📚 Published APP papers #36

LionSR · 2026-06-17T21:26:13Z

LionSR
Jun 17, 2026
Maintainer

The Agentic Publication Protocol (APP) publishes a scientific paper as a public code repository instead of only a PDF. The repository bundles the paper, its code, its data, and the information needed to run it, plus an AGENTS.md file that an AI coding assistant can read. You can open the paper in an AI agent and ask about its methods, results, and limitations, and the agent answers from the actual paper, code, and data.

This thread lists papers published with APP so people can find them. Each one is a validated, author-approved release fixed to a specific version.

To read a paper, clone its repository and open it in an AI coding agent such as Claude Code or Codex. The agent reads AGENTS.md and answers your questions about the paper.

Each summary below is copied word for word from the paper's own AGENTS.md.

1. Agentic Publication Protocol: An Attempt to Modernize Scientific Publication

Sirui Lu (Max-Planck-Institut fuer Quantenoptik; Munich Center for Quantum Science and Technology)
Xiao-Liang Qi (Leinweber Institute for Theoretical Physics, Stanford University)

Field: scientific-publication
Release: v1.0.0
Tags: agentic-publication-protocol, scientific-publication, reproducibility, paper-agents

Summary

Rather than publishing only a static paper, APP proposes a more reproducible, informative, and interactive publication format. An APP publication is an organized bundle of the research work: paper, code, data, environment information, and related context, together with an AGENTS.md instruction file that lets future readers interact with a faithful paper agent.

The goal is for scientific publications to carry not only knowledge, but also know-how: the practical understanding needed to interpret, reproduce, and build on the work, which has traditionally been difficult to transfer faithfully. The paper defines the protocol, describes agent skills for preparing APP publications, and reports a small compare-app evaluation in which APP paper agents show stronger grounding and honesty than a general repository-aware agent.

2. Perfect Nonreciprocal Axion-polaritons

Abhinava Chatterjee, Chao-Xing Liu (Department of Physics, The Pennsylvania State University)

arXiv: 2606.04341
Field: condensed-matter-physics
Release: v1.0.0
Tags: axion-polaritons, nonreciprocity, optical-isolator, topological-materials, axion-electrodynamics, magnon-polaritons

Summary

Under appropriate static electric (E₀ ‖ ŷ) and magnetic (B₀ ‖ ẑ) fields applied simultaneously to a dynamical axion insulator, axion-polaritons — hybrid axion-photon collective modes — acquire a nonreciprocal dispersion ω(k) ≠ ω(−k). This arises because the axion-photon coupling is direction-dependent: photons propagating in opposite directions hybridize with the axion with different strengths (g₊ ≠ g₋). Neither field alone is sufficient; the simultaneous breaking of inversion symmetry (by E₀) and time-reversal symmetry (by B₀) produces the term 2𝓔𝓑kω in the quartic dispersion (Eq. 4) that is the microscopic origin of nonreciprocity.

The paper identifies a special regime of perfect nonreciprocity when E₀ = c′B₀: here ω = c′k is an exact solution of the quartic, meaning the right-moving photon is completely decoupled from the axion source while the counter-propagating photon hybridizes strongly — a one-way coupling with no analogue in prior axion-polariton work. This direction-dependent coupling manifests directly as an optical isolator: a finite slab transmits light left-to-right with high efficiency while right-to-left transmission is exponentially suppressed near the axion resonance. The results propose nonreciprocal axion-polaritons as a new experimental probe of axion quasiparticles, with material parameters motivated by GHz-frequency magnon measurements in MnBi₂Te₄.

3. Lifshitz--Kosevich Theory of Anomalous Landau Levels in Topological Flat Bands

Chao-Xing Liu (Department of Physics, The Pennsylvania State University; Center for Theory of Emergent Quantum Matter, The Pennsylvania State University)

Field: condensed-matter physics
Release: v1.0.0
Tags: topological flat bands, Landau levels, quantum oscillations, Lifshitz-Kosevich theory, quantum geometry, moire materials

Summary

This paper develops a Lifshitz--Kosevich description for quantum oscillations arising from anomalous Landau levels of topological flat bands. In contrast with ordinary dispersive bands, where the LK thermal damping scale is controlled by the cyclotron energy, the anomalous flat-band oscillations are controlled by the local Landau-level spacing at the chemical potential.

Using a minimal exactly flat topological-band model, the paper compares fixed-density magnetization oscillations in normal and anomalous regimes. The anomalous oscillations have finite but much larger and field-dependent LK effective masses. In the weak-field limit, the anomalous effective mass scales inversely with magnetic field and with the trace of the quantum metric, making thermal damping of flat-band quantum oscillations a probe of quantum geometry.

4. Beyond transversality: structure of Clifford circuits for CSS codes

Victor V. Albert (Joint Center for Quantum Information and Computer Science, NIST/University of Maryland)

arXiv: 2608.05688
Field: quantum-information
Release: v1.0.0-arxiv
Tags: CSS codes, Clifford circuits, transversal gates, logical gates, QLDPC codes, fault tolerance

Summary

The paper proves structure theorems for four nested groups of Clifford circuits
that preserve a CSS code, each relevant to fault-tolerant logical operations.
Every code-preserving Clifford circuit is a product of Z-diagonal circuits
(S and CZ gates) and their X-basis analogues. Every element of the two-fold
transversal group — generated by depth-one circuits of one- and two-qubit gates —
factors into layers that are Z-diagonal, X-diagonal, or CNOT; consequently every
transversal gate is a product of three transversal diagonal circuits (two, for
connected non-self-dual codes). Every code-preserving automorphism circuit has a
normal form: a Hadamard layer, a permutation, and two diagonal circuits. A
further two-fold automorphism group, allowing a compensating qubit permutation,
can realize strictly more logical gates than the two-fold transversal group.

As an application, the paper surveys 136 CSS codes with explicit certified
generator data: 78 codes whose two-fold transversal circuits generate the full
logical Clifford group (at distances up to 12), 58 mostly-QLDPC codes with
exactly computed logical images (e.g., ≥460,800 for the gross code), and three
new code families — bipartite grids, cut-complements, and quadrics — many of
whose members realize the full logical Clifford group this way.

5. Measuring Semantic Abstractness of SAE Features via Nonlocality

Chuqiao Lin (Rudolf Peierls Centre for Theoretical Physics, University of Oxford)
Shivaji L. Sondhi (Rudolf Peierls Centre for Theoretical Physics, University of Oxford)
Xiao-Liang Qi (Leinweber Institute for Theoretical Physics, Stanford University)

Field: mechanistic-interpretability
Release: v1.0.0
Tags: sparse-autoencoders, feature-abstractness, nonlocality, steering, jailbreak-audit

Summary

Sparse autoencoders (SAEs) decompose language-model activations into features, but knowing what a feature responds to (its description) does not settle at what level of abstraction it operates — a token-matching feature and a genuinely contextual one can carry similar descriptions. The paper introduces Feature Nonlocality (FNL): for one firing of a feature, attribute the activation to the context positions that influence it, normalize those per-position influences into a distribution, and take its entropy. A feature driven by a single token has near-zero FNL; a feature integrating a whole passage has high FNL. The paper shows FNL behaves as an abstractness measure should — it rises with network depth, is stable across text corpora once a reliability ceiling is accounted for, separates contextual from token-driven features, and predicts robustness of activation under meaning-preserving paraphrase — and then uses it in two applications: auditing a published SAE-based jailbreak mitigation (finding its features are mostly positional artifacts, not detectors of harmful intent) and selecting features for steering (steering high-FNL features improves benchmark accuracy where steering low-FNL ones does not, though gains are model-specific).

6. Blast freezing a black hole

Shoaib Akhtar (Leinweber Institute for Theoretical Physics, Stanford University)
Xiao-Liang Qi (Leinweber Institute for Theoretical Physics, Stanford University; OpenAI)

Field: high-energy-theory
Release: v1.0.0
Tags: black-hole-evaporation, SYK, bulk-reconstruction, quantum-information

Summary

The paper introduces a solvable evaporation model built from coupled SYK systems:
an initially two-sided black hole is coupled at a finite time to a larger, colder
bath. In an appropriate large-N and large-p limit, two-point functions and certain
four-point probes admit analytic treatment. Boundary correlators determine a
generalized HKLL reconstruction of the emergent bulk geometry.

Operator size and Rényi-2 mutual information track an infalling excitation.
Second Rényi entropy tracks entanglement between the evaporating eta system
and the chi bath, including its oscillatory evolution.
The paper argues that information inaccessible to simple probes after blast
freezing is preserved in nonlocal many-body degrees of freedom. Its analytic
limits, finite-p numerical evidence, and qualitative geometry interpretations
must be distinguished when explaining the result.

7. Blast freezing a black hole

Shoaib Akhtar (Leinweber Institute for Theoretical Physics, Stanford University)
Xiao-Liang Qi (Leinweber Institute for Theoretical Physics, Stanford University; OpenAI)

Field: high-energy-theory
Release: v1.0.1
Tags: black-hole-evaporation, SYK, bulk-reconstruction, quantum-information

Summary

The paper introduces a solvable evaporation model built from coupled SYK systems:
an initially two-sided black hole is coupled at a finite time to a larger, colder
bath. In an appropriate large-N and large-p limit, two-point functions and certain
four-point probes admit analytic treatment. Boundary correlators determine a
generalized HKLL reconstruction of the emergent bulk geometry.

Operator size and Rényi-2 mutual information track an infalling excitation.
Second Rényi entropy tracks entanglement between the evaporating eta system
and the chi bath, including its oscillatory evolution.
The paper argues that information inaccessible to simple probes after blast
freezing is preserved in nonlocal many-body degrees of freedom. Its analytic
limits, finite-p numerical evidence, and qualitative geometry interpretations
must be distinguished when explaining the result.

Published a paper with APP? Reply with the link to your release and we will add it here.