Formal Semantics

As "AI Scientists" emerge to drive research via the Model Context Protocol (MCP), systems relying on ephemeral scripts will fail. The sheer scale of stateful, interconnected evidence requires a machine-walkable warranty grounded in a purpose-built database architecture. Eigenius is an open-source, typed knowledge-graph DBMS built on a single premise: answering the audit question ("what do you know, and what is your warranty?") requires a unified kernel. By tightly coupling the type system, storage engine, and integration protocol, Eigenius turns data provenance into a structural invariant rather than a property reconstructed across subsystem boundaries. The kernel rests on three pillars: a dependent type theory woven through the core, institutions acting as strongly typed integration boundaries, and a content-addressed immutable storage layer. On this foundation, epistemic status (declared/observed/derived/verified) is enforced as a strict commit-time invariant. Cross-system translations (comorphisms) are checked at commit and materialized directly into the graph as durable, first-class resources. To eliminate O(N^2) polystore bottlenecks, shared on-chain intermediate representations (IRs) collapse multi-system translations to identity. Crucially, this architecture unifies both domains of scientific epistemology: it relies on justification logic for empirical science, while embedding a fast, in-process term checker to safely evaluate formal mathematical proofs (via Lean 4) without IPC overhead. In an end-to-end recomputation of a published Nature study from fragile scripts to a materialized evidence graph, all 52 derived conclusions hold from pinned data, surfacing four machine-checked discrepancies in the original study.

Just like software and hardware, business processes are susceptible to vulnerabilities that can lead to product quality issues, delays, and increased costs. Business process vulnerabilities can arise from a variety of sources, including conflicting requirements, ambiguous documentation, invalid measurement spec-ifications, omission of quality checks, or implementations that differ from speci-fications. MIRABELLE is a system that identifies and characterizes business logic (BL) vulnerabilities from available business process representations, in-cluding ISO 9000/9001 documentation, user guides, work instructions, and pro-cess execution logs. MIRABELLE leverages recent advances in AI/ML to pro-cess available business process documentation and generate attributed graph rep-resentations of the business logic that can be processed using both graph and for-mal logic approaches for identifying potential vulnerabilities. However, extract-ing the business logic (e.g., operation execution sequences, decisions, input/out-put resources) from mostly natural language artifacts is challenging due to the required domain expertise, inherent process complexity, and the sometimes very large volumes of information. This paper focuses on our experimentation with Large Language Models (LLMs) and their role within MIRABELLE. We report on the performance of several LLMs across vital stages of vulnerability detection, from grammatical and technical error-flagging in short phrasings, to complete process structure recovery and extraction.

Knowledge graph engineering often distributes accepted state, observations, constraints, processes, and hypothetical scenarios across artifacts whose combined execution contract remains external. We present PULSE, an Object-Process-Methodology-inspired language that localizes four operational roles and their write effects in one typed runtime. Here, modes denote operational roles rather than modal or deontic logic. The implemented contract fixes evidence non-overwrite, branch isolation, grounded multi-subject timers, guarded state change, and declaration-ranked event ordering over time and space; an external runner still decides whether evidence becomes an authoritative move. GeoSPARQL, SOSA, and SHACL remain generated views. A core calculus gives an effect-confinement lemma and six safety properties. Lean 4 checks kernel analogues for positions, evidence, clocks, monitors, atomicity, and branch source retention; 88 tests, 3,534 bounded checks, and 32 Lean/Python runtime-kernel cases bound the implementation claim to the checked cases. First-author implementations of a standards composition and a separate Sismic statechart reproduce the tested cold-chain trace. Across 37,440 generated temporal traces, PULSE matches a separate workflow and distinguishes ten single-field mutants. On the complete NOAA IBTrACS since1980 subset it agrees with GEOS and an event sweep on 1,476,290 transition-zone pairs, including 4,800 sampled and 12,831 duration-qualified events. Project-specific GeoSPARQL probes measure interface coverage. Overall, the results support contract localization, safety arguments, and trace parity for the tested fragment; language superiority and usability remain outside the evaluation.

Languages with rich static semantics, such as Rust, provide stronger guarantees for AI-generated code, but their strictness makes generation more difficult. Off-the-shelf compilers can provide useful feedback post-generation, but does not guide intermediate generation steps, such as those during autoregressive LLM decoding. Constrained decoding intervenes earlier by rejecting invalid tokens during sampling, but requires white-box model access and costly reimplementation for semantic constraints.We introduce generative compilation, the first approach to obtaining compiler feedback on partial programs during generation. The core technical device is a sealor: a lightweight, mostly syntax-guided transformation that converts partial programs into complete ones that standard compilers can diagnose. It is designed such that possible-to-complete partial programs are never rejected, while preserving enough code context to catch genuine dead ends early. We construct such a sealor on a core Rust-like calculus and prove that it satisfies these properties, all mechanized in Lean. We extend it to the first partial-program checker for real Rust. We evaluate our method on challenging repository-level Rust coding tasks, across both frontier black-box and open-weight models. We show that generative compilation reduces non-compiling outputs and improves functional correctness, relative to standard post-generation feedback. It does so by detecting a broad range of errors close to their source and early during generation, thereby reducing errors cascades and enabling focused diagnostics. More broadly, generative compilation is a step toward making compilers a first-class citizen of AI-assisted programming active during generation, rather than a separate post-generation check.

This paper defines TRACE (Typed Reasoning And Commitment Evidence): a typed, versioned schema for recording reasoning traces, a reference procedure for writing records against it, and one operating discipline, no durable state change without a record. The paper argues in three layers that reasoning is not in the language model: the autoregressive mechanism natively computes association; chain-of-thought and reinforcement learning inherit its limits; and the formal constructs of reasoning theory, from Socratic procedure to Pearl's ladder, are absent as machinery. The schema answers the absence with fields and tests: the TraceRecord and its causal specialization, an eight-stage reference writer, a gate-first measurement regime, the TRACE-Bench protocol, and the consumers, memory admission, plan gating, temporal regret, and verdict reuse, whose more auditable decisions are the measure of the record. A record-consumer contract states what a record guarantees and what a consumer must honor in return, making the schema an operational interface rather than a passive document. Two worked examples run in the main text: a music-lessons argument traced from sentence to typed verdict, separating association, intervention, and prescription; and a flood search-and-rescue vignette in which a predictive world model reports confident plan success that its own support and out-of-distribution scores contradict, so the record defers the commitment, requests a bounded observation, revises append-only, and clears a different branch. The vignette is illustrative, not empirical; closed-loop evaluation is left to future work, so the contribution is the schema and its contract, not a performance claim. Appendices carry the full schema, writer algorithms and cost model, clinical and policy illustrations, the benchmark protocol, convergence metrics, and usage scenarios.

Large language model (LLM) applications increasingly use explicit workflows for tool use, retrieval, branching, checkpointing, and human approval. Existing workflow systems already address many execution concerns. This paper proposes a Lisp-inspired but language-independent conceptual model: symbolic forms, object identity, and live-image thinking are used as explanatory lenses, not implementation commitments. In this model, workflow definitions, workflow instances, inference records, context snapshots, and dependency relations are represented as persistent knowledge objects in a shared knowledge substrate. Its central semantic distinction is between derive and infer: derive is deterministic computation over available state; infer is mediated LLM judgment under declared context and executor-controlled capability policy. The result is a preliminary conceptual account of semantic persistence: workflows do not merely produce knowledge and leave traces, but can themselves be represented as inspectable, resumable, and reviewable knowledge objects, while formal transition semantics remain future work.

Distributed knowledge is a notion of group knowledge studied in multi-agent epistemic logic. Semantically, the distributed knowledge of a group is interpreted via an accessibility relation given by the intersection of the epistemic accessibility relations of the agents in that group. This paper investigates sequent calculi for epistemic logics of distributed knowledge based on K45, KD45, and S5. While cut elimination holds in existing sequent calculi for modal logics K45 and KD45, it fails in all the systems mentioned above. Instead, we establish the analytic cut property for all three systems by adapting Takano' s (2018) strategy, which restricts the cut formulas to the set of subformulas of the conclusion of the cut rule. As a corollary, the Craig interpolation theorem holds for all logics considered. We also show that all proof-theoretic results remain valid when the empty group is allowed for the distributed-knowledge operator, in which case the distributed knowledge for the empty group is interpreted as the global modality.

This article develops an architecture that creates a formally verifiable reward signal to train legal AI, adapting the LLM proposes, verifier disposes paradigm from mathematical AI to the distinctive demands of law. We present an architecture comprising LLM-driven autoformalization into a formal legal calculus extending Catala, a verification kernel, and explanation generation grounded in formal proof traces. For the computational components of law, the architecture provides provable correctness. For open-textured legal analysis, it provides structural guarantees: every required stage of the legal argument is addressed, argumentation is exercised at the correct stages and not omitted, and the deductive links between steps are valid. We demonstrate the architecture on procedural deadline calculations in German law, Commerce Clause analysis in U.S. constitutional law, and cross-jurisdictional sanction proportionality. We further show that the same architecture has a structural advantage for legal AI training: a deterministic external verifier supplies verifiable outcomes for legal problems and thereby closes the traditional reinforcement-learning loop gap in law.

A fundamental problem in science is identifying underlying patterns of complex systems in the form of concise mathematical formulas. Current Artificial Intelligence (AI)-based methods have shown strong performance in single-scale systems, yet remain limited in identifying scale-specific formulas in multiscale complex systems. We present Deflex, an end-to-end AI method to automatically extract multiscale formulas with potentially different forms, including invariants and distributions, from complex systems. Deflex consists of two subsystems named Deflexformer and Deflexpressor. Deflexpressor is a lambda-calculus symbolic regression model for higher-order formulas. Deflexformer is a decomposable deep energy model for learning unified representations across scales. Deflexpressor generates synthetic data to pre-train Deflexformer, which then guides formula discovery by decoupling multiscale latent relationships. Across six representative complex systems with diverse behaviors, Deflex achieves up to 7-fold higher efficiency than the state-of-the-art methods while enabling automated multiscale discovery. Our work could be a useful tool for scientific discovery across disciplines.

Equipping Large Language Models (LLMs) to execute reliable multi-step workflows has become a central challenge in artificial intelligence. Despite recent advances in LLMs' agentic capabilities, most agent systems still lack formal methods for specifying, verifying, and debugging their workflow and execution trajectories. This challenge mirrors a long-standing problem in mathematics, where the ambiguity of natural languages (NLs) motivates the development of formal languages (FLs). Inspired by this paradigm, we propose Lean4Agent, to the best of our knowledge, the first framework that uses Lean4, a dependent-type FL to model and verify agent behavior. Lean4Agent launches FormalAgentLib, an extensible Lean4 library for formally modeling and verifying agent workflows' semantic consistency under explicit assumptions, and enabling localization of execution-time failures revealed by trajectories. Building on FormalAgentLib, we further develop LeanEvolve, which applies results in FormalAgentLib to revise workflows to enhance its capability. Extensive experiments on a hard problem subset of SWE-Bench-Verified and a subset of ELAIP-Bench across 5 leading LLMs indicate that the verification-passing workflows outperform the failing ones by an average of 11.94%, and LeanEvolve further improves SWE performance by 7.47% on average. Furthermore, Lean4Agent establishes a foundation for a new field of using expressive dependent-type FL to formally model and verify agent behavior.

The do-calculus defines a general system of inference for interventional queries, allowing causal quantities to be transformed through successive applications of its rules. This process induces a rich space of equivalent interventional expressions, but combining and ordering these rules remains challenging. In this work, we introduce derivation graphs, which represent how do-calculus rules are applied and combined, and characterize the full space of observational and interventional probabilities which are equivalent under the do-calculus. The structure of these graphs yields a simple procedure that uses at most four applications of do-calculus rules. Finally, we show how applying identification algorithms to equivalent causal queries produces multiple valid estimands for the same causal quantity, eventually yielding more efficient estimators.

We propose ZX-Calculus (Knowledge Evolution Calculus), a conservative extension of Martin-Lof Dependent Type Theory (MLTT) integrating trace-indexed types, presheaf non-monotone semantics, and constructive AGM belief revision. A Coq mechanisation accompanies the paper (34 complete proofs; zero admits for the two central results). (I) Trace types. FinTrace(s0,sn) is an inductive family of typed execution traces. FinTrace and Star(Step) are isomorphic as path types but not judgementally equal; TraceElim exposes the event label e:Event explicitly, giving a more ergonomic interface for event-driven induction. We prove the Trace-Reachability Correspondence, Deterministic Replay, and a canonicity framework via reducibility candidates with a Transport Lemma (RC-elim deferred; all other Core results are Coq-verified). (II) Sheaf semantics. Trace-indexed propositions are contravariant sheaves over the free trace partial-order category Tf. A Separation Theorem (explicit countermodel) distinguishes proof-theoretic monotonicity from semantic non-monotonicity. The term model is an initial CwF (syntactic universal property, not classical completeness). (III) AGM belief revision. We give an explicit constructive partial meet contraction algorithm verified against (C1)-(C4). All eight AGM postulates (R1)-(R8) are theorems. Proofs of R7 and R8 use the Disjunctive Entrenchment Lemma, given a self-contained constructive derivation. (IV) Integration. B^AGM fails the sheaf composition law BP-comp for sequential revision (explicit countermodel, Coq-verified). We introduce Single-Step Revision Systems (SSRS), prove B^AGM is a valid SSRS (Coq-verified), and show this suffices for trace morphisms, retraction characterisation, and revision witnesses. The BP-comp failure reveals a fundamental tension between path-dependent belief revision and functor consistency, not previously identified.

Architecture diagrams are ubiquitous in deep learning, but they are usually only representational: the tensor-program identities they suggest are still proved by prose and tensor-axis manipulation. We introduce a formal graphical calculus for the structural fragment of tensor programming underlying einops, making such diagrams proof-enabling. Our calculus represents tensor axes as nested graded tubes around a base type. The tube boundary recovers the undirected tensor-network view of axes, while the directed interior retains the operational reading of computation graphs. The key rewrite is grade-naturality: sliding spectacles over tubes. Standard equivariance proofs become short diagrammatic derivations. We additionally demonstrate how our rewrite system may be applied to convert attention masks into pre-processing operations, recovering efficient implementations of sparse attention blocks.

Large Language Models (LLMs) are being employed widely to automate tasks across the software development life-cycle. It is, however, unclear whether these tasks are performed consistently with respect to the semantics of the artefacts being handled. This question is particularly under-researched concerning architectural design specification. In this paper, we address this question for High-Level Message Sequence Charts (HMSCs). These are visual models with a rigorous formal semantics that have been used for various purposes, including as a foundation for Sequence Diagrams in the Unified Modelling Language (UML). We examine whether LLMs "understand" the semantics of HMSCs by examining three LLMs (Gemini-3, GPT-5.4, and Qwen-3.6) on how they perform 129 semantic tasks ranging from querying basic semantic constructs in HMSCs (i.e., events and their ordering) to semantic-preserving abstractions and compositions, and calculating the set of traces and trace-equivalent labelled transition systems. The results show that LLMs only have a modest understanding of the formal semantics of HMSCs (ca. 52% overall accuracy), with great variability across different semantic concepts: while LLMs seem to understand the basic semantic concepts of MSCs (ca. 88% accuracy), they struggle with semantic reasoning in tasks involving abstraction and composition (ca. 36% accuracy) and traces and LTSs (ca. 42% accuracy). In particular, all three LLMs struggle with the notions of co-region and explicit causal dependencies and never employed them in semantic-preserving transformations.

AI systems increasingly synthesize executable structure at runtime: LLMs generate programs, agents construct workflows,self-improving systems modify their own behavior. In classical homoiconic and staged languages, the transition from code representation to execution is unrestricted. eval is a language primitive, not a governed operation. We argue that in governed intelligent systems, this transition is an authority amplification: it converts symbolic structure into executable authority and must be mediated like any other effect. We present governed metaprogramming, a language design where program representations (machine forms) are first-class values, form manipulation is pure computation, and materialization (the transition from form to executable machine) is a governed effect subject to structural inspection. The governance system analyzes the proposed program's capability requirements, policy compliance, and resource estimates before permitting execution. We formalize two judgments: pure form evaluation (which emits no directives) and governed materialization (which emits exactly one governed directive). We prove three properties: purity of form manipulation, the no-bypass theorem, and boundary preservation. We implement the design in mashinTalk, a DSL for AI workflows compiling to BEAM byte code, and report on integration with 454 existing machine-checked Rocq theorems. The central contribution is reclassifying eval from a language primitive into a governed effect.

We present an algebraic semantics for governed execution in which governance is axiomatized, compositional, and coterminous with expressibility. The framework, mechanized in 32 Rocq modules (~12,000 lines, 454 theorems, 0 admitted), is built on interaction trees and parameterized coinduction. A three-axiom GovernanceAlgebra record (safety, transparency, properness) induces a symmetric monoidal category with verified pentagon, triangle, and hexagon coherence, where every tensor composition preserves governance. An algebraic effect system constrains the handler algebra so that only governance-preserving handlers can be constructed in the safe fragment; programs in the empty capability set provably emit only observability directives. Capability-indexed composition bundles programs with machine-checked capability bounds, and a dual guarantee theorem establishes that within_caps and gov_safe hold simultaneously under all composition operators. The capstone result is the coterminous boundary: within our formal model, every program expressible via the four primitive morphism constructors is governed under interpretation, and every governed program is the image of such a program. Turing completeness is preserved inside governance; unmediated I/O is excluded from the governed fragment. Governance denial is modeled as safe coinductive divergence. The governance algebra is parametric: any system instantiating the three axioms inherits all derived properties, including convergence, compositional closure, and goal preservation. Extracted OCaml runs as a NIF in the BEAM runtime, with property-based testing (70,000+ random inputs, zero disagreements) confirming behavioral equivalence between the specification and the runtime interpreter.

We present five results in the theory of structural governance for cognitive workflow systems. Three are mechanized in Coq 8.19 using the Interaction Trees library with parameterized coinduction; two are proved on paper with explicit reductions. The Coinductive Safety Predicate (gov_safe) is a coinductive property that captures governance safety for infinite program behaviors, indexed by a boolean permission flag that is provably false for ungoverned I/O and true for governed interpretations (mechanized). The Governance Invariance Theorem establishes that governance is uniform across the meta-recursive tower: governance at level n+1 reduces to governance at level n by definitional equality of the type (mechanized). The Sufficiency Theorem proves that four atomic primitives (code, reason, memory, call) are expressively complete for any discrete intelligent system, formalized as compositional closure of a Kleisli category (mechanized). The Alternating Normal Form provides a canonical decomposition of any machine into alternating code and effect layers, with a confluent rewriting system (paper proof). The Necessity Theorem proves via explicit reduction to Rice's theorem that an architecturally opaque component (the reason primitive) is mathematically necessary for problems requiring semantic judgment (paper proof). A sixth contribution connects the abstract model to the deployed runtime: the Verified Interpreter Specification formalizes the BEAM runtime's trust, capability, and hash chain logic in Coq, then tests the running system against this specification using property-based testing with over 70,000 randomly generated directive sequences and zero disagreements. The mechanization comprises approximately 12,000 lines across 36 modules with 454 theorems and zero admitted lemmas.

We present a formally verified framework for patent analysis as a hybrid AI + Lean 4 pipeline. The DAG-coverage core (Algorithm 1b) is fully machine-verified once bounded match scores are fixed. Freedom-to-operate, claim-construction sensitivity, cross-claim consistency, and doctrine-of-equivalents analyses are formalized at the specification level with kernel-checked candidate certificates. Existing patent-analysis approaches rely on manual expert analysis (slow, non-scalable) or ML/NLP methods (probabilistic, opaque, non-compositional). To our knowledge, this is the first framework that applies interactive theorem proving based on dependent type theory to intellectual property analysis. Claims are encoded as DAGs in Lean 4, match strengths as elements of a verified complete lattice, and confidence scores propagate through dependencies via proven-correct monotone functions. We formalize five IP use cases (patent-to-product mapping, freedom-to-operate, claim construction sensitivity, cross-claim consistency, doctrine of equivalents) via six algorithms. Structural lemmas, the coverage-core generator, and the closed-path identity coverage = W_cov are machine-verified in Lean 4. Higher-level theorems for the other use cases remain informal proof sketches, and their proof-generation functions are architecturally mitigated (untrusted generators whose outputs are kernel-checked and sorry-free axiom-audited). Guarantees are conditional on the ML layer: they certify mathematical correctness of computations downstream of ML scores, not the accuracy of the scores themselves. A case study on a synthetic memory-module claim demonstrates weighted coverage and construction-sensitivity analysis. Validation against adjudicated cases is future work.

We introduce causal-temporal event graphs (CTEGs) as a formal model for fully resolved recursive agent execution records under single-parenthood causal semantics. We formalise direct event emissions and recursive subagent invocations as extension procedures on generic typed temporal graphs and show that the recursive closure $\mathscr{E}_\infty$ of the induced maximal dynamics starting from single causal roots consists entirely of finite sequences of CTEGs. A CTEG is a rooted arborescence whose nodes carry timestamps and event types, subject to the constraint that timestamps be strictly increasing along causal paths. We realise $\mathscr{E}_\infty$ as the increasing union of a recursive hierarchy $\mathscr{E}_0 \subseteq \mathscr{E}_1 \subseteq \cdots$ of agent execution levels parametrised by recursion depth, which is recognised as the ascending Kleene chain of a monotone operator $\varphi$ admitting $\mathscr{E}_\infty$ as its least fixed point. Although the introduction of the full hierarchy is natural, stabilisation occurs already at $\mathscr{E}_1$ if one insists that the internal construction of a subagent execution trace be a delegated and opaque computational unit. The CTEG formalism supports compositional construction of globally well-formed execution traces from local agent behaviour without centralised coordination, preserves well-formedness under partial execution failure, and admits a natural relational database encoding. The arborescent structure of CTEGs is further compatible with cryptographic Merkle tree commitments for tamper-evident session verification.

Type annotations are essential when printing terms in a way that preserves their meaning under reparsing and type inference. We study the problem of complete and minimal type annotations for rank-one polymorphic $λ$-calculus terms, as used in Isabelle. Building on prior work by Smolka, Blanchette et al., we give a metatheoretical account of the problem, with a full formal specification and proofs, and formalize it in Isabelle/HOL. Our development is a series of experiments featuring human-driven and AI-driven formalization workflows: a human and an LLM-powered AI agent independently produce pen-and-paper proofs, and the AI agent autoformalizes both in Isabelle, with further human-hinted AI interventions refining and generalizing the development.

The emergence of large language model agents capable of invoking external tools has created urgent need for formal verification of agent protocols. Two paradigms dominate this space: Schema-Guided Dialogue (SGD), a research framework for zero-shot API generalization, and the Model Context Protocol (MCP), an industry standard for agent-tool integration. While both enable dynamic service discovery through schema descriptions, their formal relationship remains unexplored. We present the first process calculus formalization of SGD and MCP, proving they are structurally bisimilar under a well-defined mapping Phi. We demonstrate that the reverse mapping Phi-1 is partial and lossy, revealing critical gaps in MCP's expressivity. Through bidirectional analysis, we identify four principles - semantic completeness, explicit action boundaries, failure mode documentation, and inter-tool relationship declaration -- as necessary and sufficient conditions for full behavioral equivalence. We formalize these principles as type-system extensions MCP+, proving MCP+ is fully equivalent to SGD. Our work provides the first formal foundation for verified agent systems and establishes schema quality as a provable safety property. Practically, this means that the current MCP specification has expressiveness gaps compared to SGD and would benefit from the proposed extensions.

Data fusion, the process of combining observational and experimental data, can enable the identification of causal effects that would otherwise remain non-identifiable. Although identification algorithms have been developed for specific scenarios, do-calculus remains the only general-purpose tool for causal data fusion, particularly when variables are present in some data sources but not others. However, approaches based on do-calculus may encounter computational challenges as the number of variables increases and the causal graph grows in complexity. Consequently, there exists a need to reduce the size of such models while preserving the essential features. For this purpose, we propose pruning (removing unnecessary variables) and clustering (combining variables) as preprocessing operations for causal data fusion. We generalize earlier results on a single data source and derive conditions for applying pruning and clustering in the case of multiple data sources. We give sufficient conditions for inferring the identifiability or non-identifiability of a causal effect in a larger graph based on a smaller graph and show how to obtain the corresponding identifying functional for identifiable causal effects. Examples from epidemiology and social science demonstrate the use of the results.