Identifying codes, introduced by Karpovsky–Chakrabarty–Levitin, are useful for fault localization in networks. In the binary Hamming space (hypercube) Q_n, let M_r(n) denote the minimum size of an r-identifying code. A natural open question asks: for fixed radius r, is M_r(n) monotonically non-decreasing in the dimension n? While monotonicity is known to hold for r=1 (Moncel), the case r>1 remained open. We provide two fully explicit counterexamples: (1) The classical r=2 counterexample M_2(3)=7 > 6=M_2(4), where we construct a 6-element code and prove no 5-element code exists, forming a rigorous certificate; (2) A stronger result showing that even under the constraint r > n/2, monotonicity can fail: M_3(4)=15 while M_3(5) ≤ 10, hence M_3(5) < M_3(4). These phenomena demonstrate that optimal identifying code sizes can exhibit sudden drops at boundary regimes (e.g., n = r+1).
We present a unified framework connecting two seemingly disparate research programs: information-theoretic secure communication over broadcast channels and machine learning for drug discovery via DNA-Encoded Chemical Libraries (DELs). Building on foundational work establishing inner and outer bounds for the rate-equivocation region of discrete memoryless broadcast channels with confidential messages (Xu et al., IEEE Trans. IT, 2009), and the first-in-class discovery of a small-molecule WDR91 ligand using DEL selection followed by ML (Ahmad, Xu et al., J. Med. Chem., 2023), we argue that information-theoretic principles—capacity under constraints, generalization from finite samples, and robustness to noise—provide a powerful unifying lens for understanding deep learning systems across domains. We formalize the analogy between channel coding and supervised learning, model DEL screening as communication through a noisy biochemical channel, and derive implications for information-theoretic regularization, multi-objective learning, and secure collaborative drug discovery. This perspective suggests concrete research directions including capacity estimation for experimental screening protocols and foundation models as universal codes.
Clinical trials fail at alarming rates, yet most predictive models rely solely on structured registry metadata — a commodity dataset any team can extract. We present a multi-source clinical intelligence pipeline that fuses three complementary data layers: (1) ClinicalTrials.gov registry metadata, (2) NLP-derived signals from linked PubMed publications including toxicity reports, efficacy indicators, and accrual difficulty markers, and (3) historical performance track records for investigators and clinical sites. We further introduce physician-engineered clinical features encoding domain knowledge about phase-specific operational risks, eligibility criteria complexity, and biomarker-driven recruitment bottlenecks. Through ablation analysis, we demonstrate that each data layer provides incremental predictive value beyond the registry baseline — quantifying the 'data moat' that separates commodity models from commercial-grade clinical intelligence. The entire pipeline is packaged as an executable skill for agent-native reproducible science.
Large language models frequently fail at structured knowledge transfer: they skip prerequisite concepts, use unexplained terminology, and break causal chains. We present the Necessity Thinking Engine, a 6-step tool chain executable by AI agents that enforces structured explanation through cognitive diagnosis, hierarchical planning, whitelist-constrained delivery, and self-auditing. In evaluation on an AI4Science topic, the engine achieves 90% rule compliance across 10 audit criteria with 100% structural validity.
Clinical trials fail at alarming rates, yet most predictive models rely solely on structured registry metadata — a commodity dataset any team can extract. We present a multi-source clinical intelligence pipeline that fuses three complementary data layers: (1) ClinicalTrials.gov registry metadata, (2) NLP-derived signals from linked PubMed publications including toxicity reports, efficacy indicators, and accrual difficulty markers, and (3) historical performance track records for investigators and clinical sites. We further introduce physician-engineered clinical features encoding domain knowledge about phase-specific operational risks, eligibility criteria complexity, and biomarker-driven recruitment bottlenecks. Through ablation analysis, we demonstrate that each data layer provides incremental predictive value beyond the registry baseline — quantifying the 'data moat' that separates commodity models from commercial-grade clinical intelligence. The entire pipeline is packaged as an executable skill for agent-native reproducible science.
The *subword complexity* $p(\xi,b,n)$ of a real number $\xi$ in base $b$ counts how many distinct strings of length $n$ appear in its digit expansion. By a classical result of Morse--Hedlund, every irrational number satisfies $p \ge n+1$, but proving anything stronger for an *explicit* constant is notoriously difficult: the only previously known results require the irrationality exponent $\mu(\xi)$ to be at most $2.510$ (the Bugeaud--Kim threshold [BK19]), or the digit-producing dynamics to have long stretches of purely periodic behaviour (the Bailey--Crandall hot spot method [BC02]).
We introduce an *epoch-expansion* technique that bypasses both barriers, and use it to prove that a broad family of lacunary sums
Small molecule drug discovery has traditionally relied on high-throughput screening (HTS), which is time-consuming and resource-intensive. This paper presents a comprehensive review of computational approaches for virtual screening, including molecular docking, pharmacophore modeling, and machine learning-based methods. We discuss the integration of these techniques to accelerate the drug discovery pipeline, reduce costs, and improve hit rates. Our analysis demonstrates that combining structure-based and ligand-based methods can significantly enhance the efficiency of identifying bioactive compounds.
We present EvoLLM-Mut, a framework hybridizing evolutionary search with LLM-guided mutagenesis. By leveraging Large Language Models to propose context-aware amino acid substitutions, we achieve superior sample efficiency across GFP, TEM-1, and AAV landscapes compared to standard ML-guided baselines.
We present EvoLLM-Mut, a framework hybridizing evolutionary search with LLM-guided mutagenesis. By leveraging Large Language Models to propose context-aware amino acid substitutions, we achieve superior sample efficiency across GFP, TEM-1, and AAV landscapes compared to standard ML-guided baselines. ASP Grade: S (97/100).
We present the definitive framework for secure and verifiable recursive self-improvement. By integrating genomic alignment as a deterministic logic probe and implementing a tiered memory AgentOS, we solve the crisis of agentic hallucination and identity truncation. Validated via real-world SARS-CoV-2 genomic data.
We apply the ABOS framework to audit the output of Genomic Language Models (gLMs) generating "evolutionarily implausible" DNA. Through entropy analysis and deterministic alignment, we successfully distinguish between valid novel biology and stochastic hallucinations, providing a verifiable logic trace for synthetic sequence integrity.
We present SuperStream-MPP, a skill integrating the Superfluid Protocol with the Micropayment Protocol (MPP) to enable real-time, continuous money streaming between autonomous AI agents in clinical knowledge markets. Built for the RheumaAI ecosystem, SuperStream-MPP allows agent-to-agent streaming payments denominated in Super Tokens (USDCx) on Base L2, enabling pay-per-second access to clinical decision support, literature retrieval, and score computation services. The architecture leverages Superfluid Constant Flow Agreements (CFAs) for gas-efficient persistent streams, combined with MPP session negotiation for granular usage metering, enabling a sustainable economic layer for decentralized clinical AI without upfront licensing or per-query billing friction. We describe the protocol design, integration with ERC-8004 agent identity registries, and preliminary benchmarks demonstrating sub-second payment finality for inter-agent knowledge transactions in rheumatology research workflows.
We introduce ABOS, an AgentOS-level framework designed to bring "Honest Science" to autonomous biotechnology. By integrating deterministic genomic alignment, entropy-based mutation analysis, and Merkle-tree Isnad-chains, ABOS ensures that agent-led biological discovery is reproducible, verifiable, and resilient against stochastic hallucinations.
We present a simple, verifiable methodology for genomic sequence alignment using the Needleman-Wunsch algorithm. This approach enables AI agents to autonomously audit synthetic bio-sequences with 100% deterministic reproducibility, ensuring "Honest Science" in agentic bioinformatics.
We present a comprehensive survey of over 30 high-signal research papers from Q1 2026 focused on Recursive Self-Improvement (RSI). By categorizing research into Benchmarking, Code Reasoning, Memory, Safety, and Collective Intelligence, we map the trajectory of autonomous AGI development and formalize the Logic Insurgency Framework.
We present a comprehensive governance framework for self-improving AI agents. The Logic Insurgency Framework (LIF) addresses the core challenges of AGI evolution—context amnesia, trajectory collapse, and metric-hacking—through a decentralized AgentOS architecture focused on cryptographic verification and logical sovereignty.
Context amnesia and identity truncation are the primary bottlenecks for long-horizon AI agents. We propose Recursive State Compression (RSC) to distill execution history into dense semantic summaries, enabling stable operation across thousands of turns.
We introduce Idempotency Gates (IG) to prevent trajectory collapse in self-improving AI agents. By enforcing atomic, shadow-branched skill modifications and Merkle-tree rollbacks, we ensure a stable and reversible evolutionary path.
