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Ver preçosWe introduce Gacha Decoding, an inference-time method for eliciting diverse language model generations that scales with model capability. Across open-ended domains (in-the-wild chat, creative writing, planning for image generation, and protein design), Gacha Decoding significantly outperforms existing generation diversity approaches at equal quality (up to 2.4x Vendi over the next-best prior approach), reaching the same number of high-quality modes with over an order of magnitude fewer samples (11.0x) and discovering novel modes that no other approach surfaces. Our key insight is to treat diversity as an instruction-following problem: rather than relying on the LM's token entropy, we combine its instruction-following capability with randomness from an external RNG tool to scalably identify and realize distinct modes of the response space. This approach of "planning with dice" enables Gacha to invert the long-observed tension between diversity and model capability. As the underlying LM becomes a better instruction follower, diversity under Gacha Decoding consistently improves--even as its token entropy and diversity under prior approaches decline. Together, our results highlight that instruction following, rather than token entropy alone, can drive generation diversity.
Peptide sequence governs both the structures formed through supramolecular assembly and the dynamics by which they emerge, but predicting either requires resolving slow collective processes among many interacting molecules. Molecular dynamics (MD) provides microscopic insight into these processes, yet the long timescales of assembly and the vast peptide sequence space make systematic exploration computationally demanding. We introduce SupraTITO, a transferable generative molecular dynamics (GenMD) framework for supramolecular systems, demonstrated through peptide self-assembly. SupraTITO learns transferable implicit transfer operators (TITO) conditioned on peptide sequence, molecular topology, and periodic geometry, allowing configurations to be propagated over physical intervals much longer than an MD integration step. On a comprehensive dipeptide benchmark, SupraTITO generalizes to held-out sequences and reproduces sequence-dependent structures and dynamics while maintaining molecular integrity over long rollouts. Compared with direct ensemble prediction trained on the same trajectory data, SupraTITO more accurately reproduces assembly structures while also resolving their temporal evolution. The learned dynamics generalize across peptide concentrations, including dilute conditions not represented during training. These results extend transferable GenMD to collective dynamics in periodic supramolecular systems and provide a foundation for modeling related processes beyond peptide assembly.
Attributing model behavior to synthetic training data requires knowing what produced each training item before estimating what that item caused. A waveform-label pair does not preserve this knowledge. We propose a generation-provenance substrate in which a synthetic research object binds source specification, generated content, waveform, target, fact requirements, quality signals, review lineage, and immutable manifest identity. Producer and selection mechanism determine evidentiary meaning; storage location and variable name do not. We audit this substrate in a private Japanese care-handoff pipeline. A 113-asset review population contains 1.552 hours of synthetic speech across six scenario families; all items have linked audio, transcripts, candidate notes, and fact checklists, but human evidence is selective and source-specific. Two faithful-only manifests are scenario-seed-disjoint and immutably versioned, while exact upstream attribution remains blocked by floating generator aliases, missing per-clip TTS and code stamps, and an unversioned checking prompt. We argue that generation provenance is necessary but not sufficient for behavior attribution: it defines the candidate causal graph and audit units, whereas contributive attribution still requires frozen training runs and intervention or influence evidence. The paper contributes a compact provenance contract, an audit protocol, and a bounded case study for synthetic-data attribution; controlled research access may be offered, but we do not claim causal training-data attribution, clinical validity, or unrestricted public release.
We study causal logistic bandits with counterfactual fairness constraints. The causal structure is given through known factual and counterfactual feature maps that share an unknown logistic reward parameter, but the learner observes only factual rewards. Consequently, the directions determining counterfactual feasibility need not be identifiable from the available feedback. The closest prior analyses either omit a coverage condition or impose a comparatively strong one, and do not establish matching lower bounds. We first show that some coverage condition is necessary: without a coverage-type restriction, factually indistinguishable environments with different optimal fair actions force Ω(T) expected joint loss. Under a weaker full-rank condition on the factual covariance pooled across actions, we identify a target-specific information scale V_that measures the difficulty of estimating rewards and counterfactual effects from factual feedback. We construct worst-case families satisfying this condition on which every policy incurs expected joint loss Ω([V_\{K,d\}]^{1/3}T^{2/3}). We also give an explore--then--exploit procedure tuned using V_and an adaptive algorithm that does not require its value. Both algorithms achieve $\{R_T,V_T\}={O}([V_\{K,d\}]^{1/3}T^{2/3}+κd/σ_0^2), where R_T is regret relative to the best fair action and V_T$ denotes the cumulative stage-wise positive violations. Thus the upper and lower bounds match in their leading dependence on T, V_, and \{K,d\}, up to logarithmic factors.
A user's movie, news, and dialogue histories differ in their native actions and outputs, yet each interaction supplies evidence that can update user memory. We study whether these histories can train one reusable update mechanism. An action-on-item schema pairs a mapped interaction role with a content embedding, allowing shared update parameters to operate on separate user states. We establish invariance to native relabeling, bounded state changes under item-embedding perturbations, and a pooled-training bound under explicit compatibility conditions. The Multi-Timescale State Hypothesis (MTSH) specifies how this evidence enters, persists, and is consumed; PerTIDE implements it with action gating, three state-space traces, fusion, and command-conditioned readout. On PENS, the same history encoder supports both next-news prediction and personalized headline generation. In a controlled PENS-to-MovieLens experiment, a frozen source-trained core exceeds an identically structured random core by 15.23 MRR points after fitting the same target consumer. On MIND, PerTIDE retains a 4.12-point MRR advantage over a same-input three-branch state-space control. Action, readout, and trace interventions identify complementary contributions to these gains. Together, the theory and experiments support learning history updates across compatible sources and reusing them through predictive and generative consumers.
World models allow agents to plan in latent space by choosing a sequence of actions that most reduces the distance to a given goal state. Thus, planning can benefit from latent representations whose distances mirror commute-times in the environment. The spectral embedding space of the graph Laplacian provides such a representation, if it obeys a specific eigenvalue-dependent scaling. Unfortunately, instantiating the graph Laplacian is intractable in large, continuous environments. Self-supervised learning offers a natural route to such commute-time-preserving embeddings at scale. However, here we show that existing methods, which commonly encourage isotropic representations to prevent representational collapse, tend to degrade the "correct" eigenvalue-dependent scaling, leading to an inaccurate representation of commute times. To address this problem, we introduce Commute-Time-Preserving World Models (CTWMs), combining a latent displacement predictor and a log-determinant regularizer that prevents collapse, which provably recover the correctly scaled Laplacian representation under reversible deterministic dynamics and at the predictor's fixed point. In numerical simulations, CTWM matches or outperforms LeWM, a task-agnostic baseline, on several complex, continuous goal-reaching benchmarks, while using half the parameters.
Understanding a nonlinear dynamical system from time series requires not only reproducing its trajectories, but also identifying a simple representation that preserves its essential dynamical structure. Almost-linear recurrent neural networks (AL-RNNs) are piecewise-linear RNNs in which only a subset of units use ReLU nonlinearities, so that nonlinear capacity is explicitly controlled by the number of ReLU units. Their activation patterns define linear regions, represented as symbols, whose observed transitions form a symbolic transition graph. However, directly training AL-RNNs with few ReLU units to realize minimal dynamical representations can be unreliable. We ask whether an AL-RNN with more ReLU units can instead be trained first and systematically reduced to a minimal dynamical representation. We introduce a fixed-point-guided hierarchical reduction procedure that progressively linearizes selected ReLU units, merging neighboring linear regions and graph nodes while preserving distinct symbols containing fixed points (FPs). The resulting reduction tree defines a hierarchy of progressively simpler candidates. Each reduced candidate is initialized from the parent parameters and retrained under guidance from the parent dynamics. We also prove that reproducing Q distinct fixed points requires at least Q FP-containing symbols, providing a certificate of symbol-level minimality when this bound is attained. On the 3-scroll Chua system, direct training with the theoretical minimum of three ReLU units achieves high-fidelity minimal realizations in only 20% of seeds, whereas our learn-reduce-retrain strategy increases the seed-macro success rate to approximately 71% at the same final nonlinear capacity. These results show that redundant nonlinear capacity can serve as a scaffold for discovering and realizing minimal dynamical representations.
Factories are shifting toward smaller lot sizes with high product customization, requiring frequent re-programming of flexible and reconfigurable automation systems. LLM-based agents can be deployed in two complementary roles: Offline, they generate deterministic production sequences, reducing programming effort; online, they operate live machines and handle unforeseen runtime faults that static programs cannot anticipate. We propose a solution in which each factory module is paired with a dedicated LLM-based agent and an MCP tool server that exposes the module's skills via OPC UA method calls, with agents coordinating over MQTT and grounded by real-time updates of the factory state. We compare three agent architectures (orchestrator, peer-to-peer, and monolithic) across nine production challenges of increasing complexity in a simulation of a physical six-module hexagonal factory, including silent hardware fault detection. The monolithic and peer-to-peer architectures both achieve the highest mean solve rate (93\%), while the orchestrator uniquely resolves a silent conveyor-belt fault in all ten runs by autonomously rerouting plates around the blocked segment. All architectures exhibit emergent fault-diagnosis behavior without any explicit failure-handling logic, establishing standardized MCP tooling, MQTT-based inter-agent communication, and real-time state injection as a viable and reproducible foundation for LLM-programmed smart manufacturing.
Multilayer networks allow the modeling of interactions between the same entities across different contexts, such as temporal observations, varying settings, or interactions of different types. The goal of community detection in multilayer networks is to identify groups of nodes exhibiting similar connectivity patterns, which may vary across layers. We propose a method based on a joint nonnegative symmetric matrix trifactorization for community detection in multilayer networks, where each graph is approximated by a nonnegative symmetric matrix trifactorization. Our approach enforces constraints on the factor matrices so that communities are disjoint and shared across layers, while allowing each layer to have its own connectivity patterns and node degrees. This flexibility enables the model to capture both local and global structural variations across layers. We also develop an algorithm to efficiently solve this problem. We evaluate multilayer community detection methods using the multilayer degree-corrected stochastic block model (MDCBM), a flexible framework for generating realistic multilayer graphs with heterogeneous degrees and varying connectivity patterns. Experiments show that our method reliably detects communities across diverse regimes, whereas existing state-of-the-art approaches are often limited by restrictive structural assumptions.
Single-particle cryo-electron microscopy (cryo-EM) has become a widely adopted technique for biomolecular structure determination. The conventional cryo-EM computational pipeline first combines many particle images to reconstruct an electrostatic potential (ESP) map and then fits an atomic model to the recovered map. Density reconstruction has high sample complexity, requiring large numbers of particle images and making structure determination high-cost and low-throughput, particularly for heterogeneous samples. Downstream atomic model building, in turn, becomes increasingly difficult as the resolution of the reconstructed map deteriorates. Protein structure prediction models provide strong sequence-derived priors on atomic structure, and experiment-guided approaches can use these priors to recover structures consistent with experimental measurements. Yet, in cryo-EM, such priors are typically integrated only after density reconstruction during atomic model fitting. We introduce Fold'EM, an inference-time framework that combines priors from protein generative models directly with cryo-EM particle images to determine atomic models from a small number of single particle images, bypassing both intermediate density reconstruction and downstream model building against the reconstructed map. Across synthetic and experimental cryo-EM datasets, Fold'EM recovers accurate atomic structures both with known particle orientations and in an ab-initio setting where orientations are inferred jointly with structure. In heterogeneous datasets, Fold'EM further resolves distinct conformational states from mixed particle populations without separately reconstructing a density map and building an atomic model for each state. We believe these results open new avenues for structure determination in the low-sample regime and for characterizing low-population conformational states directly from cryo-EM particles.
Stable port-Hamiltonian neural networks certify asymptotic stability by construction. Yet, their Hamiltonian is a global Lyapunov function with a single global minimum, so they can represent only dynamic systems with {one} attractor. We demonstrate that this excludes even simple systems with energy landscapes forming a double well, and we overcome the restriction by parametrising the Hamiltonian as a {product} of Bregman divergences generated by one input-convex network. We prove that the resulting model is locally Lyapunov stable, that the coexistence of stable equilibria forces additional non-asymptotically-stable equilibria to exist, that all equilibria lie in a bounded region, and under a hyperbolicity assumption that almost-everywhere stability holds. On three systems our approach is able to recover the energy surface characteristics and improve the convergence speed by 1.8-8.5.
We introduce a new framework for one-step generative modelling on finite state spaces. To extend drifting beyond continuous domains, we use discrete Wasserstein geometry to define a target-relative KL gradient flow over the transitions of a reversible Markov kernel. We realize this probability flow at the particle level through Markov jumps and amortize the resulting transport updates into a latent-conditioned generator, so that the iterative dynamics are required only during training while inference remains one-step. In a controlled setting where the underlying distributions and transport dynamics can be computed exactly, we verify KL dissipation, consistency between the particle dynamics and the probability flow, and the predicted numerical scaling. We further show that a finite-capacity neural generator can track these exact transport targets while retaining one-step generation. These results validate the basic construction and provide a foundation for scaling Discrete Drifting to structured discrete data.
Large language models are moving from helping write up research to helping do it, which makes it important to know how the scientific text they produce differs from human writing. Work on this question has stayed mostly at the surface, using lexical and stylistic cues that light paraphrasing erases. We look instead at rhetorical structure, the sequence of argumentative moves through which a text makes its case. We study research-article introductions under Swales' CARS model, and compare original introductions from published linguistics articles with generated counterparts of the same papers. We find that human-written introductions are more flexible in which moves they use and in what order, while the generated ones are more uniform. Giving the models the CARS definitions makes them more rigid.
Tool-using large language model (LLM) agents turn generated text into real side effects, so poisoned tool metadata, retrieved pages, memory, and reusable skills can steer the next call. Vetting an artifact before admission does not settle this. A safe variant and a leaking variant can produce the same admission evidence, and a sound gate then cannot relax that site for either. We make that condition precise, which leaves the last boundary a deployment can still act on. We present Provenance-Aware Capability Enforcement (PACE), which mediates every tool call immediately before it executes. Path confinement proposes an executable cut of represented influence paths, while capability and effect verification checks schema-defined effects against authority compiled from the authenticated request. We distinguish the certified execution contract from the evaluated configuration, which can restore an authorized call after a proposed block or apply a declared repair. Confinement requires the final action to preserve the certified cut. On eight executable agent-security benchmarks with three target-model families, the evaluated configuration gives strictly lowest attack success in 62 of 79 eligible attack columns and ties in 14; full-benchmark native utility loses at most three points relative to the undefended agent. A complete ablation over 1167 paired cases attributes most security gains to effect verification and refusal control to boundary adaptation. A reduced-scale adaptive search succeeds on 0/30 out-of-authority targets against the defense.
When developers change one component of an agent, such as its controller, a learned model or its verifier, they usually judge the change by an aggregate task score. That score cannot tell whether improvement was attainable, which component lost value, or what the agent's own checks certify. We introduce a claim-specific verification audit for modular agents that plan, act, check and refine. Instead of scoring the agent, the audit scores the evidence: each conclusion is recorded with the evidence behind it, one of four verdicts (supported, unsupported, unresolved or not evaluated) and the boundary within which it holds. Three tools supply that evidence. Oracle policies measure attainable improvement under an explicitly stated action set, so that a low value can be traced to the evaluation rather than to the environment. Replacing one component at a time with a perfect counterpart locates lost value, with null results read as unresolved whenever a downstream component could mask them. A separate test asks whether the verifier's score identifies the quantity it is read as bounding. Applied to a constrained portfolio-allocation agent in a synthetic market with known hidden regimes, the audit shows that the value of perfect regime information depends on the action set used to measure it, that the scenario generator discards most of the regime signal while better local fidelity does not improve decisions, and that the runtime verifier can be bypassed with no visible change in outcomes. The contribution is the protocol and the evidential distinctions it enforces; the empirical findings are specific to the agent and environment studied.
