John Paisley

Jian Xu, Chao Li, Guang Lin et al.

Two recent results have reshaped quantum Gaussian processes (QGPs). On the one hand, \citet{lowe2025assessing} rule out the exponential speedups claimed by HHL-based QGP regression in the typical, well-conditioned regime; on the other, an independent line of work shows that highly expressive quantum kernels suffer posterior pathologies that break Bayesian optimization. We show that these seemingly unrelated phenomena are governed by the same quantity: the normalized spectral entropy $S(K)/\log n$ of the kernel Gram matrix. We prove a Cauchy--Schwarz tail bound on Nyström approximation error, a finite-sample variance-contraction identity in terms of Bach's degrees of freedom $d_σ(K)$, and a characterization of the \emph{target-dependent} optimal entropy via the intrinsic dimension of the target in the kernel eigenbasis. Empirically, the diagnostic is kernel-agnostic: hardware-efficient, matchgate, IQP \emph{and} RBF/Matérn/RFF/deep-kernel families all collapse onto identical $S/\log n$ curves on dequantization, ECE, and variance-contraction panels. The NLL sweet spot lives at high entropy for smooth targets and at low entropy for band-limited quantum-data targets. The diagnostic transfers from simulator to IBM Heron hardware with median absolute error $3.2\%$ and mean $5.2\%$ in $S/\log n$ across $24$ configurations at $n_q = 4$, with matchgate and IQP within $5\%$ mean and a single HE configuration returning a $30\%$ outlier that drops to $0.5\%$ on rerun (attributed to calibration drift); the same diagnostic transfers to a second Heron backend (mean error $2.7\%$) and to a $n_q = 6$ scale-up on the original backend (mean error $1.7\%$). No error mitigation is applied throughout.

Jian Xu, Delu Zeng, John Paisley et al.

Generative models -- diffusion and flow matching -- are increasingly used to solve partial differential equation (PDE) inverse problems, enforcing the governing physics as a \emph{hard constraint} (via projection or guidance) and reporting the resulting samples as a Bayesian posterior with calibrated uncertainty. We show that this widely adopted recipe samples the wrong distribution. Conditioning a generative prior on a hard PDE constraint is conditioning on a measure-zero manifold -- an operation that is intrinsically ambiguous (the Borel--Kolmogorov paradox) and whose physically correct resolution, the small-residual-noise limit, carries a co-area (Fixman) Jacobian factor $[det(JJ^{\top})]^{-1/2}$ that projection- and guidance-based methods silently omit. We make the bias precise, show that it grows with the heterogeneity of the constraint sensitivity, and validate it on controlled problems against an \emph{i.i.d.} ground-truth arbiter. The omitted factor is not a second-order detail: removing it inflates the posterior error to $20\times$ the sampling-noise floor; minimal-displacement projection (as in PCFM) is biased at $9\times$ the floor; and a naive scalar reweighting does not fix it. We introduce \textbf{CoCoS}, a measure-aware constrained sampler that targets the correct co-area posterior, and show that it matches the gold-standard posterior to within sampling noise. Our results imply that ``satisfying the physics'' is not the same as ``sampling the posterior,'' and give a principled correction for uncertainty-aware scientific inference.

Wei Chen, Jiacheng Li, Shigui Li et al.

Score-based methods are powerful across machine learning, but they face a paradox: theoretically path-independent, yet practically path-dependent. We resolve this by proving that practical training objectives differ from the ideal, ground-truth objective by a crucial, overlooked term: the path variance of the score function. We propose the MVP (**M**imum **V**ariance **P**ath) Principle to minimize this path variance. Our key contribution is deriving a closed-form expression for the variance, making optimization tractable. By parameterizing the path with a flexible Kumaraswamy Mixture Model, our method learns data-adaptive, low-variance paths without heuristic manual selection. This principled optimization of the complete objective yields more accurate and stable estimators, establishing new state-of-the-art results on challenging benchmarks and providing a general framework for optimizing score-based interpolation. Our code can be found in https://github.com/Hoemr/OpenDRE.git.

Jian Xu, Shian Du, Junmei Yang et al.

Recently, Gaussian processes have been used to model the vector field of continuous dynamical systems, referred to as GPODEs, which are characterized by a probabilistic ODE equation. Bayesian inference for these models has been extensively studied and applied in tasks such as time series prediction. However, the use of standard GPs with basic kernels like squared exponential kernels has been common in GPODE research, limiting the model's ability to represent complex scenarios. To address this limitation, we introduce normalizing flows to reparameterize the ODE vector field, resulting in a data-driven prior distribution, thereby increasing flexibility and expressive power. We develop a data-driven variational learning algorithm that utilizes analytically tractable probability density functions of normalizing flows, enabling simultaneous learning and inference of unknown continuous dynamics. Additionally, we also apply normalizing flows to the posterior inference of GP ODEs to resolve the issue of strong mean-field assumptions in posterior inference. By applying normalizing flows in both these ways, our model improves accuracy and uncertainty estimates for Bayesian Gaussian Process ODEs. We validate the effectiveness of our approach on simulated dynamical systems and real-world human motion data, including time series prediction and missing data recovery tasks. Experimental results show that our proposed method effectively captures model uncertainty while improving accuracy.

Wei Chen, Yubing Wu, Junmei Yang et al.

Preference optimization is widely used to align large language models (LLMs) with human preferences. However, many margin-based objectives suppress the chosen response along with the rejected one, a phenomenon known as likelihood displacement, and no general mechanism currently prevents this across objectives. We bridge this gap by presenting a unified \emph{incentive-score decomposition} of preference optimization, revealing that diverse objectives share identical local update directions and differ only in their scalar weighting coefficients. Building on this decomposition, by analyzing the dynamics of the chosen/rejected likelihoods, we identify the \emph{disentanglement band} (DB), a simple, testable condition that characterizes when training can avoid likelihood displacement by realizing the preferred pathway: suppressing the loser while maintaining the winner, possibly after an initial transient. Leveraging the DB, we propose a plug-and-play \emph{reward calibration} (RC) that adaptively rebalances chosen versus rejected updates to satisfy the DB and mitigate likelihood displacement, without redesigning the base objective. Empirical results show that RC steers training toward more disentangled dynamics and often improves downstream performance across a range of objectives. Our code is available at https://github.com/IceyWuu/DisentangledPreferenceOptimization.

San Gultekin, Brendan Kitts, Aaron Flores et al.

We introduce a novel nonlinear Kalman filter that utilizes reparametrization gradients. The widely used parametric approximation is based on a jointly Gaussian assumption of the state-space model, which is in turn equivalent to minimizing an approximation to the Kullback-Leibler divergence. It is possible to obtain better approximations using the alpha divergence, but the resulting problem is substantially more complex. In this paper, we introduce an alternate formulation based on an energy function, which can be optimized instead of the alpha divergence. The optimization can be carried out using reparametrization gradients, a technique that has recently been utilized in a number of deep learning models.

Arunesh Mittal, Kai Yang, Paul Sajda et al.

Several approximate inference methods have been proposed for deep discrete latent variable models. However, non-parametric methods which have previously been successfully employed for classical sparse coding models have largely been unexplored in the context of deep models. We propose a non-parametric iterative algorithm for learning discrete latent representations in such deep models. Additionally, to learn scale invariant discrete features, we propose local data scaling variables. Lastly, to encourage sparsity in our representations, we propose a Beta-Bernoulli process prior on the latent factors. We evaluate our spare coding model coupled with different likelihood models. We evaluate our method across datasets with varying characteristics and compare our results to current amortized approximate inference methods.

Jian Xu, Delu Zeng, John Paisley et al.

Approximate inference over inducing variables is the central computational bottleneck of Deep Gaussian Processes (DGPs). Existing methods either fit an explicit density $q_ϕ(\bU)$ by an ELBO (DSVI, IPVI, DDVI, DBVI) or sample by MCMC (SGHMC). We instead frame DGP inference as \emph{posterior transport}: learn a deterministic sampler that maps a tractable reference measure to posterior-relevant inducing variables, regularised by a path prior derived from the Doob-bridged reference diffusion. Our realisation, \textbf{OM-Path} (formally FBVI-bridge-Path), uses Song's probability-flow ODE applied to DBVI's Doob-bridged forward SDE; the reference drift is closed-form from the bridge marginal coefficients (no score matching) and the path regulariser is the \textbf{Onsager--Machlup action}. At the finite-$ε$ value used at training, the objective is the negative log unnormalised density of a tempered Doob-bridge path posterior, and Theorem 1 identifies it with the same posterior's small-noise MAP path via the Freidlin--Wentzell LDP. Two strict path-space ELBO variants on the same bridge backbone (FFJORD log-det; OM-regularised CNF) are derived as ablations. Under a matched-seed paired Wilcoxon test against DBVI on seven UCI regression benchmarks, OM-Path delivers statistically significant wins on the two largest datasets (\textit{power}: $p\!=\!0.014$, NLL $\mathbf{0.012}$ matching the DSVI baseline of $0.017$; \textit{protein}: $p\!=\!0.002$, RMSE $\mathbf{0.716}$ vs.\ $0.764$, NLL $\mathbf{1.086}$ vs.\ $1.149$), statistical ties on \textit{yacht} / \textit{qsar}, and concedes \textit{boston} / \textit{energy} / \textit{concrete} to DBVI on small-$N$ noisy data. The strict-ELBO variants do not clear DBVI on any UCI metric: in this regime, reducing the variance of the path objective dominates exact-density tracking.

Jian Xu, Delu Zeng, John Paisley

Deep Gaussian processes (DGPs) provide a robust paradigm for Bayesian deep learning. In DGPs, a set of sparse integration locations called inducing points are selected to approximate the posterior distribution of the model. This is done to reduce computational complexity and improve model efficiency. However, inferring the posterior distribution of inducing points is not straightforward. Traditional variational inference approaches to posterior approximation often lead to significant bias. To address this issue, we propose an alternative method called Denoising Diffusion Variational Inference (DDVI) that uses a denoising diffusion stochastic differential equation (SDE) to generate posterior samples of inducing variables. We rely on score matching methods for denoising diffusion model to approximate score functions with a neural network. Furthermore, by combining classical mathematical theory of SDEs with the minimization of KL divergence between the approximate and true processes, we propose a novel explicit variational lower bound for the marginal likelihood function of DGP. Through experiments on various datasets and comparisons with baseline methods, we empirically demonstrate the effectiveness of DDVI for posterior inference of inducing points for DGP models.

Wei Chen, Qibin Zhao, John Paisley et al.

Density ratio estimation (DRE) is a useful tool for quantifying discrepancies between probability distributions, but existing approaches often involve a trade-off between estimation quality and computational efficiency. Classical direct DRE methods are usually efficient at inference time, yet their performance can seriously deteriorate when the discrepancy between distributions is large. In contrast, score-based DRE methods often yield more accurate estimates in such settings, but they typically require considerable repeated function evaluations and numerical integration. We propose One-step Score-based Density Ratio Estimation (OS-DRE), a partly analytic and solver-free framework designed to combine these complementary advantages. OS-DRE decomposes the time score into spatial and temporal components, representing the latter with an analytic radial basis function (RBF) frame. This formulation converts the otherwise intractable temporal integral into a closed-form weighted sum, thereby removing the need for numerical solvers and enabling DRE with only one function evaluation. We further analyze approximation conditions for the analytic frame, and establish approximation error bounds for both finitely and infinitely smooth temporal kernels, grounding the framework in existing approximation theory. Experiments across density estimation, continual Kullback-Leibler and mutual information estimation, and near out-of-distribution detection demonstrate that OS-DRE offers a favorable balance between estimation quality and inference efficiency.

Jian Xu, Chao Li, Delu Zeng et al.

Estimating an $N \times N$ quantum kernel from circuit fidelities requires $Θ(N^2 S)$ measurement shots, the dominant bottleneck for deployment on near-term hardware. Existing budget-saving methods (Nyström-QKE, ShoFaR, kernel-target alignment) sub-sample \emph{which} entries to measure but allocate shots \emph{uniformly} within their chosen subset, ignoring how much each entry drives the downstream classifier. We close this gap with two contributions. \textbf{First, a complete regime decomposition} for shot-budgeted quantum kernel learning: a principled menu of when each allocator wins. Our method, \emph{AQKA}, dominates the budget-limited regime ($B \lesssim 16 n_{\mathrm{pairs}}$) on sparse-sensitivity KRR, with the gap \emph{growing} from $+8$ to $+25$ pts over uniform as $N$ scales $225{\to}1000$ and reaching $+26$--$32$ pts on an \texttt{ibm\_pittsburgh} (156-qubit Heron) hardware kernel; Nyström-QKE wins at saturating budgets on planted-sparse via low-rank reconstruction; ShoFaR is competitive only at extreme low budgets. \textbf{Second, a closed-form pair-level acquisition theory}: $s_{ij}^{\star} \propto |g_{ij}|\sqrt{K_{ij}(1-K_{ij})}$ with explicit gradient $g_{ij}$ for KRR (Lemma~1, $|β_iα_j+β_jα_i|\sqrt{K_{ij}(1-K_{ij})}$) and SVM via the envelope theorem ($|η_i^*η_j^*|\sqrt{K_{ij}(1-K_{ij})}$); a \emph{corrected} sparsity-aware Cauchy--Schwarz rate $ρ\le 2m/N$ matching empirics (vs.\ the naive $m^2/N^2$); an explicit-constant plug-in regret bound (Theorem~2); and a tighter SVM ceiling $ρ^{\mathrm{SVM}} \le m_{\mathrm{sv}}^2/N^2$. We close with the first multi-seed live online adaptive shot allocation on quantum hardware: $+17.0 \pm 4.8$ pts at $N{=}20$ on \texttt{ibm\_aachen} ($3.5σ$, 5 seeds), with the advantage holding at $N{=}30$ at higher budget on \texttt{ibm\_berlin} ($+14.0 \pm 8.5$ pts, 5 seeds).

Wei Chen, Shian Du, Shigui Li et al.

Normalizing Flows (NFs) are widely used in deep generative models for their exact likelihood estimation and efficient sampling. However, they require substantial memory since the latent space matches the input dimension. Multi-scale architectures address this by progressively reducing latent dimensions while preserving reversibility. Existing multi-scale architectures use simple, static channel-wise splitting, limiting expressiveness. To improve this, we introduce a regularized, feature-dependent $\mathtt{Shuffle}$ operation and integrate it into vanilla multi-scale architecture. This operation adaptively generates channel-wise weights and shuffles latent variables before splitting them. We observe that such operation guides the variables to evolve in the direction of entropy increase, hence we refer to NFs with the $\mathtt{Shuffle}$ operation as \emph{Entropy-Informed Weighting Channel Normalizing Flow} (EIW-Flow). Extensive experiments on CIFAR-10, CelebA, ImageNet, and LSUN demonstrate that EIW-Flow achieves state-of-the-art density estimation and competitive sample quality for deep generative modeling, with minimal computational overhead.

Jian Xu, Zhiqi Lin, Min Chen et al.

Deep Gaussian process models typically employ discrete hierarchies, but recent advancements in differential Gaussian processes (DiffGPs) have extended these models to infinite depths. However, existing DiffGP approaches often overlook the uncertainty in kernel hyperparameters by treating them as fixed and time-invariant, which degrades the model's predictive performance and neglects the posterior distribution. In this work, we introduce a fully Bayesian framework that models kernel hyperparameters as random variables and utilizes coupled stochastic differential equations (SDEs) to jointly learn their posterior distributions alongside those of inducing points. By incorporating the estimation uncertainty of hyperparameters, our method significantly enhances model flexibility and adaptability to complex dynamic systems. Furthermore, we employ a black-box adaptive SDE solver with a neural network to achieve realistic, time varying posterior approximations, thereby improving the expressiveness of the variational posterior. Comprehensive experimental evaluations demonstrate that our approach outperforms traditional methods in terms of flexibility, accuracy, and other key performance metrics. This work not only provides a robust Bayesian extension to DiffGP models but also validates its effectiveness in handling intricate dynamic behaviors, thereby advancing the applicability of Gaussian process models in diverse real-world scenarios.

Jian Xu, Zhiqi Lin, Shigui Li et al.

Bayesian Last Layer (BLL) models focus solely on uncertainty in the output layer of neural networks, demonstrating comparable performance to more complex Bayesian models. However, the use of Gaussian priors for last layer weights in Bayesian Last Layer (BLL) models limits their expressive capacity when faced with non-Gaussian, outlier-rich, or high-dimensional datasets. To address this shortfall, we introduce a novel approach that combines diffusion techniques and implicit priors for variational learning of Bayesian last layer weights. This method leverages implicit distributions for modeling weight priors in BLL, coupled with diffusion samplers for approximating true posterior predictions, thereby establishing a comprehensive Bayesian prior and posterior estimation strategy. By delivering an explicit and computationally efficient variational lower bound, our method aims to augment the expressive abilities of BLL models, enhancing model accuracy, calibration, and out-of-distribution detection proficiency. Through detailed exploration and experimental validation, We showcase the method's potential for improving predictive accuracy and uncertainty quantification while ensuring computational efficiency.

Jian Xu, Delu Zeng, John Paisley

Recently, a sparse version of Student-t Processes, termed sparse variational Student-t Processes, has been proposed to enhance computational efficiency and flexibility for real-world datasets using stochastic gradient descent. However, traditional gradient descent methods like Adam may not fully exploit the parameter space geometry, potentially leading to slower convergence and suboptimal performance. To mitigate these issues, we adopt natural gradient methods from information geometry for variational parameter optimization of Student-t Processes. This approach leverages the curvature and structure of the parameter space, utilizing tools such as the Fisher information matrix which is linked to the Beta function in our model. This method provides robust mathematical support for the natural gradient algorithm when using Student's t-distribution as the variational distribution. Additionally, we present a mini-batch algorithm for efficiently computing natural gradients. Experimental results across four benchmark datasets demonstrate that our method consistently accelerates convergence speed.

Jian Xu, Wei Chen. Chao Li, Jingyuan Zheng et al.

In quantum machine learning (QML), classical data are often encoded as quantum pure states and processed directly as quantum representations, motivating representation-level generative modeling that samples new quantum states from an underlying pure-state ensemble rather than re-preparing them from perturbed classical inputs. However, extending \emph{score-based} diffusion models with well-defined reverse-time samplers to quantum pure-state ensembles remains challenging, due to the non-Euclidean geometry of the complex projective space $\mathbb{CP}^{d-1}$ and the intractability of transition densities. We propose \emph{Stochastic Schrödinger Diffusion Models} (SSDMs), an intrinsic score-based generative framework on $\mathbb{CP}^{d-1}$ endowed with the Fubini--Study (FS) metric. SSDMs formulate a forward Riemannian diffusion with a stochastic Schrödinger equation (SSE) realization, and derive reverse-time dynamics driven by the Riemannian score $\nabla_{\mathrm{FS}} \log p_t$. To enable training without analytic transition densities, we introduce a local-time objective based on a local Euclidean Ornstein--Uhlenbeck approximation in FS normal coordinates, yielding an analytic teacher score mapped back to the manifold. Experiments show that SSDMs faithfully capture target pure-state ensemble statistics, including observable moments, overlap-kernel MMD, and entanglement measures, and that SSDM-generated quantum representations improve downstream QML generalization via representation-level data augmentation.

Wei Zhang, Brian Barr, John Paisley

Deep neural networks have revolutionized many fields, but their black-box nature also occasionally prevents their wider adoption in fields such as healthcare and finance, where interpretable and explainable models are required. The recent development of Neural Additive Models (NAMs) is a significant step in the direction of interpretable deep learning for tabular datasets. In this paper, we propose a new subclass of NAMs that use a single-layer neural network construction of the Gaussian process via random Fourier features, which we call Gaussian Process Neural Additive Models (GP-NAM). GP-NAMs have the advantage of a convex objective function and number of trainable parameters that grows linearly with feature dimensionality. It suffers no loss in performance compared to deeper NAM approaches because GPs are well-suited for learning complex non-parametric univariate functions. We demonstrate the performance of GP-NAM on several tabular datasets, showing that it achieves comparable or better performance in both classification and regression tasks with a large reduction in the number of parameters.

Wei Chen, Shigui Li, Jiacheng Li et al.

Density ratio estimation is fundamental to tasks involving $f$-divergences, yet existing methods often fail under significantly different distributions or inadequately overlapping supports -- the density-chasm and the support-chasm problems. Additionally, prior approaches yield divergent time scores near boundaries, leading to instability. We design $\textbf{D}^3\textbf{RE}$, a unified framework for \textbf{robust}, \textbf{stable} and \textbf{efficient} density ratio estimation. We propose the dequantified diffusion bridge interpolant (DDBI), which expands support coverage and stabilizes time scores via diffusion bridges and Gaussian dequantization. Building on DDBI, the proposed dequantified Schr{ö}dinger bridge interpolant (DSBI) incorporates optimal transport to solve the Schr{ö}dinger bridge problem, enhancing accuracy and efficiency. Our method offers uniform approximation and bounded time scores in theory, and outperforms baselines empirically in mutual information and density estimation tasks.

Wei Zhang, Brian Barr, John Paisley

Explainable machine learning has attracted much interest in the community where the stakes are high. Counterfactual explanations methods have become an important tool in explaining a black-box model. The recent advances have leveraged the power of generative models such as an autoencoder. In this paper, we propose a novel method using a Gaussian process to construct the auto-encoder architecture for generating counterfactual samples. The resulting model requires fewer learnable parameters and thus is less prone to overfitting. We also introduce a novel density estimator that allows for searching for in-distribution samples. Furthermore, we introduce an algorithm for selecting the optimal regularization rate on density estimator while searching for counterfactuals. We experiment with our method in several large-scale tabular datasets and compare with other auto-encoder-based methods. The results show that our method is capable of generating diversified and in-distribution counterfactual samples.

Jian Xu, Wei Chen, Shigui Li et al.

Diffusion models have achieved remarkable success in low-light image enhancement through Retinex-based decomposition, yet their requirement for hundreds of iterative sampling steps severely limits practical deployment. While recent consistency models offer promising one-step generation for \textit{unconditional synthesis}, their application to \textit{conditional enhancement} remains unexplored. We present \textbf{Consist-Retinex}, the first framework adapting consistency modeling to Retinex-based low-light enhancement. Our key insight is that conditional enhancement requires fundamentally different training dynamics than unconditional generation standard consistency training focuses on low-noise regions near the data manifold, while conditional mapping critically depends on large-noise regimes that bridge degraded inputs to enhanced outputs. We introduce two core innovations: (1) a \textbf{dual-objective consistency loss} combining temporal consistency with ground-truth alignment under randomized time sampling, providing full-spectrum supervision for stable convergence; and (2) an \textbf{adaptive noise-emphasized sampling strategy} that prioritizes training on large-noise regions essential for one-step conditional generation. On VE-LOL-L, Consist-Retinex achieves \textbf{state-of-the-art performance with single-step sampling} (\textbf{PSNR: 25.51 vs. 23.41, FID: 44.73 vs. 49.59} compared to Diff-Retinex++), while requiring only \textbf{1/8 of the training budget} relative to the 1000-step Diff-Retinex baseline.

Jian Xu, Qibin Zhao, John Paisley et al.

Deep Gaussian processes (DGPs) enable expressive hierarchical Bayesian modeling but pose substantial challenges for posterior inference, especially over inducing variables. Denoising diffusion variational inference (DDVI) addresses this by modeling the posterior as a time-reversed diffusion from a simple Gaussian prior. However, DDVI's fixed unconditional starting distribution remains far from the complex true posterior, resulting in inefficient inference trajectories and slow convergence. In this work, we propose Diffusion Bridge Variational Inference (DBVI), a principled extension of DDVI that initiates the reverse diffusion from a learnable, data-dependent initial distribution. This initialization is parameterized via an amortized neural network and progressively adapted using gradients from the ELBO objective, reducing the posterior gap and improving sample efficiency. To enable scalable amortization, we design the network to operate on the inducing inputs, which serve as structured, low-dimensional summaries of the dataset and naturally align with the inducing variables' shape. DBVI retains the mathematical elegance of DDVI, including Girsanov-based ELBOs and reverse-time SDEs,while reinterpreting the prior via a Doob-bridged diffusion process. We derive a tractable training objective under this formulation and implement DBVI for scalable inference in large-scale DGPs. Across regression, classification, and image reconstruction tasks, DBVI consistently outperforms DDVI and other variational baselines in predictive accuracy, convergence speed, and posterior quality.

Wei Chen, Shigui Li, Jiacheng Li et al.

Estimating density ratios is a fundamental problem in machine learning, but existing methods often trade off accuracy for efficiency. We propose \textit{Interval-annealed Secant Alignment Density Ratio Estimation (ISA-DRE)}, a framework that enables accurate, any-step estimation without numerical integration. Instead of modeling infinitesimal tangents as in prior methods, ISA-DRE learns a global secant function, defined as the expectation of all tangents over an interval, with provably lower variance, making it more suitable for neural approximation. This is made possible by the \emph{Secant Alignment Identity}, a self-consistency condition that formally connects the secant with its underlying tangent representations. To mitigate instability during early training, we introduce \emph{Contraction Interval Annealing}, a curriculum strategy that gradually expands the alignment interval during training. This process induces a contraction mapping, which improves convergence and training stability. Empirically, ISA-DRE achieves competitive accuracy with significantly fewer function evaluations compared to prior methods, resulting in much faster inference and making it well suited for real-time and interactive applications.

Wei Zhang, Brian Barr, John Paisley

Counterfactual explanations methods provide an important tool in the field of {interpretable machine learning}. Recent advances in this direction have focused on diffusion models to explain a deep classifier. However, these techniques have predominantly focused on problems in computer vision. In this paper, we focus on tabular data typical in finance and the social sciences and propose a novel guided reverse process for categorical features based on an approximation to the Gumbel-softmax distribution. Furthermore, we study the effect of the temperature $τ$ and derive a theoretical bound between the Gumbel-softmax distribution and our proposed approximated distribution. We perform experiments on several large-scale credit lending and other tabular datasets, assessing their performance in terms of the quantitative measures of interpretability, diversity, instability, and validity. These results indicate that our approach outperforms popular baseline methods, producing robust and realistic counterfactual explanations.

Jian Xu, Yican Liu, Qibin Zhao et al.

Learning stochastic functions from partially observed context-target pairs is a fundamental problem in probabilistic modeling. Traditional models like Gaussian Processes (GPs) face scalability issues with large datasets and assume Gaussianity, limiting their applicability. While Neural Processes (NPs) offer more flexibility, they struggle with capturing complex, multi-modal target distributions. Neural Diffusion Processes (NDPs) enhance expressivity through a learned diffusion process but rely solely on conditional signals in the denoising network, resulting in weak input coupling from an unconditional forward process and semantic mismatch at the diffusion endpoint. In this work, we propose Neural Bridge Processes (NBPs), a novel method for modeling stochastic functions where inputs x act as dynamic anchors for the entire diffusion trajectory. By reformulating the forward kernel to explicitly depend on x, NBP enforces a constrained path that strictly terminates at the supervised target. This approach not only provides stronger gradient signals but also guarantees endpoint coherence. We validate NBPs on synthetic data, EEG signal regression and image regression tasks, achieving substantial improvements over baselines. These results underscore the effectiveness of DDPM-style bridge sampling in enhancing both performance and theoretical consistency for structured prediction tasks.

John Paisley, Ghazal Fazelnia, Brian Barr

We exploit the observation that stochastic variational inference (SVI) is a form of annealing and present a modified SVI approach -- applicable to both large and small datasets -- that allows the amount of annealing done by SVI to be tuned. We are motivated by the fact that, in SVI, the larger the batch size the more approximately Gaussian is the noise of the gradient, but the smaller its variance, which reduces the amount of annealing done to escape bad local optimal solutions. We propose a simple method for achieving both goals of having larger variance noise to escape bad local optimal solutions and more data information to obtain more accurate gradient directions. The idea is to set an actual batch size, which may be the size of the data set, and an effective batch size that matches the increased variance of a smaller batch size. The result is an approximation to the maximum entropy stochastic gradient at a desired variance level. We theoretically motivate our ``SVI+'' approach for conjugate exponential family model framework and illustrate its empirical performance for learning the probabilistic matrix factorization collaborative filter (PMF), the Latent Dirichlet Allocation topic model (LDA), and the Gaussian mixture model (GMM).

John Paisley, Wei Zhang, Brian Barr

We propose a nonparametric density estimator based on the Gaussian process (GP) and derive three novel closed form learning algorithms based on Fisher divergence (FD) score matching. The density estimator is formed by multiplying a base multivariate normal distribution with an exponentiated GP refinement, and so we refer to it as a GP-tilted nonparametric density. By representing the GP part of the score as a linear function using the random Fourier feature (RFF) approximation, we show that optimization can be solved in closed form for the three FD-based objectives considered. This includes the basic and noise conditional versions of the Fisher divergence, as well as an alternative to noise conditional FD models based on variational inference (VI) that we propose in this paper. For this novel learning approach, we propose an ELBO-like optimization to approximate the posterior distribution, with which we then derive a Fisher variational predictive distribution. The RFF representation of the GP, which is functionally equivalent to a single layer neural network score model with cosine activation, provides a useful linear representation of the GP for which all expectations can be solved. The Gaussian base distribution also helps with tractability of the VI approximation and ensures that our proposed density is well-defined. We demonstrate our three learning algorithms, as well as a MAP baseline algorithm, on several low dimensional density estimation problems. The closed form nature of the learning problem removes the reliance on iterative learning algorithms, making this technique particularly well-suited to big data sets, since only sufficient statistics collected from a single pass through the data is needed.

Huangxing Lin, Yihong Zhuang, Delu Zeng et al.

We devise a new regularization, called self-verification, for image denoising. This regularization is formulated using a deep image prior learned by the network, rather than a traditional predefined prior. Specifically, we treat the output of the network as a ``prior'' that we denoise again after ``re-noising''. The comparison between the again denoised image and its prior can be interpreted as a self-verification of the network's denoising ability. We demonstrate that self-verification encourages the network to capture low-level image statistics needed to restore the image. Based on this self-verification regularization, we further show that the network can learn to denoise even if it has not seen any clean images. This learning strategy is self-supervised, and we refer to it as Self-Verification Image Denoising (SVID). SVID can be seen as a mixture of learning-based methods and traditional model-based denoising methods, in which regularization is adaptively formulated using the output of the network. We show the application of SVID to various denoising tasks using only observed corrupted data. It can achieve the denoising performance close to supervised CNNs.

Elizabeth A. Gibson, Sebastian T. Rowland, Jeff Goldsmith et al.

Environmental health researchers may aim to identify exposure patterns that represent sources, product use, or behaviors that give rise to mixtures of potentially harmful environmental chemical exposures. We present Bayesian non-parametric non-negative matrix factorization (BN^2MF) as a novel method to identify patterns of chemical exposures when the number of patterns is not known a priori. We placed non-negative continuous priors on pattern loadings and individual scores to enhance interpretability and used a clever non-parametric sparse prior to estimate the pattern number. We further derived variational confidence intervals around estimates; this is a critical development because it quantifies the model's confidence in estimated patterns. These unique features contrast with existing pattern recognition methods employed in this field which are limited by user-specified pattern number, lack of interpretability of patterns in terms of human understanding, and lack of uncertainty quantification.

Huangxing Lin, Yihong Zhuang, Yue Huang et al.

The effectiveness of existing denoising algorithms typically relies on accurate pre-defined noise statistics or plenty of paired data, which limits their practicality. In this work, we focus on denoising in the more common case where noise statistics and paired data are unavailable. Considering that denoising CNNs require supervision, we develop a new \textbf{adaptive noise imitation (ADANI)} algorithm that can synthesize noisy data from naturally noisy images. To produce realistic noise, a noise generator takes unpaired noisy/clean images as input, where the noisy image is a guide for noise generation. By imposing explicit constraints on the type, level and gradient of noise, the output noise of ADANI will be similar to the guided noise, while keeping the original clean background of the image. Coupling the noisy data output from ADANI with the corresponding ground-truth, a denoising CNN is then trained in a fully-supervised manner. Experiments show that the noisy data produced by ADANI are visually and statistically similar to real ones so that the denoising CNN in our method is competitive to other networks trained with external paired data.

Arunesh Mittal, Scott Linderman, John Paisley et al.

We propose a hierarchical Bayesian recurrent state space model for modeling switching network connectivity in resting state fMRI data. Our model allows us to uncover shared network patterns across disease conditions. We evaluate our method on the ADNI2 dataset by inferring latent state patterns corresponding to altered neural circuits in individuals with Mild Cognitive Impairment (MCI). In addition to states shared across healthy and individuals with MCI, we discover latent states that are predominantly observed in individuals with MCI. Our model outperforms current state of the art deep learning method on ADNI2 dataset.

Arunesh Mittal, Paul Sajda, John Paisley

We propose a deep generative factor analysis model with beta process prior that can approximate complex non-factorial distributions over the latent codes. We outline a stochastic EM algorithm for scalable inference in a specific instantiation of this model and present some preliminary results.

Huangxing Lin, Weihong Zeng, Xinghao Ding et al.

We propose a new framework called Noise2Blur (N2B) for training robust image denoising models without pre-collected paired noisy/clean images. The training of the model requires only some (or even one) noisy images, some random unpaired clean images, and noise-free but blurred labels obtained by predefined filtering of the noisy images. The N2B model consists of two parts: a denoising network and a noise extraction network. First, the noise extraction network learns to output a noise map using the noise information from the denoising network under the guidence of the blurred labels. Then, the noise map is added to a clean image to generate a new "noisy/clean" image pair. Using the new image pair, the denoising network learns to generate clean and high-quality images from noisy observations. These two networks are trained simultaneously and mutually aid each other to learn the mappings of noise to clean/blur. Experiments on several denoising tasks show that the denoising performance of N2B is close to that of other denoising CNNs trained with pre-collected paired data.

San Gultekin, John Paisley

Bipartite ranking is an important supervised learning problem; however, unlike regression or classification, it has a quadratic dependence on the number of samples. To circumvent the prohibitive sample cost, many recent work focus on stochastic gradient-based methods. In this paper we consider an alternative approach, which leverages the structure of the widely-adopted pairwise squared loss, to obtain a stochastic and low cost algorithm that does not require stochastic gradients or learning rates. Using a novel uniform risk bound---based on matrix and vector concentration inequalities---we show that the sample size required for competitive performance against the all-pairs batch algorithm does not have a quadratic dependence. Generalization bounds for both the batch and low cost stochastic algorithms are presented. Experimental results show significant speed gain against the batch algorithm, as well as competitive performance against state-of-the-art bipartite ranking algorithms on real datasets.

Huangxing Lin, Weihong Zeng, Xinghao Ding et al.

The performance of a deep neural network is highly dependent on its training, and finding better local optimal solutions is the goal of many optimization algorithms. However, existing optimization algorithms show a preference for descent paths that converge slowly and do not seek to avoid bad local optima. In this work, we propose Learning Rate Dropout (LRD), a simple gradient descent technique for training related to coordinate descent. LRD empirically aids the optimizer to actively explore in the parameter space by randomly setting some learning rates to zero; at each iteration, only parameters whose learning rate is not 0 are updated. As the learning rate of different parameters is dropped, the optimizer will sample a new loss descent path for the current update. The uncertainty of the descent path helps the model avoid saddle points and bad local minima. Experiments show that LRD is surprisingly effective in accelerating training while preventing overfitting.

Jeremiah Zhe Liu, John Paisley, Marianthi-Anna Kioumourtzoglou et al.

Ensemble learning is a standard approach to building machine learning systems that capture complex phenomena in real-world data. An important aspect of these systems is the complete and valid quantification of model uncertainty. We introduce a Bayesian nonparametric ensemble (BNE) approach that augments an existing ensemble model to account for different sources of model uncertainty. BNE augments a model's prediction and distribution functions using Bayesian nonparametric machinery. It has a theoretical guarantee in that it robustly estimates the uncertainty patterns in the data distribution, and can decompose its overall predictive uncertainty into distinct components that are due to different sources of noise and error. We show that our method achieves accurate uncertainty estimates under complex observational noise, and illustrate its real-world utility in terms of uncertainty decomposition and model bias detection for an ensemble in predict air pollution exposures in Eastern Massachusetts, USA.

Adji B. Dieng, John Paisley

Training deep generative models with maximum likelihood remains a challenge. The typical workaround is to use variational inference (VI) and maximize a lower bound to the log marginal likelihood of the data. Variational auto-encoders (VAEs) adopt this approach. They further amortize the cost of inference by using a recognition network to parameterize the variational family. Amortized VI scales approximate posterior inference in deep generative models to large datasets. However it introduces an amortization gap and leads to approximate posteriors of reduced expressivity due to the problem known as posterior collapse. In this paper, we consider expectation maximization (EM) as a paradigm for fitting deep generative models. Unlike VI, EM directly maximizes the log marginal likelihood of the data. We rediscover the importance weighted auto-encoder (IWAE) as an instance of EM and propose a new EM-based algorithm for fitting deep generative models called reweighted expectation maximization (REM). REM learns better generative models than the IWAE by decoupling the learning dynamics of the generative model and the recognition network using a separate expressive proposal found by moment matching. We compared REM to the VAE and the IWAE on several density estimation benchmarks and found it leads to significantly better performance as measured by log-likelihood.

Aonan Zhang, John Paisley

The likelihood model of high dimensional data $X_n$ can often be expressed as $p(X_n|Z_n,θ)$, where $θ\mathrel{\mathop:}=(θ_k)_{k\in[K]}$ is a collection of hidden features shared across objects, indexed by $n$, and $Z_n$ is a non-negative factor loading vector with $K$ entries where $Z_{nk}$ indicates the strength of $θ_k$ used to express $X_n$. In this paper, we introduce random function priors for $Z_n$ for modeling correlations among its $K$ dimensions $Z_{n1}$ through $Z_{nK}$, which we call \textit{population random measure embedding} (PRME). Our model can be viewed as a generalized paintbox model~\cite{Broderick13} using random functions, and can be learned efficiently with neural networks via amortized variational inference. We derive our Bayesian nonparametric method by applying a representation theorem on separately exchangeable discrete random measures.

Huangxing Lin, Yanlong Li, Xinghao Ding et al.

We present a supervised technique for learning to remove rain from images without using synthetic rain software. The method is based on a two-stage data distillation approach: 1) A rainy image is first paired with a coarsely derained version using on a simple filtering technique ("rain-to-clean"). 2) Then a clean image is randomly matched with the rainy soft-labeled pair. Through a shared deep neural network, the rain that is removed from the first image is then added to the clean image to generate a second pair ("clean-to-rain"). The neural network simultaneously learns to map both images such that high resolution structure in the clean images can inform the deraining of the rainy images. Demonstrations show that this approach can address those visual characteristics of rain not easily synthesized by software in the usual way.

Mark Ibrahim, Melissa Louie, Ceena Modarres et al.

A barrier to the wider adoption of neural networks is their lack of interpretability. While local explanation methods exist for one prediction, most global attributions still reduce neural network decisions to a single set of features. In response, we present an approach for generating global attributions called GAM, which explains the landscape of neural network predictions across subpopulations. GAM augments global explanations with the proportion of samples that each attribution best explains and specifies which samples are described by each attribution. Global explanations also have tunable granularity to detect more or fewer subpopulations. We demonstrate that GAM's global explanations 1) yield the known feature importances of simulated data, 2) match feature weights of interpretable statistical models on real data, and 3) are intuitive to practitioners through user studies. With more transparent predictions, GAM can help ensure neural network decisions are generated for the right reasons.

Ghazal Fazelnia, Mark Ibrahim, Ceena Modarres et al.

Models for sequential data such as the recurrent neural network (RNN) often implicitly model a sequence as having a fixed time interval between observations and do not account for group-level effects when multiple sequences are observed. We propose a model for grouped sequential data based on the RNN that accounts for varying time intervals between observations in a sequence by learning a group-level base parameter to which each sequence can revert. Our approach is motivated by the mixed membership framework, and we show how it can be used for dynamic topic modeling in which the distribution on topics (not the topics themselves) are evolving in time. We demonstrate our approach on a dataset of 3.4 million online grocery shopping orders made by 206K customers.

Jeremiah Zhe Liu, John Paisley, Marianthi-Anna Kioumourtzoglou et al.

Ensemble learning is a mainstay in modern data science practice. Conventional ensemble algorithms assigns to base models a set of deterministic, constant model weights that (1) do not fully account for variations in base model accuracy across subgroups, nor (2) provide uncertainty estimates for the ensemble prediction, which could result in mis-calibrated (i.e. precise but biased) predictions that could in turn negatively impact the algorithm performance in real-word applications. In this work, we present an adaptive, probabilistic approach to ensemble learning using dependent tail-free process as ensemble weight prior. Given input feature $\mathbf{x}$, our method optimally combines base models based on their predictive accuracy in the feature space $\mathbf{x} \in \mathcal{X}$, and provides interpretable uncertainty estimates both in model selection and in ensemble prediction. To encourage scalable and calibrated inference, we derive a structured variational inference algorithm that jointly minimize KL objective and the model's calibration score (i.e. Continuous Ranked Probability Score (CRPS)). We illustrate the utility of our method on both a synthetic nonlinear function regression task, and on the real-world application of spatio-temporal integration of particle pollution prediction models in New England.

Xueyang Fu, Qi Qi, Yue Huang et al.

We propose a simple yet effective deep tree-structured fusion model based on feature aggregation for the deraining problem. We argue that by effectively aggregating features, a relatively simple network can still handle tough image deraining problems well. First, to capture the spatial structure of rain we use dilated convolutions as our basic network block. We then design a tree-structured fusion architecture which is deployed within each block (spatial information) and across all blocks (content information). Our method is based on the assumption that adjacent features contain redundant information. This redundancy obstructs generation of new representations and can be reduced by hierarchically fusing adjacent features. Thus, the proposed model is more compact and can effectively use spatial and content information. Experiments on synthetic and real-world datasets show that our network achieves better deraining results with fewer parameters.

Ceena Modarres, Mark Ibrahim, Melissa Louie et al.

Deep learning adoption in the financial services industry has been limited due to a lack of model interpretability. However, several techniques have been proposed to explain predictions made by a neural network. We provide an initial investigation into these techniques for the assessment of credit risk with neural networks.

Liyan Sun, Jiexiang Wang, Yue Huang et al.

The identification of lesion within medical image data is necessary for diagnosis, treatment and prognosis. Segmentation and classification approaches are mainly based on supervised learning with well-paired image-level or voxel-level labels. However, labeling the lesion in medical images is laborious requiring highly specialized knowledge. We propose a medical image synthesis model named abnormal-to-normal translation generative adversarial network (ANT-GAN) to generate a normal-looking medical image based on its abnormal-looking counterpart without the need for paired training data. Unlike typical GANs, whose aim is to generate realistic samples with variations, our more restrictive model aims at producing a normal-looking image corresponding to one containing lesions, and thus requires a special design. Being able to provide a "normal" counterpart to a medical image can provide useful side information for medical imaging tasks like lesion segmentation or classification validated by our experiments. In the other aspect, the ANT-GAN model is also capable of producing highly realistic lesion-containing image corresponding to the healthy one, which shows the potential in data augmentation verified in our experiments.

Aonan Zhang, Quan Wang, Zhenyao Zhu et al.

In this paper, we propose a fully supervised speaker diarization approach, named unbounded interleaved-state recurrent neural networks (UIS-RNN). Given extracted speaker-discriminative embeddings (a.k.a. d-vectors) from input utterances, each individual speaker is modeled by a parameter-sharing RNN, while the RNN states for different speakers interleave in the time domain. This RNN is naturally integrated with a distance-dependent Chinese restaurant process (ddCRP) to accommodate an unknown number of speakers. Our system is fully supervised and is able to learn from examples where time-stamped speaker labels are annotated. We achieved a 7.6% diarization error rate on NIST SRE 2000 CALLHOME, which is better than the state-of-the-art method using spectral clustering. Moreover, our method decodes in an online fashion while most state-of-the-art systems rely on offline clustering.

San Gultekin, Avishek Saha, Adwait Ratnaparkhi et al.

Area under the receiver operating characteristics curve (AUC) is an important metric for a wide range of signal processing and machine learning problems, and scalable methods for optimizing AUC have recently been proposed. However, handling very large datasets remains an open challenge for this problem. This paper proposes a novel approach to AUC maximization, based on sampling mini-batches of positive/negative instance pairs and computing U-statistics to approximate a global risk minimization problem. The resulting algorithm is simple, fast, and learning-rate free. We show that the number of samples required for good performance is independent of the number of pairs available, which is a quadratic function of the positive and negative instances. Extensive experiments show the practical utility of the proposed method.

Xueyang Fu, Borong Liang, Yue Huang et al.

Existing deep convolutional neural networks have found major success in image deraining, but at the expense of an enormous number of parameters. This limits their potential application, for example in mobile devices. In this paper, we propose a lightweight pyramid of networks (LPNet) for single image deraining. Instead of designing a complex network structures, we use domain-specific knowledge to simplify the learning process. Specifically, we find that by introducing the mature Gaussian-Laplacian image pyramid decomposition technology to the neural network, the learning problem at each pyramid level is greatly simplified and can be handled by a relatively shallow network with few parameters. We adopt recursive and residual network structures to build the proposed LPNet, which has less than 8K parameters while still achieving state-of-the-art performance on rain removal. We also discuss the potential value of LPNet for other low- and high-level vision tasks.

Delu Zeng, Yixuan He, Li Liu et al.

Although deep CNNs have brought significant improvement to image saliency detection, most CNN based models are sensitive to distortion such as compression and noise. In this paper, we propose an end-to-end generic salient object segmentation model called Metric Expression Network (MEnet) to deal with saliency detection with the tolerance of distortion. Within MEnet, a new topological metric space is constructed, whose implicit metric is determined by the deep network. As a result, we manage to group all the pixels in the observed image semantically within this latent space into two regions: a salient region and a non-salient region. With this architecture, all feature extractions are carried out at the pixel level, enabling fine granularity of output boundaries of the salient objects. What's more, we try to give a general analysis for the noise robustness of the network in the sense of Lipschitz and Jacobian literature. Experiments demonstrate that robust salient maps facilitating object segmentation can be generated by the proposed metric. Tests on several public benchmarks show that MEnet has achieved desirable performance. Furthermore, by direct computation and measuring the robustness, the proposed method outperforms previous CNN-based methods on distorted inputs.

Liyan Sun, Zhiwen Fan, Yue Huang et al.

The need for fast acquisition and automatic analysis of MRI data is growing in the age of big data. Although compressed sensing magnetic resonance imaging (CS-MRI) has been studied to accelerate MRI by reducing k-space measurements, in current CS-MRI techniques MRI applications such as segmentation are overlooked when doing image reconstruction. In this paper, we test the utility of CS-MRI methods in automatic segmentation models and propose a unified deep neural network architecture called SegNetMRI which we apply to the combined CS-MRI reconstruction and segmentation problem. SegNetMRI is built upon a MRI reconstruction network with multiple cascaded blocks each containing an encoder-decoder unit and a data fidelity unit, and MRI segmentation networks having the same encoder-decoder structure. The two subnetworks are pre-trained and fine-tuned with shared reconstruction encoders. The outputs are merged into the final segmentation. Our experiments show that SegNetMRI can improve both the reconstruction and segmentation performance when using compressive measurements.

Liyan Sun, Zhiwen Fan, Yue Huang et al.

In multi-contrast magnetic resonance imaging (MRI), compressed sensing theory can accelerate imaging by sampling fewer measurements within each contrast. The conventional optimization-based models suffer several limitations: strict assumption of shared sparse support, time-consuming optimization and "shallow" models with difficulties in encoding the rich patterns hiding in massive MRI data. In this paper, we propose the first deep learning model for multi-contrast MRI reconstruction. We achieve information sharing through feature sharing units, which significantly reduces the number of parameters. The feature sharing unit is combined with a data fidelity unit to comprise an inference block. These inference blocks are cascaded with dense connections, which allows for information transmission across different depths of the network efficiently. Our extensive experiments on various multi-contrast MRI datasets show that proposed model outperforms both state-of-the-art single-contrast and multi-contrast MRI methods in accuracy and efficiency. We show the improved reconstruction quality can bring great benefits for the later medical image analysis stage. Furthermore, the robustness of the proposed model to the non-registration environment shows its potential in real MRI applications.