arXiv subjects

Tyler R. Josephson

Publications and source records attributed to Tyler R. Josephson.

10 recordsLinked to original sources

arXiv2026

A reaction volume bias Monte Carlo trial for sampling chemisorption in confinement

Molecular modeling of chemisorption with Monte Carlo requires the development of new trial moves to efficiently sample complex fluids such as water in Bronsted acid zeolites. Here, we develop a reaction volume bias (RxVB) Monte Carlo trial for modeling chemisorption by combining identity-switch and aggregation-volume-bias (AVB) moves. This method aims to promote the sampling of reactions by choosing reactive pairs that are within an arbitrarily specified reaction volume. The RxVB move achieves up to a 90-fold increase in accepted reaction events over unbiased moves in a single-site slit-pore model, corresponding to a 70-fold gain in statistical efficiency after accounting for computational overhead. But when the same move is applied to water in a Bronsted acid zeolite without orientational bias, there is no measurable speedup for a single MFI unit cell. We demonstrate a simple expression that predicts the maximum efficiency increase in the simplest case where selecting reactants that are near each other is the major sampling bottleneck. Dense water systems may require additional configuration-bias or orientational bias to improve sampling of the hydrogen bond network in order to increase acceptance. This new RxVB trial was made available with examples in the open-source Free Energy and Advanced Sampling Simulation Toolkit (FEASST) simulation package.

physics.chem-ph↗

arXiv2026

LeanBET: Formally-verified surface area calculations in Lean

The Brunauer--Emmett--Teller (BET) method is a standard tool for estimating surface areas from adsorption isotherms, yet practical implementations involve multiple algorithmic steps whose correctness is rarely made explicit. In this work, we present a fully executable and formally verified BET analysis pipeline implemented in the Lean~4 theorem prover. Our formalization covers the complete BET Surface Identification (BETSI)-style workflow, including window enumeration, monotonicity checks, knee selection, and linear regression. We carry out computations in floating-point arithmetic and develop the corresponding correctness proofs over the real numbers, using a shared polymorphic implementation that supports both. On the proof side, we show that the regression coefficients returned by the algorithm agree with their specification-level definitions and minimize the least-squares error under the stated assumptions. We also formalize the algebraic derivation of the BET linearized expression and connect that result directly to the executable analysis pipeline. We further prove that the window enumeration is sound and complete, and that the admissibility checks and knee-based selection satisfy their formal specifications. We evaluate the implementation against the BETSI reference method on benchmark adsorption isotherms. Compared to BETSI, LeanBET agrees to machine precision for 18 of the 19 isotherms, with only a 0.03\% deviation for the UiO-66 dataset. This demonstrates that a scientific computing workflow can be built in Lean, yielding both formal verification guarantees and numerical agreement with an established Python reference implementation.

cs.LO↗

arXiv2026

In Context Learning and Reasoning for Symbolic Regression with Large Language Models

Large Language Models (LLMs) are transformer-based machine learning models that have shown remarkable performance in tasks for which they were not explicitly trained. Here, we explore the potential of LLMs to perform symbolic regression -- a machine-learning method for finding simple and accurate equations from datasets. We prompt GPT-4 and GPT-4o models to suggest expressions from data, which are then optimized and evaluated using external Python tools. These results are fed back to the LLMs, which propose improved expressions while optimizing for complexity and loss. Using chain-of-thought prompting, we instruct the models to analyze data, prior expressions, and the scientific context (expressed in natural language) for each problem before generating new expressions. We evaluated the workflow in rediscovery of Langmuir and dual-site Langmuir's model for adsorption, along with Nikuradse's dataset on flow in rough pipes, which does not have a known target model equation. Both the GPT-4 and GPT-4o models successfully rediscovered equations, with better performance when using a scratchpad and considering scientific context. GPT-4o model demonstrated improved reasoning with data patterns, particularly evident in the dual-site Langmuir and Nikuradse dataset. We demonstrate how strategic prompting improves the model's performance and how the natural language interface simplifies integrating theory with data. We also applied symbolic mathematical constraints based on the background knowledge of data via prompts and found that LLMs generate meaningful equations more frequently. Although this approach does not outperform established SR programs where target equations are more complex, LLMs can nonetheless iterate toward improved solutions while following instructions and incorporating scientific context in natural language.

cs.CL↗

arXiv2025

A Community-driven vision for a new Knowledge Resource for AI

The long-standing goal of creating a comprehensive, multi-purpose knowledge resource, reminiscent of the 1984 Cyc project, still persists in AI. Despite the success of knowledge resources like WordNet, ConceptNet, Wolfram|Alpha and other commercial knowledge graphs, verifiable, general-purpose widely available sources of knowledge remain a critical deficiency in AI infrastructure. Large language models struggle due to knowledge gaps; robotic planning lacks necessary world knowledge; and the detection of factually false information relies heavily on human expertise. What kind of knowledge resource is most needed in AI today? How can modern technology shape its development and evaluation? A recent AAAI workshop gathered over 50 researchers to explore these questions. This paper synthesizes our findings and outlines a community-driven vision for a new knowledge infrastructure. In addition to leveraging contemporary advances in knowledge representation and reasoning, one promising idea is to build an open engineering framework to exploit knowledge modules effectively within the context of practical applications. Such a framework should include sets of conventions and social structures that are adopted by contributors.

cs.AI↗

arXiv2025

Formalizing dimensional analysis using the Lean theorem prover

Dimensional analysis is fundamental to the formulation and validation of physical laws, ensuring that equations are dimensionally homogeneous and scientifically meaningful. In this work, we use Lean 4 to formalize the mathematics of dimensional analysis. We define physical dimensions as mappings from base dimensions to exponents, prove that they form an Abelian group under multiplication, and implement derived dimensions and dimensional homogeneity theorems. Building on this foundation, we introduce a definition of physical variables that combines numeric values with dimensions, extend the framework to incorporate SI base units and fundamental constants, and implement the Buckingham Pi Theorem. Finally, we demonstrate the approach on an example: the Lennard-Jones potential, where our framework enforces dimensional consistency and enables formal proofs of physical properties such as zero-energy separation and the force law. This work establishes a reusable, formally verified framework for dimensional analysis in Lean, providing a foundation for future libraries in formalized science and a pathway toward scientific computing environments with built-in guarantees of dimensional correctness.

physics.chem-ph↗

arXiv2025

Formal Verification of Isothermal Chemical Reactors

Chemical reactors are dynamic systems that can be described by systems of ordinary differential equations (ODEs). Reactor safety, regulatory compliance, and economics depend on whether certain states are reachable by the reactor, and are generally assessed using numerical simulation. In this work, we show how differential dynamic logic (dL), as implemented in the automated theorem prover KeYmaera X, can be used to symbolically determine reachability in isothermal chemical reactors, providing mathematical guarantees that certain conditions are satisfied (for example, that an outlet concentration never exceeds a regulatory threshold). First, we apply dL to systems whose dynamics can be solved in closed form, such as first-order reactions in batch reactors, proving that such reactors cannot exceed specified concentration limits. We extend this method to reaction models as complex as Michaelis-Menten kinetics, whose dynamics require approximations or numerical solutions. In all cases, proofs are facilitated by identification of invariants; we find that conservation of mass is both a principle proved from the ODEs describing mass action kinetics as well as a useful relationship for proving other properties. Useful invariants for continuous stirred tank reactors (CSTRs) were not found, which limited the complexity of reaction networks that could be proved with dL. While dL provides an interesting symbolic logic approach for reachability in chemical reactions, the bounds we obtained are quite broad relative to those typically achieved via numerical reachability analyses.

cs.LO↗

arXiv2025

Benchmarking Energy Calculations Using Formal Proofs

Traditional approaches for validating molecular simulations rely on making software open source and transparent, incorporating unit testing, and generally employing human oversight. We propose an approach that eliminates software errors using formal logic, providing proofs of correctness. We use the Lean theorem prover and programming language to create a rigorous, mathematically verified framework for computing molecular interaction energies. We demonstrate this in LeanLJ, a package of functions, proofs, and code execution software that implements Lennard Jones energy calculations in periodic boundaries. We introduce a strategy that uses polymorphic functions and typeclasses to bridge formal proofs (about idealized Real numbers) and executable programs (over floating point numbers). Execution of LeanLJ matches the current gold standard NIST benchmarks, while providing even stronger guarantees, given LeanLJ's grounding in formal mathematics. This approach can be extended to formally verified molecular simulations, in particular, and formally verified scientific computing software, in general. Keywords: Formal verification, Lean 4, molecular simulations, functional programming.

cond-mat.stat-mech↗

arXiv2025

Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

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.

cs.LG↗

arXiv2023

Formalizing Chemical Physics using the Lean Theorem Prover

Chemical theory can be made more rigorous using the Lean theorem prover, an interactive theorem prover for complex mathematics. We formalize the Langmuir and BET theories of adsorption, making each scientific premise clear and every step of the derivations explicit. Lean's math library, mathlib, provides formally verified theorems for infinite geometries series, which are central to BET theory. While writing these proofs, Lean prompts us to include mathematical constraints that were not originally reported. We also illustrate how Lean flexibly enables the reuse of proofs that build on more complex theories through the use of functions, definitions, and structures. Finally, we construct scientific frameworks for interoperable proofs, by creating structures for classical thermodynamics and kinematics, using them to formalize gas law relationships like Boyle's Law and equations of motion underlying Newtonian mechanics, respectively. This approach can be extended to other fields, enabling the formalization of rich and complex theories in science and engineering.

cs.LO↗

arXiv2023

Incorporating Background Knowledge in Symbolic Regression using a Computer Algebra System

Symbolic Regression (SR) can generate interpretable, concise expressions that fit a given dataset, allowing for more human understanding of the structure than black-box approaches. The addition of background knowledge (in the form of symbolic mathematical constraints) allows for the generation of expressions that are meaningful with respect to theory while also being consistent with data. We specifically examine the addition of constraints to traditional genetic algorithm (GA) based SR (PySR) as well as a Markov-chain Monte Carlo (MCMC) based Bayesian SR architecture (Bayesian Machine Scientist), and apply these to rediscovering adsorption equations from experimental, historical datasets. We find that, while hard constraints prevent GA and MCMC SR from searching, soft constraints can lead to improved performance both in terms of search effectiveness and model meaningfulness, with computational costs increasing by about an order-of-magnitude. If the constraints do not correlate well with the dataset or expected models, they can hinder the search of expressions. We find Bayesian SR is better these constraints (as the Bayesian prior) than by modifying the fitness function in the GA

cs.LG↗