, at three difficulty levels, across ten prompts each, providing 3,600 ratings. Text-to-image generation has seen rapid progress to the point that many recent models have demonstrated their ability to create realistic high-resolution images for various prompts. However, current text-to-image methods and the broader body of research in vision-language understanding still struggle with intricate text prompts that contain many objects with multiple attributes and relationships. We introduce a new text-to-image benchmark that contains a suite of thirty-two tasks over multiple applications that capture a model's ability to handle different features of a text prompt. For example, asking a model to generate a varying number of the same object to measure its ability to count or providing a text prompt with several objects that each have a different attribute to identify its ability to match objects and attributes correctly. Rather than subjectively evaluating text-to-image results on a set of prompts, our new multi-task benchmark consists of challenge tasks at three difficulty levels (easy, medium, and hard) and human ratings for each generated image.

cs.CV↗