Daily Papers

Bayesian Neural Networks with Latent Variables (BNN+LVs) capture predictive uncertainty by explicitly modeling model uncertainty (via priors on network weights) and environmental stochasticity (via a latent input noise variable). In this work, we first show that BNN+LV suffers from a serious form of non-identifiability: explanatory power can be transferred between the model parameters and latent variables while fitting the data equally well. We demonstrate that as a result, in the limit of infinite data, the posterior mode over the network weights and latent variables is asymptotically biased away from the ground-truth. Due to this asymptotic bias, traditional inference methods may in practice yield parameters that generalize poorly and misestimate uncertainty. Next, we develop a novel inference procedure that explicitly mitigates the effects of likelihood non-identifiability during training and yields high-quality predictions as well as uncertainty estimates. We demonstrate that our inference method improves upon benchmark methods across a range of synthetic and real data-sets.

Activation steering methods are widely used to control large language model (LLM) behavior and are often interpreted as revealing meaningful internal representations. This interpretation assumes that steering directions are identifiable and uniquely recoverable from input-output behavior. We show that, under white-box single-layer access, steering vectors are fundamentally non-identifiable due to large equivalence classes of behaviorally indistinguishable interventions. Empirically, we find that orthogonal perturbations achieve near-equivalent efficacy with negligible effect sizes across multiple models and traits, with pre-trained semantic classifiers confirming equivalence at the output level. We estimate null-space dimensionality via SVD of activation covariance matrices and validate that equivalence holds robustly throughout the operationally relevant steering range. Critically, we show that non-identifiability is a robust geometric property that persists across diverse prompt distributions. These findings reveal fundamental interpretability limits and highlight the need for structural constraints beyond behavioral testing to enable reliable alignment interventions.

Automated evaluation of free-form outputs from large language models (LLMs) is challenging because many distinct answers can be equally valid. A common practice is to use LLMs themselves as judges, but the theoretical properties of this approach are not yet well understood. We show that a geometric framework that represents both judges and candidates as points on a probability simplex can provide helpful insight on what is or is not identifiable using LLM judges. Our theoretical analysis uncovers a "phase transition" in ranking identifiability: for binary scoring systems, true rankings are identifiable even with weak judges under mild assumptions, while rankings become non-identifiable for three or more scoring levels even with infinite data, absent additional prior knowledge. This non-identifiability highlights how uncertainty in rankings stems from not only aleatoric uncertainty (i.e., inherent stochasticity in the data) but also epistemic uncertainty regarding which assumptions hold, an aspect that has received limited attention until now. To integrate both types of uncertainty, we use Bayesian inference to encode assumptions as priors and conduct sensitivity analysis of ranking estimates and credible intervals. Empirical evaluations across multiple benchmarks demonstrate that Bayesian inference yields more accurate rankings and substantially improves coverage rates. These results underscore the importance of taking a more holistic approach to uncertainty quantification when using LLMs as judges.

Recent proposals advocate using keystroke timing signals, specifically the coefficient of variation (δ) of inter-keystroke intervals, to distinguish human-composed text from AI-generated content. We demonstrate that this class of defenses is insecure against two practical attack classes: the copy-type attack, in which a human transcribes LLM-generated text producing authentic motor signals, and timing-forgery attacks, in which automated agents sample inter-keystroke intervals from empirical human distributions. Using 13,000 sessions from the SBU corpus and three timing-forgery variants (histogram sampling, statistical impersonation, and generative LSTM), we show all attacks achieve ge99.8% evasion rates against five classifiers. While detectors achieve AUC=1.000 against fully-automated injection, they classify ge99.8% of attack samples as human with mean confidence ge0.993. We formalize a non-identifiability result: when the detector observes only timing, the mutual information between features and content provenance is zero for copy-type attacks. Although composition and transcription produce statistically distinguishable motor patterns (Cohen's d=1.28), both yield δ values 2-4x above detection thresholds, rendering the distinction security-irrelevant. These systems confirm a human operated the keyboard, but not whether that human originated the text. Securing provenance requires architectures that bind the writing process to semantic content.

Large language models (LLMs) trained with Reinforcement Learning from Human Feedback (RLHF) have demonstrated remarkable capabilities, but their underlying reward functions and decision-making processes remain opaque. This paper introduces a novel approach to interpreting LLMs by applying inverse reinforcement learning (IRL) to recover their implicit reward functions. We conduct experiments on toxicity-aligned LLMs of varying sizes, extracting reward models that achieve up to 80.40% accuracy in predicting human preferences. Our analysis reveals key insights into the non-identifiability of reward functions, the relationship between model size and interpretability, and potential pitfalls in the RLHF process. We demonstrate that IRL-derived reward models can be used to fine-tune new LLMs, resulting in comparable or improved performance on toxicity benchmarks. This work provides a new lens for understanding and improving LLM alignment, with implications for the responsible development and deployment of these powerful systems.

Multiple epidemic waves are often taken as evidence that simple compartmental models are structurally inadequate. Yet the key question is not whether a simple model can reproduce multiple peaks, but how much time-varying structure is minimally required to preserve observed epidemic-wave patterns and what can legitimately be inferred from such a representation. Using the susceptible-infectious-removed (SIR) model, we develop a framework for peak-preserving dynamic parsimony linking dynamical systems, inverse problems, statistical inference, and infectious-disease modeling. We establish exact multi-wave representability under time-varying transmission, characterize conditions for epidemic peaks and resurgence, and show the incidence-only non-identifiability of time-varying transmission and removal rates. Our main methodological contribution is minimal peak-preserving complexity (MPPC): the smallest dimension of a positive time-varying transmission function whose posterior-predictive trajectories preserve salient features, including peak count, timing, height, trough depth, and whole-curve agreement. We estimate MPPC using peak-aware approximate Bayesian computation and evaluate it through six reproducible stress tests, a Philippine COVID-19 reported-case proof of concept, and short-term future-knot projection. Across diverse data-generating mechanisms, low-dimensional time-varying SIR models can preserve aggregate epidemic-wave topology with modest dynamic complexity. However, accurate trajectory compression does not imply recovery of the underlying mechanism or reliable long-term counterfactual prediction. The framework therefore separates four often-conflated questions: representability, minimal dynamic complexity, mechanistic identifiability, and projection validity, providing a basis for parsimonious modeling of complex epidemic trajectories.

Structural Causal Models (SCM) are a powerful framework for describing complicated dynamics across the natural sciences. A particularly elegant way of interpreting SCMs is do-Shapley, a game-theoretic method of quantifying the average effect of d variables across exponentially many interventions. Like Shapley values, computing do-Shapley values generally requires evaluating exponentially many terms. The foundation of our work is a reformulation of do-Shapley values in terms of the irreducible sets of the underlying SCM. Leveraging this insight, we can exactly compute do-Shapley values in time linear in the number of irreducible sets r, which itself can range from d to 2^d depending on the graph structure of the SCM. Since r is unknown a priori, we complement the exact algorithm with an estimator that, like general Shapley value estimators, can be run with any query budget. As the query budget approaches r, our estimators can produce more accurate estimates than prior methods by several orders of magnitude, and, when the budget reaches r, return the Shapley values up to machine precision. Beyond computational speed, we also reduce the identification burden: we prove that non-parametric identifiability of do-Shapley values requires only the identification of interventional effects for the d singleton coalitions, rather than all classes.

Deep representations have shown promising performance when transferred to downstream tasks in a black-box manner. Yet, their inherent lack of interpretability remains a significant challenge, as these features are often opaque to human understanding. In this paper, we propose Non-negative Contrastive Learning (NCL), a renaissance of Non-negative Matrix Factorization (NMF) aimed at deriving interpretable features. The power of NCL lies in its enforcement of non-negativity constraints on features, reminiscent of NMF's capability to extract features that align closely with sample clusters. NCL not only aligns mathematically well with an NMF objective but also preserves NMF's interpretability attributes, resulting in a more sparse and disentangled representation compared to standard contrastive learning (CL). Theoretically, we establish guarantees on the identifiability and downstream generalization of NCL. Empirically, we show that these advantages enable NCL to outperform CL significantly on feature disentanglement, feature selection, as well as downstream classification tasks. At last, we show that NCL can be easily extended to other learning scenarios and benefit supervised learning as well. Code is available at https://github.com/PKU-ML/non_neg.

Open quantum systems lose energy and phase coherence through different dissipative processes, but these processes can produce overlapping dynamical signatures. The Liouvillian spectrum summarizes how such a system relaxes, yet it is not obvious how much of that spectrum is needed to distinguish the underlying dissipation rates. We study this question for amplitude damping and dephasing in a six-qubit Lindblad model whose spectrum can be derived analytically. We retain only the slowest non-steady spectral modes and ask how many are required before each dissipative rate becomes recoverable. We show that population modes contain no dephasing information, which creates a lower bound of D = 2^n retained modes for uniform dephasing identifiability in the relevant rate regime. The measured recovery threshold reaches this bound at n = 4,5,6, while n = 3 remains above it. At n = 6, least squares achieves a mean joint absolute error of order 10^-9, compared with 4.355 x 10^-4 for four tabular learning methods. Robustness tests show that this advantage weakens when the spectra are perturbed and when a transverse field breaks the commuting structure. These results show that the amount and structure of retained spectral information can determine whether dissipative parameters are recoverable, independently of the estimator used. The present conclusions apply to noise-free simulator spectra rather than measurement-derived spectra.

We study the class of location-scale or heteroscedastic noise models (LSNMs), in which the effect Y can be written as a function of the cause X and a noise source N independent of X, which may be scaled by a positive function g over the cause, i.e., Y = f(X) + g(X)N. Despite the generality of the model class, we show the causal direction is identifiable up to some pathological cases. To empirically validate these theoretical findings, we propose two estimators for LSNMs: an estimator based on (non-linear) feature maps, and one based on neural networks. Both model the conditional distribution of Y given X as a Gaussian parameterized by its natural parameters. When the feature maps are correctly specified, we prove that our estimator is jointly concave, and a consistent estimator for the cause-effect identification task. Although the the neural network does not inherit those guarantees, it can fit functions of arbitrary complexity, and reaches state-of-the-art performance across benchmarks.

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

The sufficiently scattered condition (SSC) is a key condition in the study of identifiability of various matrix factorization problems, including nonnegative, minimum-volume, symmetric, simplex-structured, and polytopic matrix factorizations. The SSC allows one to guarantee that the computed matrix factorization is unique/identifiable, up to trivial ambiguities. However, this condition is NP-hard to check in general. In this paper, we show that it can however be checked in a reasonable amount of time in realistic scenarios, when the factorization rank is not too large. This is achieved by formulating the problem as a non-convex quadratic optimization problem over a bounded set. We use the global non-convex optimization software Gurobi, and showcase the usefulness of this code on synthetic data sets and on real-world hyperspectral images.

Recent advances to combine structured regression models and deep neural networks for better interpretability, more expressiveness, and statistically valid uncertainty quantification demonstrate the versatility of semi-structured neural networks (SSNs). We show that techniques to properly identify the contributions of the different model components in SSNs, however, lead to suboptimal network estimation, slower convergence, and degenerated or erroneous predictions. In order to solve these problems while preserving favorable model properties, we propose a non-invasive post-hoc orthogonalization (PHO) that guarantees identifiability of model components and provides better estimation and prediction quality. Our theoretical findings are supported by numerical experiments, a benchmark comparison as well as a real-world application to COVID-19 infections.

The algebraic diversity framework generalizes temporal averaging over multiple observations to algebraic group action on a single observation for second-order statistical estimation. The central open problem in this framework is group selection: given an M-dimensional observation with unknown covariance structure, find the finite group whose spectral decomposition best matches the covariance. Naive enumeration of all subgroups of the symmetric group S_M requires exponential time in M. We prove that this combinatorial problem reduces to a generalized eigenvalue problem derived from the double commutator of the covariance matrix, yielding a polynomial-time algorithm with complexity O(d^2M^2 + d^3), where d is the dimension of a generator basis. The minimum eigenvector of the double-commutator matrix directly constructs the optimal group generator in closed form, with no iterative optimization. The reduction is exact: the double-commutator minimum eigenvalue is zero if and only if the optimal generator lies in the span of the basis, and its magnitude provides a certifiable optimality gap when it does not. This problem does not appear in the standard catalogs of computational complexity (Garey and Johnson, 1979) and represents a new class linking group theory, matrix analysis, and statistical estimation. We establish connections to independent component analysis (JADE), structured matrix nearness problems, and simultaneous matrix diagonalization, and we show that the double-commutator formulation is the unique approach that is simultaneously polynomial-time, closed-form, and certifiable. We extend the framework to non-Abelian symmetry recovery via a Sequential GEVP with deflation, and add two identifiability theorems characterizing the commutant-lattice ambiguity and the dichotomy on whether Aut(R) recovers a generative subgroup or only a supergroup.

The remarkable achievements of large language models (LLMs) have led many to conclude that they exhibit a form of intelligence. This is as opposed to explanations of their capabilities based on their ability to perform relatively simple manipulations of vast volumes of data. To illuminate the distinction between these explanations, we introduce a novel generative model that generates tokens on the basis of human-interpretable concepts represented as latent discrete variables. Under mild conditions, even when the mapping from the latent space to the observed space is non-invertible, we establish an identifiability result, i.e., the representations learned by LLMs through next-token prediction can be approximately modeled as the logarithm of the posterior probabilities of these latent discrete concepts given input context, up to an invertible linear transformation. This theoretical finding not only provides evidence that LLMs capture underlying generative factors, but also provide a unified prospective for understanding of the linear representation hypothesis. Taking this a step further, our finding motivates a reliable evaluation of sparse autoencoders by treating the performance of supervised concept extractors as an upper bound. Pushing this idea even further, it inspires a structural variant that enforces dependence among latent concepts in addition to promoting sparsity. Empirically, we validate our theoretical results through evaluations on both simulation data and the Pythia, Llama, and DeepSeek model families, and demonstrate the effectiveness of our structured sparse autoencoder.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.