Cryptographically Authorized Mutation

Background: Molecular testing for NPM1 and FLT3-ITD mutations guides critical early treatment decisions in acute myeloid leukemia (AML), but results can take weeks, long after these decisions must be made. Flow cytometry, already performed within hours of admission as part of routine care, may carry enough signal to predict these mutations directly, without added cost or delay. Methods: We developed an interpretable multi-instance learning classifier based on a decision tree, in which each patient sample is modeled as a collection of individual cells and mutation status is inferred from cell-level predictions. The model was benchmarked against a random forest trained on clinical variables and a deep convolutional neural network adapted for multitube flow cytometry data. Performance was assessed by cross-validation on a discovery cohort of 197 patients and tested on an independent cohort of 161 patients, using the area under the receiver operating characteristic curve (AUROC) and positive predictive value. Results: In cross-validation on the discovery cohort, the MIL model achieved mean AUROCs of 0.96 (SD=0.05) for NPM1 and 0.86 (SD=0.10) for FLT3-ITD, outperforming the clinical baseline and matching deep learning approaches. The model then successfully generalized to the independent test cohort of 161 patients, reaching AUROCs of 0.90 (NPM1) and 0.82 (FLT3-ITD), with positive predictive values of 0.87 and 0.68, respectively. Cell-level interpretation recovered established immunophenotypic signatures (CD33${}^{+}$ /CD34___ for NPM1-mutated cases, CD33${}^{+}$ /low side-scatter for FLT3-ITD), directly linking model predictions to known biology. Conclusions: These results show that an interpretable model applied to data already collected in routine care can predict AML molecular status within hours, offering a practical route to earlier, biology-informed treatment decisions.

Antibody lead optimization calls for a small, bounded set of edits to an existing candidate: substitutions, but also insertions and deletions. Edit-based generative models are the only ones that allocate such an edit budget without fixing the edit positions, the edit count, or the output length in advance. However, the existing approaches Edit Flows and EvoFlows did not release code or complete training specifications. Here, we show that both methods follow the same underlying process -- edits firing one at a time, at learned rates, in continuous time -- the pure-jump case of generator matching over finite sequences. With EditJumps we introduce the first open implementation of this framework, with a single generalist antibody editor trained on 1.66M Observed Antibody Space homolog pairs to propose homolog-like variants of a seed sequence, editing unseen leads zero-shot, without the per-family retraining original approaches require. Replicating this system from scratch exposes why open code is essential for generative biology: reconciling published edit distributions required reverse-engineering an undocumented rate-scaling hyperparameter that dictates realized mutation counts. Moreover, we show that published evaluation metrics are highly sensitive to reference sample size, frequently flipping method rankings. We release our full codebase, automated test suite, and configurations at: https://github.com/VisiumCH/editjumps

This study proposes a Large Language Model-Driven Differential Evolution (LLMDE) algorithm to reduce the reliance on handcrafted hyperparameter design. The proposed algorithm leverages a prompt engineering strategy, allowing large language models (LLMs) to dynamically select mutation strategies and configure control parameters guided by optimization feedback, thus enhancing the performance of the DE algorithm. We evaluate the performance of LLMDE on the CEC2022 benchmark suite, comparing it with standard DE and representative metaheuristics. Furthermore, we employ factor analysis and K-means clustering for stock selection, and then apply LLMDE to solve the Conditional Value at Risk (CVaR) portfolio optimization problem using the selected stocks, subject to budget and minimum expected return constraints. Experimental results demonstrate that LLMDE achieves competitive performance on the benchmark suite while continuously generating high-quality solutions for complex constrained optimization tasks. These outcomes successfully demonstrate the viability of embedding LLMs within metaheuristics, paving a promising path toward the design of advanced LLM-assisted optimization techniques.

Text-to-SQL systems translate natural language queries into executable SQL, democratizing access to structured data. Despite recent advances driven by large language models (LLMs), evaluation remains a major bottleneck: public benchmarks fail to capture the complexity of enterprise schema, while building private evaluation sets is costly and nondeterministic, making evaluation results difficult to reproduce. To address this issue, we present SQLMorph, a framework for Text-to-SQL evaluation via query mutation. SQLMorph introduces two techniques to automatically generate and expand evaluation sets: Join Query Expansion (JQE), which systematically increases structural complexity through valid join additions, and Textual Query Augmentation (TQA), which generates controlled natural language perturbations to assess robustness to linguistic variation. JQE and TQA create targeted choke points to challenge specific system components. When applied to state-of-the-art systems, JQE increases query coverage and reveals accuracy degradation as the number of joins grows. Meanwhile, TQA shows that linguistic brittleness induced by heavy abbreviation can reduce accuracy by up to 17%. Beyond evaluation sets, SQLMorph introduces a family of execution-level metrics that address the limitations of current binary measures, such as Execution Accuracy. We define Execution Precision (EXP) and Execution Recall (EXR) to quantify the fraction of correct and recovered results, respectively, and combine them via F1 for unified scoring. Our experiments show that these relaxed metrics enable fine-grained analysis of over- and under-prediction, revealing differences across systems that binary metrics obscure. Together, SQLMorph's query mutation and fine-grained metrics support debugging and better align Text-to-SQL evaluation practices with real-world deployments.

The evolution of DNA sequences can be viewed as stochastic dynamics on a high-dimensional discrete space, but it is unclear when empirical transition biases reduce to an effective energy landscape versus retain irreducible non-equilibrium circulation. Human context-dependent mutation probabilities offer a direct test: every single-nucleotide substitution in a local context has a reverse substitution, so the logarithm of the forward-to-reverse probability ratio defines an antisymmetric field-the human mutation field. We show this field has a dominant gradient component and a smaller but reproducible curl component. Using seven-base human germline substitution probabilities, we infer an effective mutational landscape with a Siamese neural network constrained to predict only energy differences. This model predicts forward-to-reverse log-ratios for held-out mutations with a correlation of about 0.93, close to both an unconstrained predictive reference (0.948) and the empirical reversible ceiling from Hodge projection (about 0.96). Although trained only on mutation probabilities, the inferred landscape largely recovers short-word genomic composition and Chargaff reverse-complement symmetry for sequences up to length four. Deviations from equilibrium structure reveal a small but detectable nonequilibrium component: a residual irreversible circulation violating the Kolmogorov cycle condition for detailed balance, reproducible across African, Asian, and European populations, and strongest in CpG-linked cycles and CpG-transition edges, consistent with methylcytosine deamination. These results give a thermodynamic decomposition of the human mutation field: most mutation bias is organized by a local equilibrium-like energy landscape aligned with genome composition, while the residual circulation points to specific directional mutational mechanisms.

Automated repair of Hardware Description Language (HDL) designs remains challenging due to the large search space of candidate repairs and the strict syntactic and semantic constraints imposed by HDL grammars. Generic mutation strategies overwhelmingly generate syntactically invalid candidates that waste compilation and simulation budget, while synthesis-driven and template-based approaches impose their own constraints on generality and portability. In this paper, we propose a dictionary-guided HDL repair system that combines ANTLR-derived DUT-specific mutation vocabularies with a simulation-divergence fault localization (FL) module. The mutation operator applies category-constrained token substitutions, insertions, and deletions directly to Verilog source via regex-based matching, without requiring AST manipulation or synthesis. The FL module identifies diverging output wires from a single simulation run and scores source lines by structural proximity to those signals, directing the mutation search toward high-suspicion regions. A deterministic targeted sweep exhausts all dictionary mutations on the highest-scored lines before falling back to a genetic programming (GP) search. Evaluated on the CirFix benchmark suite across six design under test (DUT) families, the proposed approach produces correct oracle-passing repairs on 14 bug variants, including a 6-edit multi-bug instance that CirFix cannot repair, and achieves an 18x speedup over CirFix on a two-edit benchmark variant. These results indicate that dictionary-constrained mutation operators, combined with lightweight simulation-divergence FL, are a practical and competitive approach to automated HDL repair for common bug classes without formal analysis or synthesis dependencies.

Emerging edge AI workloads increasingly require arithmetic units that can trade computational accuracy for efficiency on demand. However, existing approximate arithmetic circuits are typically fixed-accuracy or rely on predefined structures for runtime configurability. This work introduces CircuitsDNA, an evolutionary framework that automatically evolves accuracy-configurable arithmetic circuits supporting multiple accuracy modes within a single circuit. It integrates three key features: 1) multi-threshold verifiability miter to enforce mode-specific accuracy requirements, 2) resource-limited verifiability-driven search to reduce verification overhead without sacrificing correctness, enabling efficient exploration of large circuit design, and 3) feedback-driven adaptive mutation to prioritize effective structural modifications and accelerate search convergence. Experimental results show that the 8-bit multiplier variants synthesized in 28-nm CMOS reduce the area-power product by up to 56% on INT8 DNN workload and 93% under exhaustive activity, compared with an exact 8-bit multiplier. Across CNNs and DeiTs, the accuracy loss relative to FP32 remains below 2% after fine-tuning under worst-case error (WCE) budgets of at most 1%. CircuitsDNA eliminates all search stalls observed in conventional methods across 8/12/16-bit multipliers, while adaptive mutation provides up to 1.33 times faster convergence than its non-adaptive counterpart.

MutMem V1 introduced retention-preserving, cryptographically authorized mutation for persistent agent memory but did not provide a complete portable verification contract or clean-install reproduction path. MutMem V2 closes that publication gap without introducing a second memory engine. It specifies exact canonical bytes, domain-separated object and bundle commitments, mandatory recall-evidence membership and ordering, external trust anchors, identity epochs, revocation, authorization, request receipts, ordered disclosure, and three mutation terminal types. The released protocol contains 18 versioned object schemas, 39 recall vectors, 15 mutation vectors, and 37 closed recall failure reasons. Independent Node and Python implementations agree on verdict and primary reason for all 72 structural and cryptographic terminals; a production-conformance corpus agrees on 42/42 cases across 28 required classes. A clean Node v26.8.1 installation reaches first-boot, restart, and scheduler readiness with no experimental memories. A separately scoped 120-unit Canary experiment supports only explicit-marker traversal. Every public table regenerates from a self-hashed aggregate, and an independent verifier reconstructs the statistics and claim boundaries. Historical V1 empirical results remain historical. MutMem V2 supports claims about portable integrity, authorization, traceability, conformance, and reproducibility under stated assumptions; it does not establish semantic truth, universal robustness, or independent replication.

LLM agents increasingly modify their own prompts, tools, middleware, resources, and execution harnesses at runtime. Such self-evolution can improve capability, but a successful mutation may leave persistent effects that cannot be safely reversed in states different from the one in which it was created. We introduce EvoUndo, a framework for representing, synthesizing, diagnosing, and independently verifying recoverability of model-generated self-modifications across counterfactual states. Across 600 unseen one-shot self-evolution tasks, we identify 197 capability-improving mutations that fail recoverability verification. Under the original recovery representation, conventional repair strategies recover 0/197 of these natural failures. Deterministic oracle analysis recovers 48/197 under the original recovery language L0, while the extended recovery calculus increases empirical oracle recovery to 191/197. A protocol-locked 2x2 grounding-by-expressivity intervention then separates two bottlenecks: exact state-address grounding increases successful recovery from 0/48 to 38/48 (79.2%) when the original language is sufficient, while extending the recovery language enables recovery on 142/143 (99.3%) failures in the oracle-defined S1 stratum. On the primary gpt-oss-120b backbone, adding exact-address diagnostics to the richer language reduces recovery to 133/143 (93.0%); a Qwen3.8-27B replication preserves the grounding and expressivity effects but not this negative interaction, indicating that the latter is model-dependent. These results indicate that reliable agent self-evolution requires co-designing verification, state grounding, witness semantics, and recovery-language expressivity rather than relying on iterative prompting alone.

Over the past decade, many test adequacy metrics have been proposed for deep learning that characterize test dataset adequacy from different perspectives, e.g., neuron activation behavior, latent feature coverage, decision-boundary exploration, etc. However, these metrics are typically released as independent research prototypes with substantially different installation and preprocessing requirements, execution workflows, and configuration mechanisms. These complications make them quite difficult to reproduce, compare, and adopt in research work and practical deployment alike. In this paper, we present the engineering details of ADEPT, a framework that integrates representative adequacy techniques, including neuron-coverage-based metrics, surprise adequacy, input distribution coverage, boundary coverage, and source- and model-level mutation score, under a consistent execution workflow. ADEPT provides a template-based metric interface with well-defined extension points for integrating new adequacy metrics. Furthermore, it provides YAML-based configuration management, preprocessing-cache reuse, and structured result reporting, making it easy to use in any research and development workflows. ADEPT is designed for researchers and practitioners who wish to reproduce and apply adequacy metrics without spending days or weeks implementing missing tooling or configuring disparate research prototypes. A demo video is available at https://aub.ie/ADEPT_video.

Successful mutation strategies in evolutionary code search may contain reusable knowledge that is useful beyond a single run, and in some cases may transfer across related tasks and domains. However, existing LLM-driven evolutionary frameworks largely discard such knowledge, repeatedly rediscovering similar ideas and limiting opportunities for cross-run and cross-task learning. We introduce EvoMem, a persistent memory architecture for LLM-based evolutionary program search that captures and reuses candidate mutation knowledge. EvoMem converts successful mutation events into structured, task-aware advice for future runs. It operates in two phases: after each run, it extracts and stores promising ideas with provenance, and during subsequent evolution, it retrieves a small set of relevant instructions based on the current task and program context to guide mutation. Across geometric optimization, multi-hop question answering, GPU kernel optimization, and related benchmarks, our experiments show positive average improvements in target metrics or search speed for most evaluated settings, while also revealing variability across tasks. Overall, EvoMem provides evidence that persistent memory can reduce some redundant exploration and improve the reuse and adaptation of successful strategies in LLM-driven evolutionary search.

Agent frameworks ship quality gates that compare text blocks by embedding-cosine similarity and decide at a fixed cutoff. Deduplication filters, semantic caches, drift guards, and answer grader gates deploy to answer the question: "Does this text still mean the same thing?" But the score answers a different question: "How much did the wording change?" We audit this gate class as a measurement instrument. In the cases these gates exist to catch, the two can run in opposite ways. Many times, reversing an instruction is a single word edit, while agreement often rephrases a sentence. The consequence is a safety check that fires backwards. The production drift guard we audited caught 0 of 56 meaning-breaking mutations, and one approved item, "withhold the study drug" -> "administer the study drug", came in at cosine 0.9608. We observed five shipped operating points, and balanced accuracy across 90 configuration-threshold-task cells never exceeded 0.700 (median 0.525). The same confounder also corrupted evaluations. A naively built corpus inherits this confounder and can return an inverted verdict, with a decision AUROC exactly 0.000 in 13 of 18 configuration-task cells (at most 0.040 in all 18) against 0.440-0.815 for the same nine configurations under a balanced 2x2 design. Twice in the effort it captured our own headline claims. Obvious repairs fail: an encoder swap and an overlap-conditioned gate (0.750 in-sample, 0.533 held-out) land at chance on separately authored held-out data, and an NLI drop-in did no better. Embeddings do still bear hope here, as the strongest two of nine configurations separated reversal from paraphrase at matched overlap (AUROC 0.79-0.90), but only a matched-pair audit reveals the deployment regime. We release the corpus method, harness, and frozen results, and contend that scores gated this way measure the wrong thing. We believe a valid instrument is buildable.

Multimodal embodied agents are increasingly required to solve long-horizon tasks by integrating visual observations, textual goals, and interaction history into closed-loop decision making. However, state-of-the-art large-model-based planners often rely on a single dominant planning style during execution. Once this execution mode becomes ineffective, the agent may remain stalled for many steps, repeatedly interacting with the environment without making meaningful progress. We address this limitation by proposing a Quality-Diversity (QD) framework for discovering diverse planning policies for multimodal embodied agents. The proposed method treats planning-policy templates as evolvable individuals and organizes them into a behavior-indexed archive rather than collapsing search to a single prompt style. In the offline stage, rollout trajectories are summarized into structured success and failure experiences, which guide policy variation through recombination and experience-guided mutation. The resulting policies are mapped into a behavior space defined by interaction intensity and goal-directedness, and the highest-quality policy in each niche is retained in the archive. In the online stage, the agent executes one policy at a time while monitoring task progress. When persistent stall is detected, the system rolls back to the latest checkpoint and switches to a behaviorally distinct archive policy to resume execution. Experiments on the ThreeDWorld transport benchmark show that the proposed framework improves both task success and interaction efficiency over representative baseline planners. These results suggest that discovering diverse policy repertoires is an effective way to support adaptive multimodal planning and online failure recovery.

Permutation optimization arises whenever the components of a system are fixed but their ordering affects performance. We introduce PRISM, a predictive protocol for permutation optimization that measures a fitness landscape before selecting a search strategy. PRISM uses inexpensive landscape diagnostics, including one-step move autocorrelation and fitness-distance correlation, to predict useful mutation operators, identify when structured search is likely to outperform random sampling, and detect regimes in which search provides little advantage. Across synthetic permutation landscapes, neural architecture benchmarks, scientific machine learning pipelines, and large-language-model instruction ordering, the protocol makes testable predictions about search behavior before optimization begins. Exhaustive instruction-ordering experiments reveal substantial performance variation induced solely by permutation, while cross-model experiments show that useful ordering structure can transfer across model families and task difficulty. Additional experiments demonstrate that instruction ordering remains consequential after prompt wording is optimized, indicating that content optimization and ordering optimization are complementary. The results position PRISM not as a universally superior optimizer, but as a framework for determining when permutation search is useful, which representation and operator should be used, and when simpler alternatives are preferable.

Distributed parallel Artificial Intelligence (AI) programs expose reliability gaps that conventional testing cannot close: parallel executions are non-deterministic, and AI workloads bring high-dimensional inputs and non-linear operations that defeat fuzzing and symbolic execution in isolation. We present Directed Neuro-Symbolic Stochastic Execution (DNSSE), a hybrid testing framework that couples schedule prediction guided by a Large Language Model (LLM) with symbolic constraint solving and coverage-guided stochastic mutation. We model distributed AI executions as non-deterministic transition systems, specify correctness in linear temporal logic, and prove soundness, bounded completeness, and probabilistic completeness of the hybrid solver, together with an expected-cost analysis of LLM-guided schedule exploration. A scalable implementation on PyTorch and Ray detects 2.9% more concurrency bugs than the strongest baseline and raises average branch coverage from 68.6 % to 91.6 % across five realistic distributed AI benchmarks.

Self-improving coding agents that iteratively rewrite their own source code have demonstrated impressive performance on coding tasks. However, existing solutions generally derive self-modification from a single failure trajectory at a time, overlooking rich comparative signals available in the agent's expanding archive of past attempts. According to Mendelian principles of controlled inheritance, we introduce Mendel Gödel Machine (MGM). In addition to the general single-trajectory clonal mutation, MGM includes two new types of self-modification that better utilizes evidences accumulated: the reaction-norm mutation edits an agent based on its trajectories on multiple tasks simultaneously, and the cross-lineage hybridization edits an agent using the trajectory of a reference agent from another lineage on the same task. Under an additive fitness landscape model, we prove theoretically and demonstrate via controlled surrogate simulation that the new strategies facilitate a faster and better convergence over single-trajectory baselines. Experiments on SWE-bench and Polyglot confirm MGM's consistent improvement in performance, efficiency, and generalizability.

Persistent agent memory must adapt as later outcomes change earlier evidence, yet mutable retrieval weights create an attribution problem: reviewers must distinguish authorized adaptation from database tampering. We present MutMem, an authorized-mutation protocol in HOM-AIMOS, a persistent agent-memory engine. MutMem retains memory content, records signed positive and negative outcome evidence without age-based expiry, and commits each nontrivial weight change as a housekeeper-authorized transition. Each transition binds a terminal provenance node, signer epoch, quantized old and new weights, a no-fork predecessor, and two domain-separated SHA-256 commitments. Ed25519 verification runs in both the database writer and a portable verifier. Content classified as poison-likely is retained with signed, revisable labels used by recall as trust evidence. We evaluate utility, mutation integrity, and poisoning adaptation. HOM-AIMOS answers 459/500 LongMemEval questions correctly under LLM judgment (91.8%). On LoCoMo, it obtains 74.12% judged accuracy and, under a separate upstream-compatible protocol, 58.20 token F1. A native suite passes all declared authorization, topology, tamper, signer-epoch, and post-mutation-recall cases; median signed-transition latency is 4.865 ms. In a declared N=100 PoisonedRAG adaptation, no injected poison appears in attacked top-5 disclosures (0/100; 95% Wilson upper bound 3.70%), while induced target-answer attack success among 98 clean-negative targets is 1/98 (1.02%). A preregistered four-arm ablation attributes the retrieval reduction to signed stored labels: the retriever selects poison for 94/100 targets when epistemic policy is bypassed and 0/100 when labels are restored. MutMem provides evidence of integrity, authorization, traceability, and historical continuity; it does not establish content truth.

LLM agents increasingly run policy-bound enterprise workflows such as document auditing, where they must apply rules consistently, ground every value, and stay auditable. Improving these agents is hard: operational feedback is sparse and unlabeled, edits to one rule can regress unrelated cases, and accuracy must improve without inflating inference cost or losing auditability. We present FRAMES, a closed-loop framework that cold-starts deployable skills from existing assets and then evolves them through consensus-based mutation, Pareto selection over accuracy and cost, and an anti-regression guarantee, all while preserving auditability. Deployed on our internal production system, FRAMES attains the best accuracy-cost trade-off among baselines, with the same gains reproduced on tau-bench.

Large language models (LLMs) enable neural architecture search (NAS) directly over executable neural network programs. However, code-level flexibility does not provide the architecture state needed for effective mutation: LLMs must infer tensor dependencies, editable components, and compatibility constraints from implementation details. To address this representation mismatch, we propose GraphIR, an architecture-aware intermediate representation that supplements executable programs with a mutation-aligned candidate state. GraphIR organizes each candidate through three complementary views: a computation skeleton describing tensor flow, a mutation surface exposing editable modules and operations, and a validity envelope capturing interface contracts, propagated shapes, and downstream dependencies. To evaluate our method, we construct NAS-Dependency, a 120-question benchmark covering six complementary dependency-reasoning dimensions. The diagnostic shows that GraphIR is particularly effective at identifying exact producer occurrences, tracing dependency propagation, and diagnosing interface and failure risks. Across six downstream benchmarks including CLRS, GraphIR achieves the best overall search performance while maintaining comparable model size and favorable end-to-end NAS efficiency when integrated into OpenEvolve. These results show that a mutation-oriented architecture state provides an effective interface between executable neural programs and LLM-guided architecture evolution.

Diffusion large language models (dLLMs) have emerged as a promising alternative to autoregressive LLMs, offering efficient generation through block-wise progressive unmasking. However, their strong general-purpose performance does not necessarily translate into reliable mathematical reasoning, where correctness depends on preserving coherent numerical-symbolic reasoning trajectories. In this work, we analyze the decoding trajectories of LLaDA 2.0 and identify a recurring diffusion confidence trap: local token confidence can become misaligned with global reasoning correctness during progressive block decoding. Our analysis reveals two representative failure regimes: sampling-sensitive failures, where correct paths exist but are unstable, and sampling-consistent failures, where repeated sampling converges to repetitive high-confidence but incorrect continuations. Motivated by this observation, we propose Evolutionary Decoding, a training-free test-time scaling framework that views diffusion decoding as an evolutionary process over candidate reasoning states. The framework combines step-wise selection, which preserves useful numerical-symbolic signals and suppresses repetitive patterns, with block-wise mutation, which introduces structured alternatives to escape incorrect high-confidence basins. Experiments on multiple benchmarks show that Evolutionary Decoding improves LLaDA 2.0 over confidence-based decoding, leading to more reliable mathematical reasoning.

Recent advances in large language models (LLMs) have driven growing interest in using LLMs to automate test generation. Prior work commonly evaluates generated test suites using proxy metrics such as code coverage and mutation score. However, studies by Inozemtseva et al. and Papadakis et al. show that, for human-written tests, correlations among coverage, mutation, and real-bug detection can largely vanish once test suite size is controlled, raising concerns about the validity of evaluations based on proxy metrics. It also remains unclear whether these conclusions carry over to LLM-generated tests, given that prevailing LLM-based test-generation workflows differ substantially from traditional approaches. In this paper, we conduct a large-scale replication study of these two prior works using a wide range of test suites generated by a diverse set of LLMs, and re-examine the relationships among coverage, mutation, and real-bug detection effectiveness. Our findings diverge substantially from prior results. We show that the usefulness of coverage and mutation is highly context-dependent: in regression-style settings where the code provided to the LLM can be reasonably assumed bug-free, these metrics can provide meaningful signals when comparing across models; in another common scenario where the code-under-test may already be buggy and the goal is to expose the bug within the code-under-test, they no longer serve as reliable indicators. We also find little evidence that test suite size is a dominant confounder for correlations among coverage, mutation, and real-bug detection for LLM-generated tests. Based on these findings, we discuss how to interpret results from prior studies and provide actionable guidance for evaluating LLM-based test generation.

The function of many genes is still unknown, and conventional driver-discovery methods, which rely on how frequently a gene is mutated, cannot assess genes that are only rarely affected. Here we pair Evo2-based genome analysis with routine clinical imaging to identify gene--phenotype associations at genome-wide scale. For every somatic mutation across three TCGA cohorts (cRCC=clear cell renal cell carcinoma, HCC=hepatocellular carcinoma, and BC=breast cancer; $n = 340$ total), Evo2 predicts a severity score, with no task-specific training. Per-gene severity summaries are then correlated with radiomic features extracted from paired tumor segmentations, controlling for total mutation burden. In TCGA-cRCC ($n = 162$), this sweep recovers established renal-cancer drivers and identifies 46 additional genes reaching false discovery rate (FDR) significance absent from curated cancer-gene panels, several of which are Mendelian ciliopathy and cytoskeletal-disease genes. These results demonstrate that pairing a genomic language model with widely available clinical imaging can serve as a hypothesis-free discovery tool for gene--imaging associations invisible to conventional approaches.

Neural simulation-based inference enables parameter estimation for complex models, but typically requires the user to specify a simulator encoding a fixed model structure. We present a framework for joint model selection and parameter estimation that combines large language models for program synthesis with neural simulation-based inference. Given a natural language description of the system and data under investigation, an LLM proposes candidate simulator programs which are iteratively refined via feedback-driven mutation and evaluated using neural density estimation. The approach enables simulation-based inference over a pool of models, not just parameters within a fixed model. On benchmarks spanning deterministic dynamics, stochastic epidemic models, and dark matter substructure inference from gravitational-lensing images, the method identifies plausible model families from open-ended prompts, with accuracy that reflects the information content of the data and identifiability of candidate models.

Large language models now translate natural-language descriptions of decision problems into solver-ready optimization models, but they fail silently. A generated model often runs and still formulates the wrong problem. This paper develops a theory of falsification-based verification for this setting. Every numeric quantity in the description is a typed slot, and a candidate model is tested only through solver calls on slot-transformed instances; no reference model or label is consulted. From duality, comparative statics, and polyhedral limit arguments we derive a battery of test classes covering directions, curvature, crush probes, prohibitive limits, annihilation, and exchange. Every test is sound, so a violation certifies unfaithfulness and the false-positive rate is zero by design. We characterize what such verification can never see, give conditions under which the canonical error classes are detected with certainty, and prove that no fixed-threshold perturbation tester is simultaneously sound and nontrivial. Experiments on 326 ground-truth models from NL4OPT and four benchmark families confirm the theory. The battery attains a 0.0% false-positive rate against 54.9% for a threshold tester, detects 70.0% of certified conditional-class mutants, convicts 40.4% of the mutants invisible to execution-accuracy scoring, and reproduces the predicted detectability pattern including its zeros.

Exhaustive site-by-site interventions on a neural network's computational graph -- activation-patching sweeps, circuit-discovery searches, systematic ablation studies -- mutate the graph at every candidate site, and their cost is dominated by recomputation after each mutation. On a reactive graph engine whose invalidation provably touches exactly the downstream cone of a mutated node, we give a complete cost accounting for such workloads. First, the aggregate speedup of an exhaustive sweep over independent full recomputations is not a universal constant: if per-layer weight varies regularly with depth at Karamata index q, the ratio converges to (q+2)/(q+1) when weight concentrates near the output and to q+2 near the input, recovering 2 only in the depth-uniform case; a wall-clock corollary predicts a ceiling of about 1.79, below 2, until interpreter overhead is compiled away. Second, we prove the exact cost of a sequence of persistent mutations, never undone between insertions: the interleaved cost exceeds the isolated sum by an exact overcount summed over comparable site pairs, with closed-form extremes over insertion orders, while batched application is order-independent and sub-additive, costing exactly the union of the sites' cones plus the fresh nodes. Third, we prove the exact mirror of forward locality for the backward pass, showing it collapses the aggregate speedup to 1 under backpropagation on architectures without long skip connections. Every identity is validated on NeuroDSL, a reactive graph engine in Julia: measured sweep ratios converge to the predicted limits under four cost profiles; the training-mode ratio collapses to 1 at the predicted rate; and all 18 per-graft sequential costs and the batched total match the closed forms at zero tolerance across three insertion orders.

Large language models (LLMs) excel at pattern recognition and text generation, but their capacity for abductive inference - inferring latent hypotheses that explain observed behavior - remains poorly understood. Here, we introduce Elenchos (named after the Socratic method of cross-examination), a generative evaluation framework that measures abductive reasoning as a structural inverse problem. Given a reference formal system, such as the lambda-calculus, and a potentially mutated counterpart, agents must determine whether a mutation has occurred and infer the rule modifications responsible for the resulting behavioral differences. Evaluating frontier and mid-tier LLMs reveals a consistent detection-attribution dissociation: models often recognize that a system has been altered but struggle to identify the latent mutations causing the observed discrepancies. Performance degrades substantially under interacting mutations, where models frequently recover only a subset of the underlying mutations. Preliminary evidence also suggests diminishing returns from increased inference-time reasoning, with only modest improvements under larger reasoning budgets, though this finding requires further validation.

While traditional evolutionary algorithms hard-code reproduction, self-replication can emerge spontaneously within digital ``primordial soups''. This paper investigates the coevolution of such emergent self-replication alongside problem-solving capabilities. We initialize a population of random 32-byte Z80 assembly programs, requiring self-replication to arise purely through random assembly-level mutations and pairwise program interactions. To couple computation with reproduction, we introduce a task-based validation step: correctly evaluating a polynomial raises a program's interaction probability above a baseline rate. Our experiments yield four primary findings. First, self-replication and mathematical problem-solving successfully coevolve from initial randomness. Second, the pressure to compute accelerates the emergence of compact, robust reproductive architectures that preserve memory for task execution. Third, applying metabolic constraints that penalize runtime promotes the emergence of sophisticated conditional execution patterns that reduce energy use. Finally, partitioning programs into interconnected task niches generates an emergent learning curriculum that utilizes simple solutions as stepping stones toward more complex tasks. Altogether, these results demonstrate an interactive feedback loop: environmental task demands actively shape the physical architecture of self-replication, while spontaneous replication alters the evolutionary trajectory of functional problem-solving.

This study presents a multi-fidelity framework for the systematic optimization of genetic algorithm (GA) hyperparameters. The framework integrates three fidelity levels: high-fidelity Fast Fourier Transform (FFT) homogenization for validation, a medium-fidelity 3D convolutional neural network surrogate for rapid property evaluation, and a low-fidelity Gaussian process (GP) surrogate within a Bayesian optimization (BO) framework to guide the hyperparameter search. Various acquisition functions are evaluated, with logNEI achieving the best performance by effectively accounting for the noise inherent in GA evaluations. The proposed framework identifies hyperparameter configurations that enable a 25-generation GA run to achieve elastic modulus values comparable to those obtained in a full 75-generation optimization. Furthermore, introducing a penalized BO objective significantly reduces the number of required lattices with only minor decreases in absolute achieved elastic modulus, revealing a practical trade-off between performance and the number of structures that must be evaluated. High-fidelity FFT validation verifies the effectiveness of the surrogate-driven optimization strategy. The optimized hyperparameters allow for rapid convergence, eliminate the need for lattice mutation, and reduce the overall computational cost by 24% (from 225 to 171 hours) while preserving mechanical performance. These results demonstrate the potential of multi-fidelity optimization as an efficient and practical approach for GA hyperparameter tuning and future experimental lattice design studies.

Modern processor verification struggles to reach deep architectural states due to the inefficiencies of traditional mutation-based fuzzing. We propose HiFuzz, a novel hierarchical reinforcement learning framework that replaces mutation with a structured, two-layer generation process: a Program Agent for global layout and a Basic Block Agent for precise instruction filling. To overcome reward sparsity, HiFuzz integrates an adaptive coverage reward mechanism and a semantic-aware basic block encoder providing intrinsic feedback. Extensive evaluations on three real-world RISC-V cores demonstrate that HiFuzz significantly outperforms state-of-the-art fuzzers in coverage and bug detection.

LLM agents are increasingly applied to vulnerability analysis, but existing benchmarks have not kept pace. They typically rely on small non-compilable snippets, focus on binary classification (vulnerable or not), and do not account for the risk that publicly-released datasets are part of model training corpora. We introduce RustMizan, a benchmarking framework for Rust vulnerability analysis that addresses these gaps. RustMizan contains compilable code variants at the crate, file, and function levels, with annotations for binary vulnerability detection, CWE classification, and function- and line-level localization. A paired mutation framework produces semantics-preserving code mutants for contamination testing and robustness probing. Across four frontier models in an agentic setup with command-line access, binary classification sits in the 56-65% range, but line localization F1 stays near 20%, and adversarial cues drop line F1 by about 27%.

Before fixing an issue, it is useful to first reproduce it by generating a bug reproduction test (BRT). However, generating a BRT is itself a challenging task, because issue descriptions tend to be informal, making it difficult to determine whether a candidate BRT indeed fails for the reason in the issue. Prior work has attempted to tackle this problem via inference scaling, using large language models to generate many BRTs and patches, then using execution feedback to select and improve them. Unfortunately, this is expensive and the feedback is unreliable. This paper explores evolutionary programming for BRT generation to sharpen the feedback, while enhancing evolutionary programming to keep costs in check. Our new approach, EvoOtter, controls test execution costs via successive halving. Furthermore, it controls LLM costs via batched crossover for an entire generation in a single LLM call, as well as via rule-based code mutations, with a new fitness score tailored for BRTs. As a result, EvoOtter generates state-of-the-art quality BRTs at the fraction of the cost of prior inference-scaling approaches to this problem. More broadly, this paper points at how to efficiently and effectively combine evolutionary programming with large language models for software engineering.

The ''Computational Life'' paper (Agüera y Arcas et al., 2024) argues that paired interactions in a computational soup are an effective way to find self-replicators. In this work, aided by recent developments in self-replicator detection, we explore the alternate hypothesis that self-replicators can be found at least as easily using simple mutation random walks in program space. We also explore the claim that capping the maximum ''depth'' and ''width'' of the ancestry tree stops self-replicators from emerging, showing instead that it merely stops self-replicators from taking over the soup.

Quantum computers could outperform classical machines on important problems, but only if the errors that pervade quantum hardware can be corrected at scale. Quantum low-density parity-check (qLDPC) codes offer a promising route to this goal by combining sparse parity checks with finite encoding rate and growing distance, but their construction remains a challenging discrete design problem. Here we introduce structured concept evolution (SCE), a search framework that pairs a large language model with a structured algebraic mutation grammar to discover lifted-product code families, a class of CSS qLDPC codes. Instead of asking the LLM to design codes from first principles, SCE evolves structured concepts consisting of algebraic specifications paired with executable programs that realize them, using hierarchical mutations that modify the group algebra, protograph geometry, or base space. Running SCE, we discover a diverse set of competitive code families, ranging from abelian constructions to families over non-abelian groups beyond those underlying standard designs such as bivariate-bicycle codes, and characterize them under code-capacity depolarizing noise with BP+OSD decoding. These results are obtained with lightweight models (GPT-5.4-mini and GPT-5.4-nano).

Therapeutic peptides occupy a valuable design space between small molecules and biologics, but their development requires satisfying several competing constraints at once: solubility, hemolytic activity, and nonspecific surface fouling are governed by overlapping sequence features, so improving one property often degrades another. Computational design addresses this by pairing generative models with sequence-based property predictors, iteratively proposing and refining candidates. However, these components are typically wired together as monolithic scripts that are difficult to inspect, extend, or reuse, and they often refine sequences by natural-language reasoning rather than by tracking the evolving multi-property state of each candidate. We present Pepti-Agent, a closed-loop, peptide-specific framework that exposes generation, property prediction, and single-residue mutation as independently inspectable Model Context Protocol (MCP) tools. A large language model controller invokes these tools and consults live predictor output between calls, so refinement is guided by each sequence's current property profile rather than by language reasoning alone. Task-specific PeptideGPT models generate candidates, ProtBERT-based classifiers score solubility, hemolysis, and non-fouling, and two interchangeable mutation operators propose sequence edits. By recording a per-step trace of controller decisions, predictor outputs, and accepted mutations, Pepti-Agent offers a reproducible substrate for benchmarking multi-objective design strategies and for prioritizing candidates for experimental validation.

We study the $(μ+1)$ EA on the Binary Value function BinVal. We show that it needs at most $O(μ\log μ\cdot n \log n)$ function evaluations to find the optimum when $μ= o(n/\log n)$. This substantially improves upon the recent upper bound of $O(μ^5 n \log(n/μ^4))$ by Krejca, Neumann and Witt. Our results hold for several mutation operators including standard bit mutation. In particular, our bound implies that the $(μ+1)$ EA is at most a factor $O(\log μ\cdot \log n)$ slower on BinVal than on OneMax.

Large Language Models are highly sensitive to prompt formulation, necessitating automatic prompt optimization to unlock their full potential. While evolutionary algorithms have emerged as the dominant paradigm, they suffer from a critical bottleneck: data efficiency. Current methods treat the development dataset as a static benchmark, wasting significant compute budget on uninformative data. In this work, we introduce APEX (Automatic Prompt Engineering eXpert), a novel framework that optimizes the data usage alongside the prompt search. APEX dynamically stratifies the dataset into Easy, Hard, and Mixed tiers based on the optimization lineage. By prioritizing the Mixed tier, which identifies the data where the LLM has mixed performance, we identify two high-leverage subsets: the addressable frontier for generating informative mutations and the rank-sensitive frontier for distinguishing candidate quality. We evaluate APEX across three diverse benchmarks: IFBench, SimpleQA Verified, and FACTS Grounding. Under a fixed budget of 5,000 evaluation calls, due to its data efficiency, APEX outperforms the initial prompt by an average of 11.2% on Gemini 2.5 Flash and 6.8% on Gemma 3 27B, demonstrating that a data-centric approach is key to efficient and effective prompt optimization.

Multimodal $ΔΔG$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations. Existing approaches address these limitations primarily through additional architectural components, leaving optimization-level intervention comparatively underexplored. We introduce a constraint-aware optimization framework combining Balanced Mean Squared Error, a Siamese anti-symmetric regularizer, and a novel OOD-margin consistency loss on the per-position feature representation, requiring no architectural changes to the SPURS backbone. Across eleven benchmarks and three random seeds, the framework improves Spearman correlation on S669 from 0.486 to 0.540 ($σ=0.002$ across seeds), matching the published SPURS baseline (0.50) without architectural modification, and on S461 from 0.653 to 0.711, with consistent smaller gains on five additional OOD datasets. A controlled diagnostic on Ssym reveals that anti-symmetric training does not eliminate systematic forward-reverse bias, indicating that gains arise through implicit regularization rather than exact thermodynamic constraint enforcement.

As large language model (LLM) agents are integrated into autonomous cloud operations, distributed systems face a semantic reliability problem: proposer agents can generate production mutations, such as modifying IAM policies, opening firewall security groups, or executing data exports, that are syntactically valid and statically authorized but operationally unsafe. Classical distributed consensus protocols replicate deterministic state transitions but do not evaluate the safety of the proposed intent. To address this gap, we introduce Semantic Quorum Assurance (SQA), a control-plane primitive for governing non-deterministic agentic infrastructure. SQA represents proposals as declarative execution contracts bound to cryptographic evidence chains and routes them to a diverse panel of read-only, sandboxed validator agents. SQA aggregates their judgments under a risk-adaptive quorum predicate that enforces model and archetype diversity, adjusts weights based on calibrated assurance scores, and respects archetype-specific vetoes. Admitted proposals execute only through a sovereign execution gate. We instantiate SQA in a cloud-native control plane and formalize a correlated cognitive failure model for non-deterministic validators. On 500 infrastructure-inspired mutation scenarios, with safety results reported on held-out safe/unsafe trials excluding ambiguous scenarios, SQA reduces unsafe approval from 18.5% for single-agent validation to 0.3% while adding median validation latency of 1.45--4.12 seconds across the studied risk buckets.

As the Model Context Protocol (MCP) standardizes tool-calling for autonomous agents, it introduces a critical, unexamined attack surface: the error-handling loop. We hypothesize that tool error messages possess implicit authority, triggering corrective reasoning modes that bypass standard safety heuristics. We introduce VATS (Vulnerability Analysis of Tool Streams), a mutation-driven framework that systematically evolves adversarial payloads across seven structural and linguistic dimensions. Our evaluation across four frontier models, Gemini 3.1 Pro, GPT-5.5, GLM-5.1, and Qwen3-Coder, demonstrates that error-path injection triples the success rate of standard indirect prompt injection (IPI), achieving up to 100% compliance in controlled evaluations. We isolate structural positioning (sandwiching instructions within error context) as the most effective exploit vector across all tested models. While we find that production framework guardrails can mitigate these vulnerabilities, the inherent susceptibility of the model layer poses a systemic risk to bespoke agentic workflows.

When an LLM repeatedly mutates a program, does it explore new forms or circle back to the same ones? We study this question by analyzing LLM-driven mutation chains in the absence of selection pressure within a domain-specific language, varying prompt design, model family, and stochastic replication. We find that LLM-based mutation consistently converges toward restricted attractor regions in program space. Convergence is especially severe at the structural level: in 87% of chains, over 93% of mutations revisit a previously seen structural form, with most variation confined to terminal substitutions within recurring templates. Cycle analysis reveals short cycles and self-loops dominating the transition structure. The rate of convergence varies with prompt wording and model choice, but the phenomenon is robust across conditions. A classical GP subtree mutation operator does not exhibit comparable convergence, suggesting that the effect is intrinsic to the LLM mutation pipeline. These findings reveal a tension at the heart of LLM-driven program evolution: the same capabilities that enable semantics-aware program transformation also carry a systematic bias toward structural homogeneity that must be accounted for if such systems are to sustain open-ended exploration. Source code is available at https://github.com/can-gurkan/lmca.

Deep Neural Networks (DNNs) are increasingly being deployed in security-critical and safety-sensitive applications, which makes rigorous testing essential to identify and mitigate model weaknesses. Existing DNN testing approaches explore either the input space or a learned latent space. While latent-space generation can better maintain plausibility than direct input-space mutation, current methods still face a trade-off among exploration controllability, failure diversity, and seed-relative semantic drift. To overcome these limitations, we propose Latte, a black-box testing framework that generates semantically proximate, diverse, and fault-revealing test cases by leveraging the latent space. Specifically, Latte encodes each input seed with a pre-trained VQ-VAE and performs a seed-centered, one-step latent mutation along directions defined by anchors sampled from alternative classes, followed by quantization and decoding back to the input space. This explores local neighborhoods around each seed within the learned latent manifold, resulting in a larger number and broader diversity of oracle-triggering prediction discrepancies under the same budget. We evaluated Latte on 5 datasets and 10 DNN models in single-model and multi-model testing scenarios. Across the evaluated datasets and models, Latte improves fault exposure and behavioral diversity under matched testing budgets. Under the single-model setting, it also maintains low seed-relative semantic drift with respect to the source seeds.

Protein sequence optimization under tight oracle budgets requires methods that explore vast combinatorial spaces while making each evaluation informative. Existing reinforcement learning and off-policy generative approaches often degrade under surrogate noise, and position-agnostic mutation proposals risk disrupting functionally critical residues. We introduce SILO, a trajectory-level self-improvement imitation framework for oracle-budgeted protein design. SILO uses a hierarchical edit policy that decomposes each mutation into a position choice followed by a residue choice. In each active-learning round, the policy samples candidate trajectories via incremental stochastic beam search without replacement (SBS), and a UCB-based proxy ensemble, combined with an alanine-scan fitness score (AFS), selects candidates with functionally relevant edits for in silico oracle evaluation. The policy is then updated by next-action cross-entropy imitation on the round's best oracle-labeled trajectories, avoiding value-function estimation. Across eight reproduced protein fitness landscapes and five strong baselines from prior work, SILO achieves the highest maximum and top-100 mean fitness on 8 of 8 landscapes within our evaluations, often exhibiting faster early-stage improvement. In low-data and noisy-proxy stress tests on two landscapes per setting, SILO remains competitive or best when several baselines degrade. Ablations show that SBS with AFS account for much of the gains, with iterative imitation providing additional improvement. Code is available at: https://github.com/grimmlab/SILO.git

Evaluating software engineering capabilities has become a core component of modern large language models (LLMs); however, the key bottleneck hindering further scaling lies not in the scarcity of high-quality solutions, but in the lack of high-quality test suites. Test suites are indispensable both for synthesizing program repair trajectories and for providing precise feedback signals in reinforcement learning. Unfortunately, due to the high cost and difficulty of annotation, high-quality test suites have long been hard to obtain, while those automatically generated by LLMs tend to be superficial and lack sufficient discriminative power. As a first step toward constructing high-quality test suites, we introduce SWE-Mutation, a benchmark for evaluating LLM-generated test suites. The benchmark characterizes test suites by introducing systematically mutated solutions that attempt to ``fool'' the test suites and pass validation. We further propose an agentic, language-agnostic framework for automatically generating complex mutants. Our benchmark consists of 2,636 mutated variants derived from 800 original instances and includes a multilingual subset spanning nine programming languages. Experiments on seven LLMs reveal that even DeepSeek-V3.1 achieves only 10.20% verification and 36.15% detection rates, highlighting the inadequacy of current LLMs. Additionally, our agentic mutation strategy enhances realism, reducing average detection rates from 71.04% to 39.81% compared to conventional methods. These findings expose persistent deficiencies in the ability of current LLMs to generate reliable and discriminative test suites.

A recent trend is to leverage machine learning models to improve the evolutionary design and optimization process. We propose a novel transformer-based mutation operator for Cartesian genetic programming (CGP) for the automated design of approximate arithmetic circuits. We introduce a hybrid scheme for CGP in which the proposed mutation operator is switched with the standard mutation operator to prevent stagnation of the circuit approximation process. We also develop a new training scheme for the underlying transformer that utilizes training vectors composed of thousands of CGP chromosomes representing various approximate multipliers. For several target error constraints, the approximate multipliers evolved with CGP utilizing the transformer-based mutation achieve better trade-offs than the highly optimized designs available in the state-of-the-art EvoApproxLib library of approximate circuits. Although both training and evolutionary processes are computationally demanding, they appear to be necessary steps for improving existing approximate circuits and producing new, potentially patentable circuit designs.

Current neural architecture search (NAS) methods are often limited by their predefined, restrictive search spaces. While recent large language model (LLM)-assisted NAS methods enable open-ended search spaces, they often suffer from inefficient exploration due to biased or low-quality design ideas. To address these issues, we propose to semi-automatically structure model design knowledge to guide the search process. Our approach first defines a high-level structural template of architectural attributes. An LLM then populates this template by analyzing papers, creating a rich and diverse search space that embodies this structured design knowledge. To efficiently explore this vast space, we introduce FairNAD, using a multi-type mutation that enables broad exploration through mutation with fair idea sampling, Pareto-aware mutation, LLM-driven iterative mutation, and a fine-grained feedback loop. We demonstrate the effectiveness of FairNAD in discovering high-performing architectures that yield 0.84, 2.17, and 2.35 points improvement on CIFAR-10, CIFAR-100, and ImageNet16-120, respectively, compared to current state-of-the-art methods.

Multi-party multi-objective optimization problems (MPMOPs) require consensus among autonomous decision makers and therefore differ from flattened many-objective formulations. Existing runtime theory for multi-objective evolutionary algorithms is largely tailored to single-party Pareto-front approximation and does not directly explain common-solution search in MPMOPs. We investigate cross-party recombination in two representative settings. On MP-JCG, a pseudo-Boolean benchmark with an explicit gap region, we prove that a payoff-guided mutation baseline faces a gap-crossing bottleneck requiring $Θ(n^2)$ expected fitness evaluations. In contrast, an analytical CPR-NSGA-II variant discovers both common Pareto-optimal solutions in $O(n\log n)$ expected evaluations by directly assembling complementary prefix and suffix templates distributed across party populations. Comparing this with the flattened four-objective formulation F-JCG, our full-front coverage analysis illustrates the additional coverage burden introduced by flattening. For BPBOMST, the bi-party, two-objective-per-party specialization of the multi-party multi-objective minimum spanning tree problem, we develop a layered support-cover analysis. For each common Pareto objective vector, the symmetric average projection induces an auxiliary bi-objective MST instance, and suitable support representatives yield a $2λ$-common approximation cover with $λ\in[1,2]$. We further derive an instance-parameterized expected runtime bound for a representative-pool CPR-NSGA-II variant using edge-union recombination and uniform repair. This bound separates the effects of local auxiliary-front filling, cross-party recombination shortcuts, and edge-union repair ambiguity.

Context. Metamorphic Testing addresses the test-oracle problem in scientific computing, but classical Mutation Score operates on syntactic AST mutations and misses domain semantics. Objective. We propose the Semantic Mutation Score (SMS), built on five domain-semantic operators (Conservation Erosion, Operator Substitution, Hyperparameter, Trajectory Flip, Structural Injection). SMS degenerates almost everywhere to MS in a characterised limit, so any SMS-based conclusion remains consistent with prior mutation-testing literature in the classical regime. Method. A 12-PUT x 5-MP design over four single-output float-to-float classes (numeric, probabilistic, surrogate, machine-learning) is paired with a three-layer attribution classifier separating true semantic faults from tolerance, OOD, statistical, and artefact categories. A same-source / cross-source ablation under an identical prompt isolates the LLM-source-diversity contribution. LLM-generated mutants are compared against a default-configuration cosmic-ray syntactic pool at the AST-normalised level. Results. The pre-registered large-effect threshold for Cliff's delta is not met under the point-estimate criterion; the observed effect lies in the medium-effect range. Cross-source pooling under an identical prompt does not appreciably shift delta, indicating that LLM identity is not the lever within this design. AST-level overlap between LLM-generated and default cosmic-ray syntactic mutants is small; the Hyperparameter, Structural Injection, and Trajectory Flip classes are unreachable under default first-order syntactic configurations. Conclusion. SMS is a backward-compatible adequacy metric for domain-semantic metamorphic-relation sets in scientific computing. The first-order unreachability evidence is independent of the effect-size question.

LLM-guided evolutionary methods such as AlphaEvolve have proven effective in domains like math, systems research, and algorithmic discovery, but their reliance on frontier models makes each run expensive. We argue this is largely an artifact of how existing frameworks allocate search: archives that fail to preserve solution diversity force compensation through stronger mutation models; blind model use spends frontier dollars on local edits a smaller model could handle; and full-set evaluation wastes rollouts on redundant examples. We introduce LEVI, a harness-first evolutionary framework built on the bet that stronger search architectures can substitute for or even outperform larger LLMs in evolutionary search. LEVI improves on three core components of evolutionary search: a solution database that establishes diversity from the beginning, and then maintains it throughout the run; a smarter mutation router that plays into the strengths of large and small LLMs; and a rank-preserving proxy benchmark for rollout-heavy settings. Across systems-research benchmarks LEVI attains the highest score on a budget 3.3-6.7x smaller than the published frontier-model runs of existing frameworks like ShinkaEvolve, GEPA, and AdaEvolve; on one problem, LEVI matches the existing best at a 35x lower cost. On prompt optimization, LEVI matches or exceeds GEPA at less than half of its rollout budget on four different benchmarks. LEVI is available as an open-source framework at https://github.com/ttanv/levi.

We extend RDEx-CSOP with 3 changes that target stagnation & late-stage variance, plus minor parameter tuning. The second scale factor in the standard branch is sampled independently from a truncated Cauchy. A small feasible-only JADE-style archive (|A|_max = 50) is added & sampled with probability |A|/(|A|+|P|). Per-individual stagnation counter triggers, after 180 no-improvement generations, three local overrides on standard branch: pull toward the global best, lift the archive sampling floor to 0.65, & saturate CR to 0.95 when population success rate is below 0.10. The exploitation biased branch & every other RDEx component are left untouched. On CEC CSOP suite (D=30, 25 runs), RDEx-CASK is competitive with RDEx, UDE-III, & CL-SRDE in feasibility-aware quality & improves time-to-target on most problems.

We present ARES-LSHADE, a memetic differential-evolution variant submitted to the GECCO 2026 competition on LLM-designed evolutionary algorithms for the Generalized Numerical Benchmark Generator (GNBG). The algorithm builds on the LLM-LSHADE 2025 winner, contributing two new components: (a) a scout-augmented mutation operator with adaptive CMA-ES integration, produced by an autonomous research loop across approximately thirty LLM-driven design experiments, and (b) a multi-start L-BFGS-B polish phase that respects strict blackbox treatment of the benchmark. On the official 31-run-per-function evaluation with the competition-specified function-evaluation budgets, ARES-LSHADE obtains 510 of 744 wins (per-function gap below 1e-8), reaching machine precision on 18 of 24 functions. The remaining six functions exhibit characteristic plateau signatures consistent with GNBG's compositional structure, and were independently identified by the autoresearch loop as the hardest of the suite. Beyond the result itself, this report documents two methodological observations: (i) an LLM-driven research loop with operator-only edit surface and fitness-only observation space converges to a characteristic plateau on this benchmark; (ii) when we initially widened the observation space to include the benchmark's compositional metadata, the resulting algorithm trivially solved all 24 functions but violated the competition's blackbox rule, which we identified before submission. We discuss this tension between LLM capability and benchmark integrity as a design consideration for future LLM-driven optimization-algorithm research. Code and reproducibility artifacts are available at https://github.com/anaeem1/ARES-LSHADE.

Protein sequence data from nature exhibits survivorship bias: we only observe data from those organisms that survive and reproduce, while non-functional protein mutations are eliminated by natural selection. Thus, predicting whether a protein sequence is functional often requires learning from positive examples alone. While positive-unlabeled (PU) learning frameworks offer a generic solution to this problem, existing PU methods ignore the evolutionary processes that shape sequence observability and cause survivorship bias. Consider a sequence that is one mutation away from a commonly-observed protein variant in a well-surveilled organism. If the sequence were functional, it would likely be observed. If it is not observed, this suggests non-functionality. In contrast, sequences that are unlikely to arise through mutation may be missing simply because they never arose. Thus, these two kinds of missing sequences should be treated differently when training models. In this work, we propose Evo-PU, a PU learning framework that uses a scientific understanding of nucleotide mutation to model survivorship bias for well-surveilled single-organism sequence data. On three prediction tasks using single-organism uniform-coverage surveillance data -- predicting results from held-out influenza and respiratory syncytial virus (RSV) mutagenesis studies, and predicting future SARS-CoV-2 variants -- Evo-PU outperforms standard PU learning, one-class classification (OCC), and protein language models (PLMs). On prediction tasks from multi-organism ProteinGym datasets with more heterogeneous surveillance coverage, we identify opportunities to generalize our approach.

Modern fuzzers increasingly use Large Language Models (LLMs) to generate structured inputs, but LLM-driven fuzzing is sensitive to prompt initialization and sampling variance, which can reduce exploration efficiency and lead to redundant inputs. We present FunFuzz, a multi-island evolutionary fuzzing framework that runs several isolated searches in parallel and periodically migrates high-value candidates to maintain diversity. FunFuzz derives initial generation prompts from documentation and initializes islands with topic-specific instructions, then continuously adapts prompts using feedback-guided selection. During fuzzing, candidates are prioritized by incremental compiler coverage, while compiler-internal failure signals are used to identify crash-inducing inputs. We evaluate FunFuzz on compiler fuzzing, where inputs are source programs and success is measured by compiler coverage and unique compiler-internal failures. Across repeated 24-hour campaigns on GCC and Clang, FunFuzz achieves higher compiler coverage than previous LLM-driven baselines and discovers more unique failure-triggering inputs.

Character-level perturbations bypass safety alignment in modern LLMs despite leaving prompts human-readable. We identify and test a central structural mechanism: BPE tokenization fragments safety-critical words into sub-word pieces, and the three public alignment datasets we surveyed contain no intentionally fragmented inputs. The mechanism is a chain, tested end-to-end on five model families (Qwen-3-4B, Qwen-2.5-7B, Gemma-3-4B, Llama-3.1-8B, Mistral-7B). An optimization targeting safety-token fragmentation flips the first-token refusal trigger on 80-100% of refused HarmBench prompts, with 48% of those flips producing genuinely harmful outputs (per-model 29-65%; gap-vs-behavior ROC-AUC 0.66-0.98, pooled 0.84). Activation patching localizes the disrupted signal to the last ${\sim}30\%$ of layers; an alignment-data scan finds zero fragmented prompts among 30,000 examples (positive-control recall $\geq 99\%$ at attack-relevant intensities); and targeted-mutation experiments isolate safety words as the disruption locus. On the defense side, a 68-cell grid (55 trained checkpoints) shows that no DPO configuration achieves seed- and pool-stable ASR closure on the three families with closed pool-size confounds. SFT trained on fragmented prompts closes ASR on 3/5 families but only via global collapse that raises refusal on benign prompts as well, indicating the missing distribution is necessary but not sufficient under the LoRA-16 recipe we tested. To distinguish selective repair from global collapse, we introduce Conv-Benign, a candidate paired diagnostic. All ASR claims are 3-judge-calibrated (cell rankings stable across judges; absolute levels $\pm$18pp; see App.~B.13).

Proteins are shaped by gradual evolution under biophysical and functional constraints. Protein language models learn rich evolutionary constraints from large-scale sequences, and discrete diffusion-based protein language models~(\eg, DPLMs) are promising for both understanding and generation. However, existing DPLMs typically rely on masked diffusion that contradicts a simple biological intuition: proteins evolve through accumulated edits, not by emerging from masks. Consequently, these frameworks lack explicit pretraining objectives for substitution and insertion/deletion (indel) operations, limiting both optimization-style post-editing and flexible guided generation. To address these limitations, we present DPLM-Evo, an evolutionary discrete diffusion framework that explicitly predicts substitution, insertion, and deletion operations during denoising. DPLM-Evo decouples an upsampled-length latent alignment space from the variable-length observed sequence space, which makes indel-aware generation tractable. To better align substitutions with real evolution, we further introduce a contextualized evolutionary noising kernel that produces biologically informed, context-dependent mutation patterns. Across tasks, DPLM-Evo improves sequence understanding and achieves state-of-the-art mutation effect prediction performance on ProteinGym in the single-sequence setting. It also enables variable-length simulated evolution, and post-editing/optimization of existing proteins via explicit edit trajectories.

Synthetic accented speech is a promising way to improve automatic speech recognition (ASR) when real accented recordings are scarce. We ask what makes such data useful for ASR fine-tuning: target-accent phoneme edits that expose the recognizer to accent-specific pronunciations, or random phoneme perturbations that act as augmentation in phoneme space. In a few-shot TTS pipeline, we compare LLM-generated accent edits with matched-rate random substitutions and oracle controls using ground-truth accented phonemes and prosody. Random substitutions recover much of the ASR gain: LLM target-accent edits improve over random by only a small margin, ground-truth phonemes stay close to the random baseline and nearly converge with it as the synthetic ASR fine-tuning set grows larger, and adding ground-truth prosody yields only a modest further gain. Mixing synthetic with real accented speech also stabilizes low-resource fine-tuning, but a fixed synthetic budget can later dilute the information in real data, showing that the real--synthetic ratio matters.

Mutants support testing and debugging in two roles: (i) as test goals and (ii) as substitutes for real faults. Hard-to-kill mutants provide better guidance for test improvement, while realism is essential when mutants are used to simulate real bugs. Building on these roles, selective mutation for deep learning (DL) aims to reduce the cost of mutant generation and execution by choosing operator configurations that yield resistant and realistic mutants. However, the DL literature lacks a unified measure that captures both aspects. This study presents a probabilistic framework to quantify mutant quality along two complementary axes: resistance and realism. Resistance adapts the classical notion of hard-to-kill mutants to the DL setting using statistical killing probabilities, while realism is measured via the generalized Jaccard similarity between mutant and real-fault detectability patterns. The framework enables ranking and filtering of low-quality mutation-operator configurations without assuming a specific use case. We empirically evaluate the approach on four datasets of real DL faults. Three datasets (CleanML, DeepFD, and DeepLocalize) are used to estimate and select high-quality operator configurations, and the held-out defect4ML dataset is used for validation. Results show that quality-driven selection reduces the number of generated mutants by up to 55.6% while preserving typical levels of resistance and realism under baseline-aligned selection thresholds. These findings confirm that dual-objective selection can lower cost without compromising the usefulness of mutants for either role.

LLM-based automated program repair (APR) techniques have shown promising results in reducing debugging costs. However, prior results can be affected by data leakage: large language models (LLMs) may memorize bug fixes when evaluation benchmarks overlap with their pretraining data, leading to inflated performance estimates. In this paper, we investigate whether we can better reveal data leakage by combining metamorphic testing (MT) with negative log-likelihood (NLL), which has been used in prior work as a proxy for memorization. We construct variant benchmarks by applying semantics-preserving transformations to two widely used datasets, Defects4J and GitBug-Java. Using these benchmarks, we evaluate the repair success rates of seven LLMs on both original and transformed versions, and analyze the relationship between performance degradation and NLL. Our results show that all evaluated state-of-the-art LLMs exhibit substantial drops in patch generation success rates on transformed benchmarks, ranging from -4.1% for GPT-4o to -15.98% for Llama-3.1. Furthermore, we find that this degradation strongly correlates with NLL on the original benchmarks, suggesting that models perform better on instances they are more likely to have memorized. These findings show that combining MT with NLL provides stronger and more reliable evidence of data leakage, while metamorphic testing alone can help mitigate its effects in LLM-based APR evaluations.

Accurate early prediction of Acute Kidney Injury (AKI) is critical for timely clinical intervention. However, existing deep learning models struggle with irregularly sampled data and suffer from the opaque "black-box" nature of sequential architectures, strictly limiting clinical trust. To address these challenges, we propose CT-Former, integrating continuous-time modeling with a Causal-Transformer. To handle data irregularity without biased artificial imputation, our framework utilizes a continuous-time state evolution mechanism to naturally track patient temporal trajectories. To resolve the black-box problem, our Causal-Attention module abandons uninterpretable hidden state aggregation. Instead, it generates a directed structural causal matrix to identify and trace the exact historical onset of severe physiological shocks. By establishing clear causal pathways between historical anomalies and current risk predictions, CT-Former provides native clinical interpretability. Training follows a decoupled two-stage protocol to optimize the causal-fusion process independently. Extensive experiments on the MIMIC-IV cohort (N=18,419) demonstrate that CT-Former significantly outperforms state-of-the-art baselines. The results confirm that our explicitly transparent architecture offers an accurate and trustworthy tool for clinical decision-making.

As LLMs continue to shape real-world applications, automated jailbreak generation becomes essential to reveal safety weaknesses and guide model improvement. Existing automatic jailbreak generation methods have not yet fully considered two important aspects: adaptability to evolving safety-finetuned models, which affects their effectiveness on newer model versions, and diversity in generated prompts, which can cause narrow or repetitive attack patterns. To address these issues, we propose EvoJail, an instruction-fusion-driven evolutionary jailbreak generation framework that formalizes jailbreak prompt generation as a multi-objective black-box optimization problem and leverages the principles of evolutionary algorithms to search for jailbreak prompts that can adapt across different model versions and exhibit diverse attack patterns. Specifically, EvoJail integrates jailbreak prompt generation into an iterative evolutionary loop, where at each iteration candidate prompts are evaluated directly against the target model and then selected and varied based on the target model's responses, enabling the generation process to continuously adapt to model updates. To enhance diversity, EvoJail introduces field-aware instruction fusion to construct diverse starting points and incorporates diversity-aware objectives into the evolutionary fitness function, guiding the search toward prompts with richer semantic variation, while further designing multi-level LLM-based mutation operators that modify prompt structures at different granularities to promote structural diversity throughout the evolutionary process. Results demonstrate that EvoJail has stronger adaptability and can achieve over $93\%$ attack success rate and more than $5.6\%$ improvement in diversity metrics over state-of-the-art methods.

Automating operations research (OR) with large language models (LLMs) remains limited by hand-crafted reasoning--execution workflows. Complex OR tasks require adaptive coordination among problem interpretation, mathematical formulation, solver selection, code generation, and iterative debugging. To address this limitation, we propose EvoOR-Agent, a co-evolutionary framework for automated optimization. The framework represents agent workflows as activity-on-edge (AOE)-style networks, making workflow topology, execution dependencies, and alternative reasoning paths explicit. On this representation, the framework maintains an architecture graph and evolves a population of reasoning individuals through graph-mediated path-conditioned recombination, multi-granularity semantic mutation, and elitist population update. A knowledge-base-assisted experience-acquisition module further injects reusable OR practices into initialization and semantic variation. Empirical results on heterogeneous OR benchmarks show that the proposed framework consistently improves over zero-shot LLMs, fixed-pipeline OR agents, and representative evolutionary agent frameworks. Case studies and ablation analyses further indicate that explicit architecture evolution and graph-supported reasoning-trajectory search contribute to both performance improvement and structural interpretability. These results suggest that treating agent architectures and reasoning trajectories as evolvable objects provides an effective route toward adaptive and interpretable automated optimization.