Cryptographically Authorized Mutation

Persistent language-model agents increasingly combine tool use, tiered memory, reflective prompting, and runtime adaptation. In such systems, behavior is shaped not only by current prompts but by mutable internal conditions that influence future action. This paper introduces layered mutability, a framework for reasoning about that process across five layers: pretraining, post-training alignment, self-narrative, memory, and weight-level adaptation. The central claim is that governance difficulty rises when mutation is rapid, downstream coupling is strong, reversibility is weak, and observability is low, creating a systematic mismatch between the layers that most affect behavior and the layers humans can most easily inspect. I formalize this intuition with simple drift, governance-load, and hysteresis quantities, connect the framework to recent work on temporal identity in language-model agents, and report a preliminary ratchet experiment in which reverting an agent's visible self-description after memory accumulation fails to restore baseline behavior. In that experiment, the estimated identity hysteresis ratio is 0.68. The main implication is that the salient failure mode for persistent self-modifying agents is not abrupt misalignment but compositional drift: locally reasonable updates that accumulate into a behavioral trajectory that was never explicitly authorized.

Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples. Yet most protein families are small: the median Pfam seed alignment contains only 22 sequences, a regime where learned models overfit or collapse. We propose \emph{stochastic attention} (SA), a training-free sampler that treats the modern Hopfield energy over stored sequences as a Boltzmann distribution and draws samples via Langevin dynamics. The score function is the residual of a single softmax attention operation, eliminating the need for a trained score network, pretraining data, or graphics processing units (GPUs). Across eight Pfam families spanning 37 to 420 sequences and 23 to 262 residues, SA generates sequences with low composition divergence, novelty, and structural plausibility supported by ESMFold and AlphaFold2. Compared with profile hidden Markov models (HMMs), EvoDiff, and the multiple sequence alignment (MSA) Transformer, SA is the only tested method to simultaneously achieve low composition divergence, genuine novelty, and sequence identity within each family's nearest-neighbor identity range; the others drift outside this range or produce near-copies. The critical inverse temperature is predicted from principal component analysis (PCA) dimensionality alone, enabling fully automatic operation from a seed alignment. In two domains with deep mutational scanning data, SA-generated substitutions are enriched for experimentally tolerated mutations beyond a position-matched null, and an independent language model (ESM2-650M) scores them within the natural range. Stochastic attention thus opens training-free sequence generation to the long tail of protein families too small for deep learning.

In this paper, we tackle a critical challenge in model evaluation: how to keep code benchmarks useful when models might have already seen them during training. We introduce a novel solution, dynamic benchmarking framework, to address this challenge. Given a code understanding or reasoning benchmark, our framework dynamically transforms each input, i.e., programs, with various semantic-preserving mutations to build a syntactically new while semantically identical benchmark. We evaluated 10 popular language models on our dynamic benchmarks. Our evaluation reveals several interesting or surprising findings: (1) all models perform significantly worse than before, (2) the ranking between some models shifts dramatically, and (3) dynamic benchmarks can resist against the data contamination problem.