Barry Smith

Hong Zhang, Barry Smith, Satish Balay et al.

While large language models have significantly accelerated scientific code generation, comprehensively evaluating the generated code remains a major challenge. Traditional benchmarks reduce evaluation to test-case matching, an approach insufficient for library code in HPC where solver selection, API conventions, memory management, and performance are just as critical as functional correctness. To address this gap, we introduce petscagent-bench, an agentic framework built on an agents-evaluating-agents paradigm. Instead of relying on static scripts, petscagent-bench deploys a tool-augmented evaluator agent that compiles, executes, and measures code produced by a separate model-under-test agent, orchestrating a 14-evaluator pipeline across five scoring categories: correctness, performance, code quality, algorithmic appropriateness, and library-specific conventions. Because the agents communicate through standardized protocols (A2A and MCP), the framework enables black-box evaluation of any coding agent without requiring access to its source code. We demonstrate the framework on a benchmark suite of realistic problems using the PETSc library for HPC. Our empirical analysis of frontier models reveals that while current models generate readable, well-structured code, they consistently struggle with library-specific conventions that traditional pass/fail metrics completely miss.

Jobst Landgrebe, Barry Smith

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in this journal for a thesis of this sort, on the basis of the idea (1) that where there is semantics there is also understanding and (2) that machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics \parencite{sogaard:2022}. We show that he goes wrong because he pays insufficient attention to the difference between language as used by humans and the sequences of inert of symbols which arise when language is stored on hard drives or in books in libraries.

Barry Smith, Junchao Zhang, Hong Zhang et al.

Generative AI, especially through large language models (LLMs), is transforming how technical knowledge can be accessed, reused, and extended. PETSc, a widely used numerical library for high-performance scientific computing, has accumulated a rich but fragmented knowledge base over its three decades of development, spanning source code, documentation, mailing lists, GitLab issues, Discord conversations, technical papers, and more. Much of this knowledge remains informal and inaccessible to users and new developers. To activate and utilize this knowledge base more effectively, the PETSc team has begun building an LLM-powered system that combines PETSc content with custom LLM tools -- including retrieval-augmented generation (RAG), reranking algorithms, and chatbots -- to assist users, support developers, and propose updates to formal documentation. This paper presents initial experiences designing and evaluating these tools, focusing on system architecture, using RAG and reranking for PETSc-specific information, evaluation methodologies for various LLMs and embedding models, and user interface design. Leveraging the Argonne Leadership Computing Facility resources, we analyze how LLM responses can enhance the development and use of numerical software, with an initial focus on scalable Krylov solvers. Our goal is to establish an extensible framework for knowledge-centered AI in scientific software, enabling scalable support, enriched documentation, and enhanced workflows for research and development. We conclude by outlining directions for expanding this system into a robust, evolving platform that advances software ecosystems to accelerate scientific discovery.

John Beverley, Jim Logan, Barry Smith

This paper introduces a framework for representing information about entities that do not exist or may never exist, such as those involving fictional entities, blueprints, simulations, and future scenarios. Traditional approaches that introduce "dummy instances" or rely on modal logic are criticized, and a proposal is defended in which such cases are modeled using the intersections of actual types rather than specific non existent tokens. The paper positions itself within the Basic Formal Ontology and its realist commitments, emphasizing the importance of practical, implementable solutions over purely metaphysical or philosophical proposals, arguing that existing approaches to non existent entities either overcommit to metaphysical assumptions or introduce computational inefficiencies that hinder applications. By developing a structured ontology driven approach to unreal patterns, the paper aims to provide a useful and computationally viable means of handling references to hypothetical or non existent entities.

John Beverley, David Limbaugh, Eric Merrell et al.

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding dandruff, and on and on. Among this plethora of what we can think of as mere dispositions is a subset of dispositions in whose realizations we have an interest a car responding well when driven on ice, a rabbits lungs responding well when it is chased by a wolf, and so on. We call the latter capabilities and we attempt to provide a robust ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are currently being collected in siloed fashion.

John Beverley, Giacomo De Colle, Mark Jensen et al.

Mid-level ontologies are used to integrate terminologies and data across disparate domains. There are, however, no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domain-level terms. To gain clarity, we aim to specify the necessary and sufficient conditions for a collection of one or more ontologies to inhabit what we call a mid-level architecture.

Jobst Landgrebe, Barry Smith

Since the noun phrase `artificial intelligence' (AI) was coined, it has been debated whether humans are able to create intelligence using technology. We shed new light on this question from the point of view of themodynamics and mathematics. First, we define what it is to be an agent (device) that could be the bearer of AI. Then we show that the mainstream definitions of `intelligence' proposed by Hutter and others and still accepted by the AI community are too weak even to capture what is involved when we ascribe intelligence to an insect. We then summarise the highly useful definition of basic (arthropod) intelligence proposed by Rodney Brooks, and we identify the properties that an AI agent would need to possess in order to be the bearer of intelligence by this definition. Finally, we show that, from the perspective of the disciplines needed to create such an agent, namely mathematics and physics, these properties are realisable by neither implicit nor explicit mathematical design nor by setting up an environment in which an AI could evolve spontaneously.

David Limbaugh, Jobst Landgrebe, David Kasmier et al.

Here we understand 'intelligence' as referring to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as 'items of knowledge'.

Jobst Landgrebe, Barry Smith

Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial intelligence encouraged by these successes, especially in the domain of language processing. We then show an alternative approach to language-centric AI, in which we identify a role for philosophy.