Free Energy Principle

Molecular systems have many degrees of freedom, but their metastable behavior can often be described by a few collective variables. Identifying these variables and estimating free energies along them from limited simulation data remains a challenging, important problem. Separate short trajectories may sample different metastable states without capturing transitions or establishing their relative equilibrium populations. For unbiased trajectories generated with the same Hamiltonian at a single temperature, alternate methods based on histogram reweighting cannot correct this imbalance. Here we present SPIBER, which combines the State Predictive Information Bottleneck (SPIB) with Generative Flow Networks (GFlowNets). SPIB uses deep learning to approximate slow degrees of freedom through a past-future information bottleneck, retaining information needed to predict future metastable states. We show that this compression limits conditional entropy variations in populated regions, allowing conditional mean potential energies, which are much easier to calculate, to be used to approximate free energy differences. Given sufficient local sampling to estimate these energies, they define the target distribution for GFlowNets, energy-based generative samplers that sample according to estimated thermodynamic stability rather than observed populations. For a particle in a radial double-well potential, for alanine dipeptide, and for the nine-residue peptide AIB9, SPIBER recovers free energy differences between sampled metastable states to within one thermal energy unit of reference values. The method combines collective-variable learning and free energy estimation in up to four latent dimensions, without requiring converged state populations or additional molecular dynamics simulations.

We study the Bayes-optimal spherical linear model as the ambient dimension and sample size grow proportionally, under a quantitative Marchenko--Pastur spectral-regularity condition on the design. This condition is satisfied by normalized i.i.d. designs with standardized entries of finite fourth moment, but does not require entrywise independence or impose conditions on the singular vectors. Under this condition, we prove a quantitative all-temperature TAP approximation and characterize the posterior geometry. For the natural finite-aspect-ratio TAP functional, the normalized spherical free energy and the TAP optimum differ by $O_P(p^{-1})$. Each is within $O_P(p^{-1/2})$ of its explicit deterministic equivalent, and this fluctuation scale is sharp. Uniformly over all global TAP maximizers, the normalized squared Euclidean distance to the spherical posterior mean is $O_P(p^{-1})$. We also prove that the posterior mass outside a data-dependent band determined by the ridge estimator has sharp exponential order. More precisely, uniformly over sufficiently small band widths $\varepsilon$, the logarithm of this mass is at most $-cp\varepsilon^2+O_P(1)$. For every fixed geometrically admissible width, a spherical-cap construction gives a matching exponential-order lower bound on this mass. For every deterministic sequence of widths $\varepsilon_p\gg p^{-1/2}$, the corresponding bands capture asymptotically all posterior mass.

The last decade has seen the development of powerful methods for learning complex structure from high-dimensional data. These advances have brought to the foreground fundamental connections between subdisciplines of physics, applied mathematics, and machine learning. In this review, we bring together some of these ideas, often expressed in different languages, to highlight a conceptual thread that links five distinct fields: control theory, optimal transport, probabilistic inference, non-equilibrium thermodynamics, and machine learning. A common theme is the optimization of free-energy-like functionals under dynamical or statistical constraints. We offer a guided tour through this thread and present selected applications in reinforcement learning, variational inference, and generative modeling. The review does not assume prior familiarity with these topics, and begins with principles originating from physics.

Liquids exhibit collective behavior that depends sensitively on thermodynamic conditions, interfaces and confinement, yet predicting each new state commonly requires a separate atomistic simulation. Classical density functional theory offers a reusable variational description, but its central excess free-energy functional is generally unknown, and learned approximations have largely remained restricted to planar or lower-dimensional settings. Here we show that this functional can be learned directly from fully three-dimensional equilibrium density fields while preserving spatial symmetry and variational consistency, without free-energy or chemical-potential labels. A single learned functional transfers across temperatures, system sizes and statistical ensembles, and recovers structure factors, the equation of state, liquid--vapor coexistence and interfacial broadening, none of which are used as training targets. Applied to complex three-dimensional geometries, it predicts the non-monotonic force associated with formation and rupture of a solvent-depleted bridge between colloids and adsorption in an interconnected gyroid pore. These results demonstrate that equilibrium density data can be converted into a transferable thermodynamic generator connecting microscopic liquid structure to response, phase behavior and collective phenomena.

Predictive coding offers a powerful framework for cortical computation, yet scalable implementations that respect both Bayesian exactness and neurobiological constraints remain scarce. We bridge this gap by formally connecting predictive coding to Recursive Gaussian Processes (RGPs). RGPs employ a single Gaussian process $g(t, \cdot)$ indexed by layer index and input value, preventing the representational collapse of standard deep Gaussian processes while allowing learnable cross-layer dependence via $r_{1g}$. We demonstrate that RGPs intrinsically implement hierarchical Bayesian inference, uncertainty propagation, and precision-weighted prediction error. Critically, we map RGP components---the shared GP, spike-and-slab variable selection, and MCMC dynamics---onto the canonical cortical microcircuit, providing a neurobiological substrate for these computations. Drawing on the free energy principle, we show that RGP inference minimizes variational free energy, formally linking Bayesian mechanics to neuronal dynamics. Our synthesis positions RGPs as both a principled computational tool and a candidate model for the brain's predictive machinery, generating testable predictions for laminar-specific dynamics and spectral asymmetries between feedforward and feedback processing.

Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort. Coding agents promise to automate significant portions of this workflow, yet their reliability on realistic molecular dynamics (MD) tasks remains poorly characterized. To address this issue, we introduce MDArena, a benchmark of 50 containerized tasks drawn from active biomolecular simulation projects, spanning 29 molecular systems and 14 broad research protocols, including trajectory analysis, complex system preparation, free-energy protocols, and enhanced sampling. We evaluate six model/harness configurations spanning Codex and OpenCode. Among the evaluated configurations, Codex GPT-5.5 at extra-high reasoning effort performs best, reaching 24/50 Strict-Pass@1 successes (48%), followed by Codex GPT-5.5 Medium with 21/50, and OpenCode Gemini Flash 3.5 with 20/50. Average correctness and process rewards are substantially higher than strict success rates across all configurations, indicating that agents frequently make meaningful partial progress but fail on the fine-grained details required for reproducible scientific workflows. Hard tasks remain largely unsolved, particularly membrane-protein system preparation and alchemical free-energy setup, both unsolved or near-unsolved by every evaluated configuration. MDArena thus exposes a substantial gap between the usefulness of coding agents as supervised assistants and their reliability as autonomous MD researchers, while providing a reproducible and extensible platform for tracking progress toward closing it.

Using large deviations theory, we solve and obtain a general expression for the free energy functional for a broad class of associative memories, including dense associative memories. We illustrate the method by reproducing classical results for the Hopfield model. For a finite number of patterns, we derive the temperature-dependent free energy functional for dense associative memories featuring polynomial interactions and Log-Sum-Exponential (LSE) activation. We also evaluate the disorder-averaged ground-state energy of these systems in the extensive limit. Our analytical framework reveals how memory retrieval depends on the initial state in higher-order dense networks, and gives the exact full-retrieval threshold for the LSE model. This method provides a systematic procedure for analyzing diverse, complex architectures in associative memory.

An agent acting under partial observability must decide when to gather information and which observations are worth their cost. Standard POMDPs value information only through its eventual effect on reward. The $ρ$-POMDP framework instead rewards uncertainty reduction directly, through a belief-dependent utility $ρ$, but in practice both the choice of $ρ$ and the weight placed on it are tuned by hand for every task. We show that active inference removes this tuning entirely. Minimizing Expected Free Energy (EFE) is exactly equivalent to solving a $ρ$-POMDP whose utility is expected information gain, and the exploration weight is fixed at $w=1$ because the variational bound expresses pragmatic and epistemic value in the same units (nats). We prove this equivalence for observe-then-commit POMDPs and extend it to factored observation POMDPs, a broader class that covers interleaved observe-act problems such as non-destructive testing and mobile sensing, where gathering information leaves the hidden state unchanged. Experiments support the theory. Across environments ranging from the classic Tiger problem to RockSample and a new Structural Inspection benchmark with over 65,000 states, the untuned weight matches or outperforms reward-only planning at the same horizon, avoids the over-exploration of bonuses tuned per task, and sits near the reward-maximizing knee of the success-reward Pareto frontier. The practical payoff is an exploration objective that works out of the box. In applications such as fault detection and medical screening, where every test has a price and every missed fault has a cost, EFE supplies a belief-dependent utility that is derived rather than tuned.

Joint-Embedding Predictive Architectures (JEPAs) are the dominant design for latent world models, yet they are usually justified by empirical performance rather than a normative principle. We show that the choice of anti-collapse regulariser determines whether a JEPA's training objective, a prediction loss plus a weighted embedding regulariser, is a valid Active Inference (AIF) variational free energy. We organise four non-contrastive regularisers (VICReg, LogDet, PairDist, and SIGReg) into an entropy-estimator hierarchy indexed by a prior-miscalibration gap, and show that the gap's sign, whether the estimator bounds the latent entropy from above or below, decides whether the AIF surprise bound survives: VICReg and LogDet are unsafe upper bounds, PairDist a safe lower bound, and SIGReg eliminates the gap. We then prove a correspondence theorem: under the standard constant-noise encoder model and successful SIGReg enforcement (isotropic-Gaussian embeddings), the gap vanishes, the objective becomes an exact information bottleneck, the surprise bound is preserved, and the latent goal cost becomes an exact proxy for AIF pragmatic value, whereas VICReg leaves an irreducible second-order anisotropy term. We extend the correspondence to multi-step expected free energy, ensemble epistemic value, and a learned-policy regime, and we identify the one AIF term no current JEPA world model computes: the state-epistemic value, a future-state coverage signal. The predictions differ in kind, not degree, and are stated here as theoretical consequences left for empirical test in separate work; full proofs are in Appendix A, and the algebraic core of every result is machine-verified in Lean 4 (Appendix D).

Under the free energy principle, a predictive system does not observe reality directly; it maintains a generative model of the world and experiences that model's best current hypothesis. Can a synthetic environment be made consistent enough that a predictive system's own inference machinery adopts it as this default hypothesis, permanently displacing the environment that first shaped it? We call this state ontological inversion. Because inducing and monitoring such a transition in a nervous system is neither ethical nor technically feasible, we study the underlying computational problem through a controlled proxy: a convolutional variational autoencoder paired with a recurrent latent predictor, whose evidence lower bound objective is mathematically identical, up to sign, to variational free energy itself. The network is trained first on a baseline visual domain, then on a mixed stream in which a swept rehearsal ratio r controls how much baseline content persists during transition to a target domain. Representational capacity, what the latent space can discriminate, is tracked separately from default behavior, what the system generates when left unconstrained. Across a full sweep of 90 runs, the two diverge sharply: representational accuracy stays near ceiling, 0.97 to 0.998, regardless of r, while default behavior spans nearly the system's entire range depending on r alone, a decoupling of learning from acceptance. More strikingly, at intermediate r the system's default output rises toward the target domain, then partially reverts toward the baseline while training continues unchanged, a structural failure we term cognitive relapse. Resistance to reality-adoption is not reducible to learning speed; it is a structural property with its own distinct failure modes, established here as a computational existence proof and nothing further.

We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD). This is in contrast with existing generative models that remove degrees of freedom by operating on coarse-grained, vacuum, or implicit solvent systems. Operating at this resolution allows for post-processing through force field energy evaluations and MD simulations, and enables the prediction of relevant properties in a gray-box manner (as ensemble averages of potential energy evaluations over generated samples). We demonstrate the utility of this paradigm on absolute hydration free energy (AHFE), producing estimates 4-10x faster and with comparable accuracy to standard GPU-based MD. By generating uncorrelated samples from alchemical Boltzmann distributions, we create more accurate, interpretable, and refinable ensemble predictions with calibrated uncertainty estimates, unlike regression methods which are entirely black-box predictors. Our approach also yields predictable benefits from increasing train- and test-time compute, realized by scaling model size and generating more samples, respectively. We believe that this approach demonstrates the utility of high-resolution ensemble generation for free energy estimation, with future potential to replace MD in tasks such as the prediction of lipophilicity, membrane permeability, or absolute binding free energy (ABFE) -- whose grounding and interpretability may be critical for the development of new drugs and materials.

Quantum mechanical (QM) cluster models provide an effective framework for mechanistic studies of enzymatic reactions but remain computationally demanding. Neural network potentials (NNPs) offer a promising route to reduce this cost, but enzymes present challenges beyond small molecules, including large system sizes, implicit-solvent environments, substantial polarization, and charge transfer. Here, we present an integrated software framework for efficient NNP training for mechanistic studies of enzymes, demonstrated on QM cluster models of S-adenosyl-L-methionine-dependent methyltransferases (MTases). Our Enerzyme code introduces modular electrostatics-aware NNP architectures and combines automated QM-cluster construction with reactive dataset generation. The Enerzymette subpackage automates reaction pathway exploration at both NNP and DFT levels. We show that iterative flexible scans and nudged elastic band calculations impose stricter requirements on NNPs than conventional dataset metrics. Nevertheless, NNPs trained on fewer than 1,000 system-specific datapoints reproduce reaction energetics and transition-state structures for MTase clusters containing up to 545 atoms with near-chemical accuracy. Direct supervision of atomic charges and consistent dielectric screening substantially improve simulation stability and accuracy, while multitask-learned atomic charges capture charge transfer and polarization trends and provide chemically meaningful descriptors of reactivity. Finally, transferability across chemically diverse catechol O-methyltransferase substrates indicates that NNPs learn generalizable reactivity patterns as training data expand across multiple enzymes. Together, these results establish a foundation for accelerating enzyme mechanistic studies and guide future NNP development for biomolecular reactivity.

Hallucination detection in large language models (LLMs) is deployment-critical, and recent work shows that the spectrum of attention-derived graph Laplacians carries strong signal about reasoning quality. Prior spectral diagnostics, however, summarize the Laplacian spectrum by a handful of eigenvalues or hand-picked scalars, leaving most of its structure unused. We propose Free-Energy Signatures (Fes), a spectral descriptor that treats each layer's attention Laplacian as a Hamiltonian and extracts its thermodynamic potentials partition function, free energy, spectral entropy, heat capacity together with the random-matrix-theory (RMT) spectral form factor. We prove three results: (i)~Lipschitz stability of Fes under attention perturbation; (ii)~an expressiveness result showing that Fes enriches finite spectral summaries and approximates moment-derived spectral functionals under explicit regularity and grid-resolution assumptions; and (iii)~a finite-sample PAC bound on the AUROC of a training-free detector built from Fes. Empirically, across six open-weight LLMs and six benchmarks, a lightweight probe on Fes descriptors achieves the strongest aggregate AUROC among attention-spectral baselines, improving over LapEig by $+6.5$ AUROC points and over GoR-4 by $+2.4$ points on average, while requiring no update to the underlying LLM. In the fully unsupervised setting, an RMT-deviation score achieves mean AUROC $0.71$, providing a label-free but weaker detector. A complementary RMT analysis shows that correct generations exhibit more Wigner-Dyson like spectral statistics, whereas hallucinations exhibit more Poisson-like statistics. The anonymized code and config are provided in the supplementary material.

We study the dynamics of gradient descent in the Edge of Stability regime, where the learning rate is large enough to induce persistent oscillations in the loss and the sharpness. We propose a continuous-time effective model that tracks the evolution of the average trajectory coupled with the time-averaged covariance of its fast oscillations. Our analysis reveals that the natural quantity to monitor in such unstable regimes is an effective free energy, which combines the original risk functional with a curvature-related "entropic" term. Our model allows us to track the envelope of the oscillations even in situations where its dynamics evolve on similar timescales as the averaged weights. Otherwise stated, we can track the spikes that occur during the training of some neural network architectures. For wide two-layer neural networks optimized under stable non-vanishing oscillations, we derive a mean-field limit that results in a novel kinetic equation describing the joint distribution of weights and their fluctuations. We show that this equation can be interpreted as a Wasserstein-2 gradient flow of a macroscopic free energy. Finally, we provide numerical evidence on matrix factorization and deep learning tasks (CIFAR-10) to demonstrate the model's accuracy in capturing the envelope of the oscillations and the predictive power of the effective free energy.

Active inference casts decision-making as inference, with the Expected Free Energy (EFE) unifying goal-directed and information-seeking behavior. Recent work showed that EFE minimization can be written as Variational Free Energy (VFE) minimization on a generative model augmented with epistemic priors. We prove that the VFE of the augmented model can be rewritten as the VFE of the predictive model plus explicit entropy-correction terms, making the EFE contribution transparent. We then show that proper EFE-based planning requires combining these epistemic corrections with a planning correction that turns marginal inference into policy optimization, yielding a full variational characterization of EFE-based planning. This clarifies which corrections are needed for cross-entropy planning and for full EFE-based planning. The same entropy-corrected formulation leads to a detailed message-passing scheme for EFE-based planning together with simpler ablations. Experiments on three grid-world environments show that full EFE-based planning outperforms ablations that omit either the planning correction or the epistemic corrections.

We show that computing the log-partition function (free-energy) of conditioned inhomogeneous Curie--Weiss spin Hamiltonians reduces to an unbalanced $2 \to 1$ norm computation, and design a polynomial-time SDP algorithm for this problem with a lower bound proof for the amount of unbalance achieved. Applied to the protein Ubiquitin, the framework starts from a known crystal structure, explores alternative backbone conformations across the free-energy landscape, and identifies flexible regions of the protein while preserving its native secondary structure.

Free energy estimation is a fundamental yet challenging problem, from physics to statistics. Classical approaches rely on thermodynamic transformations, ranging from direct estimation, quasistatic integration, to finite-time averaging. Recent work [He and Du et al., 2025] learns neural transports to significantly accelerate the efficiency in the finite-time regime. In this paper, we generalize this framework to arbitrary state spaces. Building on this view, we develop a generalized neural transport learning approach for efficient estimation. Experiments validate the effectiveness and efficiency of the proposed method beyond continuous settings, extending to discrete and multimodal spaces as well as autoregressive settings. Beyond free energy estimation, we establish algebraic identities and reveal a group-theoretic structure linking infinitesimal time reversal and generalized Doob's $h$-transforms, showing that their compositions form a generalized dihedral group.

Trajectory prediction methods have demonstrated remarkable capabilities in capturing complex motion patterns. However, existing methods rely on global state assumptions, suffer from insufficient belief inference under partial observability, and lack cognitive behavioral constraints in prediction. These limitations severely compromise both deployment feasibility and physical plausibility in real-world settings. In this work, we propose FEP-Diff, an agent-centric trajectory prediction framework grounded in the Free Energy Principle, aimed at achieving cognitively plausible predictions under realistic constraints. Specifically, a dual-branch spatiotemporal encoder extracts ego-motion dynamics and social interaction cues from local observations. Building upon this, a goal-conditioned belief learner infers multimodal latent belief distributions optimized via a free-energy objective, with a social consistency constraint on the local neighborhood graph to promote cognitive alignment among neighboring agents. Finally, a residual diffusion trajectory generator is conditioned on the learned belief representations with token-level proxy conditioning, producing precise and diverse future predictions. Extensive experiments on five public benchmarks demonstrate that FEP-Diff consistently outperforms state-of-the-art methods under restricted observability. Code: https://anonymous.4open.science/r/FEP-Diff-8876.

Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force (PMF), with density functional theory (DFT) accuracy is computationally expensive. Universal machine learning interatomic potentials (MLIPs) drastically reduce this cost, but their accuracy is strongly determined by their training data and hence can be uncertain for a given system. In this work, we present a systematic and scalable framework for reweighting PMFs, initially sampled with a single 'source' MLIP, across a representative suite of target MLIPs. Because traditional direct exponential reweighting fails for large system sizes due to low phase-space overlap between potentials, we deploy robust analytical corrections. Applying this to a complex 601-atom system of Li$^+$ transport in a nanoconfined electrolyte, we demonstrate that a mean energy-gap approximation effectively bypasses statistical collapse, producing a highly stable PMF matching the target PMF. Using this approach, we recover high-fidelity target thermodynamics across multiple DFT reference levels (PBE+D3, PBE-sol, r$^2$SCAN,r$^2$SCAN-D4) at a fraction of the computational cost of full simulations. Furthermore, thermodynamic analysis reveals that the studied MLIPs partition into two distinct clusters driven by their training data. Our reweighting framework successfully recovers target thermodynamic properties--specifically, reaction and activation free energies--even when the phase-space overlap between potentials is critically low. Ultimately, this approach establishes a vital diagnostic protocol to achieve affordable cross-model consensus on materials chemistry properties without redundant, resource-intensive simulations.

Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of the free-energy surface, leaving its curvature unconstrained. We introduce a framework that augments force matching with stochastic Hessian-vector product (HVP) matching, instilling second-order curvature information into CG potentials without constructing the full Hessian. We derive a decomposition of the target CG Hessian into a model-independent projected AA Hessian, precomputed once before training, and a model-dependent covariance correction computed online at negligible cost. We construct an unbiased stochastic estimator of the Hessian-matching objective by using random probe vectors. We evaluate our method by comparing against force matching on a benchmark of nine fast-folding proteins unseen during training. HVP matching outperforms plain force matching on 8 of 9 proteins on slow-mode metrics, with reductions of up to 85% in the Kullback--Leibler divergence between the CG and reference distributions along the slowest collective mode of the largest protein. Our results demonstrate that higher-order physical supervision is a practical path to more accurate and transferable CG potentials for biomolecular simulation.

Large language models rely on multihead attention, but interactions among heads remain poorly understood. We apply the Game Theoretic Free Energy Principle (GTFEP): a framework casting multiagent systems as distributed variational inference to analyze attention heads as bounded rational agents. According to GTFEP, each head minimizes its variational free energy, and collective behavior follows a Gibbs distribution over coalition structures whose energy is decomposed into Harsanyi dividends. Using a tractable approximation (uniform prior, deterministic dynamics), coalition free energy reduces to joint Shannon entropy of discretized head outputs (argmax key index). Pairwise dividends become mutual information (nonnegative), while triple dividends correspond to interaction information and can be negative. On BERT, GPT2, and Llama with GSM8K, triple dividends are consistently negative, revealing higher order redundancy. The Nash FEP correspondence guarantees that stationary points of collective free energy are epsilon Nash equilibria; thus, heads with negligible contribution can be pruned with minimal performance loss. Pruning heads with low marginal contribution reduces computational cost with minimal performance loss: for example, pruning 20% of heads in GPT2 reduces FLOPs by 18%, increases throughput by 22%, and raises perplexity only modestly (from 28.4 to 33.4 on GSM8K). Our work shows GTFEP provides a principled foundation for analyzing and optimizing transformer architectures.

Bayesian neural networks are typically trained against the evidence lower bound (ELBO), whose Jensen gap closes only when the variational posterior is exact. We instead train by local consistency: gradient descent on the Bethe free energy, driving the belief at every factor toward agreement with its neighbours rather than placing a loss on the output. The resulting objective scores each observation by its own predictive density: a strictly proper rule whose optimum is the true conditional, for any likelihood with a tractable predictive convolution. Instantiated with a Gaussian last layer over a deterministic backbone, exact inference appears as one known corner: the neural-linear marginal likelihood. That corner is evidence-optimal; the shared-cavity, free-routed interior is predictive-optimal, improving NLL and calibration over it. This instance, SCROLL (Shared-Cavity fRee-rOuting Last-Layer), is a single-pass Bayesian neural network: batchable, any-likelihood, and implicitly empirical-Bayes-prior precision, observation noise, covariance, and backbone fit in one gradient pass. Prior work enters the interior only through the ELBO and its Jensen gap, even in this conjugate setting. At a single training run and forward pass per architecture-where the validation-tuned conventional references cross-validate $λ$ and ensembles pay $5$-$50\times$ at inference-a fixed SCROLL variant is best-or-tied on NLL and calibration on 7/8 UCI regression benchmarks, and best on 4/5 across three large tabular datasets (up to 515k examples) and two frozen text/vision embeddings.

Debates about large language model post-training often treat supervised fine-tuning (SFT) as imitation and reinforcement learning (RL) as discovery. But this distinction is too coarse. What matters is whether a training procedure increases the probability of behaviors the pretrained model could already produce, or whether it changes what the model can practically reach. We argue that post-training research should distinguish between capability elicitation and capability creation. We make this distinction operational by introducing the notion of accessible support: the set of behaviors that a model can practically produce under finite budgets. Post-training that reweights behaviors within this support is capability elicitation; whereas changing the support itself corresponds to capability creation. We develop this argument through a free-energy view of post-training. SFT and RL can both be seen as reweighting a pretrained reference distribution, only with different external signals. Demonstration signals define low-energy behavior for SFT, and reward signals define low-energy behavior for RL. When the update remains close to the base model, the main effect is local reweighting, not capability creation. Within this framework, the central question is no longer whether post-training is framed as SFT or RL, but whether it reweights behaviors already within reach, or instead expands the model's reachable behavioral space through search, interaction, tool use, or the incorporation of new information.

Elastic ribbons, slender structures whose length ($L$), width ($W$), and thickness ($b$) satisfy $L \gg W \gg b$, exhibit mechanical behaviors intermediate between one-dimensional rods ($L \gg W, b$) and two-dimensional plates ($L, W \gg b$). In quadratic Kirchhoff-type rod-based frameworks, such as Discrete Elastic Rods (DER), the governing equilibrium equations are independent of width, and therefore these models cannot capture width-dependent mechanical effects. Reduced centerline-based ribbon models attempt to capture width dependence via coupled bending-twisting energies. However, their relative accuracy remain unclear due to the absence of a unified simulation framework. In this work, we formulate a framework grounded in discrete differential geometry where the energy is expressed as functions of coupled bending-twisting strain measures along the centerline, rather than a linear sum of quadratic bending and twisting energies in DER. We derive analytical gradients and Hessians of the energy that enable implicit time integration. Within this unified setting, we compare five ribbon models: Kirchhoff, Sadowsky, Wunderlich, Sano, and Audoly. As a benchmark, a straight ribbon is longitudinally constrained into a pre-buckled arch and subjected to transverse displacement, inducing a supercritical pitchfork bifurcation. Predicted bifurcation thresholds are compared against shell-based finite element simulations, with the Sano model providing the closest agreement in capturing width-dependent shifts. Our high-performance JAX-based implementation achieves $\mathcal{O}(N)$ per-iteration cost and also confirms that Sano model introduces negligible per-iteration overhead relative to standard DER.

Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical computational approaches remain prohibitively expensive due to their reliance on extensive molecular dynamics simulations, while deep learning-based methods are constrained by either less-expressive generative models or input dimensions tied to a specific system, resulting in negligible generalization. To address these challenges, we propose CARD, a generative framework that employs a novel radix-based decomposition to bijectively convert 3D coordinates into mixed discrete-continuous sequences, enabling coarse-to-fine autoregressive modeling with enhanced expressiveness. Notably, the model corresponds to a distribution with zero free energy, serving as a proposal for absolute free energy computation of arbitrary systems without relying on alchemical pathways. Experiments across diverse tasks demonstrate that CARD matches the accuracy of classical computational methods on unseen systems with diverse topologies, while achieving an approximately 40-fold speedup in inference.

The Free Energy Principle (FEP) is a leading framework for mathematically modeling self-organization and learning, while Integrated Information Theory (IIT) is a computational ontology of consciousness oriented around irreducible cause and effect. While conceptual unifications have been proposed and appear to be supported by empirical findings, the absence of a rigorous mathematical mapping places upper bounds on their precision and testability. This work proposes that information can be defined as the deviation $ψ$ of realized dynamics from a constrained maximum-caliber (MaxCal) path ensemble over a finite time horizon. Under this definition, each of the cause/effect repertoires central to IIT 3.0 emerge directly from MaxCal variational principles, allowing IIT's phenomenological calculus to be re-derived from constrained entropy-maximization (CMEP). This framework supplies a theoretical bridge to active inference, which is mathematically dual to CMEP under Langevin dynamics, and offers a principled route for extending IIT to new dynamical regimes. When the approach is applied under the Central Limit Theorem (CLT) for Markov chains and via large deviations theory (LDT) to Ising models, information $ψ$ is shown to be equivalent to prediction error under accompanying predictive coding models. This may hold relevance to the ``hill-shaped trajectory'' of $Φ$ observed in neuronal cultures adapting to sensory inputs. Together, these results provide a physically and mathematically grounded rationale for studying the convergence of FEP, IIT, and thermodynamic frameworks of cognition such as recent work grounding consciousness in violations of the Fluctuation-Dissipation Theorem (FDT).

Sparse MoE routing fails at domain transitions, where the current token belongs to one distribution and the next to another. In a controlled experiment (4 experts, 5 seeds), standard affinity routing assigns only 0.006 +/- 0.001 probability to the correct expert at the transition. Three lightweight gate modifications raise this to 0.748 +/- 0.002 (124x), cutting experts needed for 99% coverage from infeasible to a small constant: temporal memory (beta), a per-expert LIF membrane potential accumulating routing context across tokens; precision-weighted gating (Pi), a per-expert inverse variance of recent prediction error, yielding 31x contrast between reliable and unreliable experts; and anticipatory routing, a next-state predictor conditioned on the beta-accumulated hidden state. The mechanisms draw from Friston's Free Energy Principle and use LIF dynamics from spiking neural networks. An ablation across all 2^3 subsets reveals a super-additive beta x Ant interaction: anticipation alone gives nothing (+0.000 +/- 0.001); beta alone gives modest gain (+0.295 +/- 0.013); combined they close 75% of the oracle gap (+0.741 +/- 0.002, exceeding the sum by +0.446 +/- 0.014). This is structural: a stateless predictor cannot detect approaching transitions because pre-transition tokens are distributionally identical to within-domain tokens. In a character-level MoE LM (5 seeds), beta-routing reduces transition-step BPC from 6.56 +/- 0.01 (Standard) to 4.01 +/- 0.15 (beta-MoE); the beta + Ant gate places 0.86 +/- 0.02 probability on the correct domain expert before that domain appears in input, vs 0.42 +/- 0.12 for Standard MoE. Reference implementations (~200 lines each): https://github.com/russellwmy/affinity-is-not-enough

Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional methods for free energy surface sampling involve simulation in high-dimensional configuration space and projecting the resulting configurations onto the CV space. To reduce the computational costs of such sampling, we propose FES-FM, a reduced flow matching (FM) method for free energy sampling (FES). We train a dynamical transport map in the CV space, thereby enabling direct sampling of the free energy surface. For many-particle systems, we construct a prior distribution based on the Hessian at a local minimum of the potential, which ensures both rotation-translation invariance and physically meaningful configurations. We evaluate the proposed method across a variety of potential functions and collective variables. Comparative experiments demonstrate that our approach drastically reduces computational costs while delivering superior accuracy per unit sampling time.

Collective intelligence emerges across biological, physical, and artificial systems without central coordination, yet a unifying principle governing such behaviour remains elusive. The Free Energy Principle explains how individual agents adapt through variational inference, while game theory formalises strategic interactions. Here we introduce the Game-Theoretic Free Energy Principle, a unified framework showing that multi-agent systems performing local free-energy minimisation implicitly implement a stochastic game. We prove that, under bounded rationality and local information constraints, stationary points of collective free energy correspond to approximate Nash equilibria of an induced game. Conversely, a broad class of cooperative games admits a variational representation in which equilibria arise as Gibbs distributions over coalitions, establishing a bridge between Bayesian inference and strategic interaction. To characterise higher-order effects, we introduce a free-energy formulation of the Harsanyi dividend, isolating irreducible multi-agent synergy. This yields a predictive theory of cooperation, including a falsifiable non-monotonic relationship between sensory precision and agent influence. We validate this prediction across neural, biological, and artificial multi-agent systems. These results identify a common variational principle underlying inference, thermodynamics, and game-theoretic equilibrium.

Modern machine learning optimizes for accuracy without explicit treatment of internal computational cost, even though physical and biological systems operate under intrinsic energy constraints. We evaluate energy-aware learning across 2,203 experiments spanning vision, text, neuromorphic, and physiological datasets with 10 seeds per configuration and factorial statistical analysis. Three findings emerge. First, architecture alone explains negligible variance in accuracy (partial eta^2 = 0.001), while the architecture x dataset interaction is large (partial eta^2 = 0.44, p < 0.001), demonstrating that optimal architecture depends critically on task modality and rejecting the assumption of a universal best architecture. Second, a controlled lambda-sweep across lambda in {0, 1e-5, 1e-4, 1e-3, 1e-2} validates a single-parameter energy-regularized objective L = L_CE + lambda * E(theta, x): across this range, internal activation energy decreases by approximately three orders of magnitude relative to the unregularized lambda=0 baseline, with negligible accuracy change (<0.5 percentage points) on both MNIST and Fashion-MNIST. Third, energy-first architectures inspired by an action-principle framework yield 5-33% within-modality training-efficiency gains over conventional baselines. These results emerge from a research program that interprets learning through a structural correspondence between the action functional in classical mechanics, free energy in statistical physics, and KL-regularized objectives in variational inference. We frame this correspondence as a design hypothesis, not a derivation.

We propose an Expected Free Energy-based acquisition function for Bayesian optimization to solve the joint learning and optimization problem, i.e., optimize and learn the underlying function simultaneously. We show that, under specific assumptions, Expected Free Energy reduces to Upper Confidence Bound, Lower Confidence Bound, and Expected Information Gain. We prove that Expected Free Energy has unbiased convergence guarantees for concave functions. Using the results from these derivations, we introduce a curvature-aware update law for Expected Free Energy and show its proof of concept using a system identification problem on a Van der Pol oscillator. On a two-dimensional benchmark with an oscillatory landscape, our adaptive Expected Free Energy acquisition achieves competitive performance in both regret and mean squared error, unlike the typical acquisition functions that perform well in only one metric.

The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), MetaDiff (a batchwise analogue for metadynamics), and $Δ$G-Diff (free-energy differences via tilted ensembles). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system-closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.

Autonomous robotic navigation in real-world environments requires exploration to acquire environmental information as well as goal-directed navigation in order to reach specified targets. Active inference (AIF) based on the free-energy principle provides a unified framework for these behaviors by minimizing the expected free energy (EFE), thereby combining epistemic and extrinsic values. To realize this practically, we propose a deep AIF framework that integrates a diffusion policy as the policy model and a multiple timescale recurrent state-space model (MTRSSM) as the world model. The diffusion policy generates diverse candidate actions while the MTRSSM predicts their long-horizon consequences through latent imagination, enabling action selection that minimizes EFE. Real-world navigation experiments, including baseline comparisons, component ablations, and robustness evaluations, demonstrated that our framework achieved higher success rates and fewer collisions, particularly in exploration-demanding scenarios. These results highlight how AIF based on EFE minimization can unify exploration and goal-directed navigation in real-world robotic settings.

Navigation in the natural world is a feat of adaptive inference, where biological organisms maintain goal-directed behaviour despite noisy and incomplete sensory streams. Central to this ability is the Free Energy Principle (FEP), which posits that perception is a generative process where the brain minimises Variational Free Energy (VFE) to maintain accurate internal models of the world. While Deep Neural Networks (DNNs) have served as powerful analogues for biological brains, they typically lack the real-time plasticity required to handle abrupt sensory shifts. We introduce FEP-Nav, a biologically inspired framework for real-time perceptual adaptation in robust visual navigation. Motivated by the decomposition of VFE into prediction error and Bayesian surprise, FEP-Nav combines a Top-down Decoder, which provides an internal expectation of uncorrupted sensory input, with Adaptive Normalisation, which adjusts shifted feature distributions toward prior statistics. We interpret reconstruction and normalisation as approximate mechanisms for reducing the corresponding VFE-related terms during inference without gradient-based updates. Experiments across simulated and real-world visual corruptions show that FEP-Nav restores performance lost under visual corruption, outperforming non-adaptive baselines and strong adaptive methods. These results suggest that variational principles can provide a useful design perspective for robust autonomous behaviour under degraded sensory conditions.