Promit Ghosal

Xuxing Chen, Krishnakumar Balasubramanian, Promit Ghosal et al.

We conduct a comprehensive investigation into the dynamics of gradient descent using large-order constant step-sizes in the context of quadratic regression models. Within this framework, we reveal that the dynamics can be encapsulated by a specific cubic map, naturally parameterized by the step-size. Through a fine-grained bifurcation analysis concerning the step-size parameter, we delineate five distinct training phases: (1) monotonic, (2) catapult, (3) periodic, (4) chaotic, and (5) divergent, precisely demarcating the boundaries of each phase. As illustrations, we provide examples involving phase retrieval and two-layer neural networks employing quadratic activation functions and constant outer-layers, utilizing orthogonal training data. Our simulations indicate that these five phases also manifest with generic non-orthogonal data. We also empirically investigate the generalization performance when training in the various non-monotonic (and non-divergent) phases. In particular, we observe that performing an ergodic trajectory averaging stabilizes the test error in non-monotonic (and non-divergent) phases.

Sayan Banerjee, Krishnakumar Balasubramanian, Promit Ghosal

We provide finite-particle convergence rates for the Stein Variational Gradient Descent (SVGD) algorithm in the Kernelized Stein Discrepancy ($\mathsf{KSD}$) and Wasserstein-2 metrics. Our key insight is that the time derivative of the relative entropy between the joint density of $N$ particle locations and the $N$-fold product target measure, starting from a regular initial distribution, splits into a dominant `negative part' proportional to $N$ times the expected $\mathsf{KSD}^2$ and a smaller `positive part'. This observation leads to $\mathsf{KSD}$ rates of order $1/\sqrt{N}$, in both continuous and discrete time, providing a near optimal (in the sense of matching the corresponding i.i.d. rates) double exponential improvement over the recent result by Shi and Mackey (2024). Under mild assumptions on the kernel and potential, these bounds also grow polynomially in the dimension $d$. By adding a bilinear component to the kernel, the above approach is used to further obtain Wasserstein-2 convergence in continuous time. For the case of `bilinear + Matérn' kernels, we derive Wasserstein-2 rates that exhibit a curse-of-dimensionality similar to the i.i.d. setting. We also obtain marginal convergence and long-time propagation of chaos results for the time-averaged particle laws.

Promit Ghosal, Srinath Mahankali, Yihang Sun

Recently, neural networks have demonstrated remarkable capabilities in mapping two arbitrary sets to two linearly separable sets. The prospect of achieving this with randomly initialized neural networks is particularly appealing due to the computational efficiency compared to fully trained networks. This paper contributes by establishing that, given sufficient width, a randomly initialized one-layer neural network can, with high probability, transform two sets into two linearly separable sets without any training. Moreover, we furnish precise bounds on the necessary width of the neural network for this phenomenon to occur. Our initial bound exhibits exponential dependence on the input dimension while maintaining polynomial dependence on all other parameters. In contrast, our second bound is independent of input dimension, effectively surmounting the curse of dimensionality. The main tools used in our proof heavily relies on a fusion of geometric principles and concentration of random matrices.

Ye He, Krishnakumar Balasubramanian, Sayan Banerjee et al.

We derive finite-particle rates for the regularized Stein variational gradient descent (R-SVGD) algorithm introduced by He et al. (2024) that corrects the constant-order bias of the SVGD by applying a resolvent-type preconditioner to the kernelized Wasserstein gradient. For the resulting interacting $N$-particle system, we establish explicit non-asymptotic bounds for time-averaged (annealed) empirical measures, illustrating convergence in the \emph{true} (non-kernelized) Fisher information and, under a $\mathrm{W}_1\mathrm{I}$ condition on the target, corresponding $\mathrm{W}_1$ convergence for a large class of smooth kernels. Our analysis covers both continuous- and discrete-time dynamics and yields principled tuning rules for the regularization parameter, step size, and averaging horizon that quantify the trade-off between approximating the Wasserstein gradient flow and controlling finite-particle estimation error.

Kingsley Yeon, Xuefeng Liu, Promit Ghosal

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

Shixing Yu, Promit Ghosal, Kyra Gan

A critical step for reliable large language models (LLMs) use in healthcare is to attribute predictions to their training data, akin to a medical case study. This requires token-level precision: pinpointing not just which training examples influence a decision, but which tokens within them are responsible. While influence functions offer a principled framework for this, prior work is restricted to autoregressive settings and relies on an implicit assumption of token independence, rendering their identified influences unreliable. We introduce a flexible framework that infers token-level influence through a latent mediation approach for general prediction tasks. Our method attaches sparse autoencoders to any layer of a pretrained LLM to learn a basis of approximately independent latent features. Unlike prior methods where influence decomposes additively across tokens, influence computed over latent features is inherently non-decomposable. To address this, we introduce a novel method using Jacobian-vector products. Token-level influence is obtained by propagating latent attributions back to the input space via token activation patterns. We scale our approach using efficient inverse-Hessian approximations. Experiments on medical benchmarks show our approach identifies sparse, interpretable sets of tokens that jointly influence predictions. Our framework enhances trust and enables model auditing, generalizing to high-stakes domain requiring transparent and accountable decisions.

Sujai Hiremath, Jacqueline R. M. A. Maasch, Mengxiao Gao et al.

Learning the unique directed acyclic graph corresponding to an unknown causal model is a challenging task. Methods based on functional causal models can identify a unique graph, but either suffer from the curse of dimensionality or impose strong parametric assumptions. To address these challenges, we propose a novel hybrid approach for global causal discovery in observational data that leverages local causal substructures. We first present a topological sorting algorithm that leverages ancestral relationships in linear structural causal models to establish a compact top-down hierarchical ordering, encoding more causal information than linear orderings produced by existing methods. We demonstrate that this approach generalizes to nonlinear settings with arbitrary noise. We then introduce a nonparametric constraint-based algorithm that prunes spurious edges by searching for local conditioning sets, achieving greater accuracy than current methods. We provide theoretical guarantees for correctness and worst-case polynomial time complexities, with empirical validation on synthetic data.

Kingsley Yeon, Promit Ghosal, Mihai Anitescu

Efficient matrix trace estimation is essential for scalable computation of log-determinants, matrix norms, and distributional divergences. In many large-scale applications, the matrices involved are too large to store or access in full, making even a single matrix-vector (mat-vec) product infeasible. Instead, one often has access only to small subblocks of the matrix or localized matrix-vector products on restricted index sets. Hutch++ achieves optimal convergence rate but relies on randomized SVD and assumes full mat-vec access, making it difficult to apply in these constrained settings. We propose the Block-Orthonormal Stochastic Lanczos Quadrature (BOLT), which matches Hutch++ accuracy with a simpler implementation based on orthonormal block probes and Lanczos iterations. BOLT builds on the Stochastic Lanczos Quadrature (SLQ) framework, which combines random probing with Krylov subspace methods to efficiently approximate traces of matrix functions, and performs better than Hutch++ in near flat-spectrum regimes. To address memory limitations and partial access constraints, we introduce Subblock SLQ, a variant of BOLT that operates only on small principal submatrices. As a result, this framework yields a proxy KL divergence estimator and an efficient method for computing the Wasserstein-2 distance between Gaussians - both compatible with low-memory and partial-access regimes. We provide theoretical guarantees and demonstrate strong empirical performance across a range of high-dimensional settings.

Sujai Hiremath, Promit Ghosal, Kyra Gan

Inferring causal relationships from observational data is crucial when experiments are costly or infeasible. Additive noise models (ANMs) enable unique directed acyclic graph (DAG) identification, but existing sample-efficient ANM methods often rely on restrictive assumptions on the data generating process, limiting their applicability to real-world settings. We propose local search in additive noise models, LoSAM, a topological ordering method for learning a unique DAG in ANMs with mixed causal mechanisms and general noise distributions. We introduce new causal substructures and criteria for identifying roots and leaves, enabling efficient top-down learning. We prove asymptotic consistency and polynomial runtime, ensuring scalability and sample efficiency. We test LoSAM on synthetic and real-world data, demonstrating state-of-the-art performance across all mixed mechanism settings.

Dominik Meier, Shixing Yu, Sagnik Nandy et al.

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular heterogeneity. Yet, clustering accuracy, and with it downstream analyses based on cell labels, remain challenging due to measurement noise and biological variability. In standard latent spaces (e.g., obtained through PCA), data from different cell types can be projected close together, making accurate clustering difficult. We introduce a latent plug-and-play diffusion framework that separates the observation and denoising space. This separation is operationalized through a novel Gibbs sampling procedure: the learned diffusion prior is applied in a low-dimensional latent space to perform denoising, while to steer this process, noise is reintroduced into the original high-dimensional observation space. This unique "input-space steering" ensures the denoising trajectory remains faithful to the original data structure. Our approach offers three key advantages: (1) adaptive noise handling via a tunable balance between prior and observed data; (2) uncertainty quantification through principled uncertainty estimates for downstream analysis; and (3) generalizable denoising by leveraging clean reference data to denoise noisier datasets, and via averaging, improve quality beyond the training set. We evaluate robustness on both synthetic and real single-cell genomics data. Our method improves clustering accuracy on synthetic data across varied noise levels and dataset shifts. On real-world single-cell data, our method demonstrates improved biological coherence in the resulting cell clusters, with cluster boundaries that better align with known cell type markers and developmental trajectories.

Bhavya Agrawalla, Krishnakumar Balasubramanian, Promit Ghosal

Stochastic Gradient Descent (SGD) has become a cornerstone method in modern data science. However, deploying SGD in high-stakes applications necessitates rigorous quantification of its inherent uncertainty. In this work, we establish \emph{non-asymptotic Berry--Esseen bounds} for linear functionals of online least-squares SGD, thereby providing a Gaussian Central Limit Theorem (CLT) in a \emph{growing-dimensional regime}. Existing approaches to high-dimensional inference for projection parameters, such as~\cite{chang2023inference}, rely on inverting empirical covariance matrices and require at least $t \gtrsim d^{3/2}$ iterations to achieve finite-sample Berry--Esseen guarantees, rendering them computationally expensive and restrictive in the allowable dimensional scaling. In contrast, we show that a CLT holds for SGD iterates when the number of iterations grows as $t \gtrsim d^{1+δ}$ for any $δ> 0$, significantly extending the dimensional regime permitted by prior works while improving computational efficiency. The proposed online SGD-based procedure operates in $\mathcal{O}(td)$ time and requires only $\mathcal{O}(d)$ memory, in contrast to the $\mathcal{O}(td^2 + d^3)$ runtime of covariance-inversion methods. To render the theory practically applicable, we further develop an \emph{online variance estimator} for the asymptotic variance appearing in the CLT and establish \emph{high-probability deviation bounds} for this estimator. Collectively, these results yield the first fully online and data-driven framework for constructing confidence intervals for SGD iterates in the near-optimal scaling regime $t \gtrsim d^{1+δ}$.

Dominik Meier, Sujai Hiremath, Promit Ghosal et al.

Distinguishing cause and effect from bivariate observational data is a foundational problem in many disciplines, but challenging without additional assumptions. Additive noise models (ANMs) are widely used to enable sample-efficient bivariate causal discovery. However, conventional ANM-based methods fail when unobserved mediators corrupt the causal relationship between variables. This paper makes three key contributions: first, we rigorously characterize why standard ANM approaches break down in the presence of unmeasured mediators. Second, we demonstrate that prior solutions for hidden mediation are brittle in finite sample settings, limiting their practical utility. To address these gaps, we propose Bivariate Denoising Diffusion (BiDD) for causal discovery, a method designed to handle latent noise introduced by unmeasured mediators. Unlike prior methods that infer directionality through mean squared error loss comparisons, our approach introduces a novel independence test statistic: during the noising and denoising processes for each variable, we condition on the other variable as input and evaluate the independence of the predicted noise relative to this input. We prove asymptotic consistency of BiDD under the ANM, and conjecture that it performs well under hidden mediation. Experiments on synthetic and real-world data demonstrate consistent performance, outperforming existing methods in mediator-corrupted settings while maintaining strong performance in mediator-free settings.

Soham Bonnerjee, Zhen Wei, Yeon et al.

In-context learning (ICL)-the ability of transformer-based models to perform new tasks from examples provided at inference time-has emerged as a hallmark of modern language models. While recent works have investigated the mechanisms underlying ICL, its feasibility under formal privacy constraints remains largely unexplored. In this paper, we propose a differentially private pretraining algorithm for linear attention heads and present the first theoretical analysis of the privacy-accuracy trade-off for ICL in linear regression. Our results characterize the fundamental tension between optimization and privacy-induced noise, formally capturing behaviors observed in private training via iterative methods. Additionally, we show that our method is robust to adversarial perturbations of training prompts, unlike standard ridge regression. All theoretical findings are supported by extensive simulations across diverse settings.

Tianle Liu, Promit Ghosal, Krishnakumar Balasubramanian et al.

Stein Variational Gradient Descent (SVGD) is a nonparametric particle-based deterministic sampling algorithm. Despite its wide usage, understanding the theoretical properties of SVGD has remained a challenging problem. For sampling from a Gaussian target, the SVGD dynamics with a bilinear kernel will remain Gaussian as long as the initializer is Gaussian. Inspired by this fact, we undertake a detailed theoretical study of the Gaussian-SVGD, i.e., SVGD projected to the family of Gaussian distributions via the bilinear kernel, or equivalently Gaussian variational inference (GVI) with SVGD. We present a complete picture by considering both the mean-field PDE and discrete particle systems. When the target is strongly log-concave, the mean-field Gaussian-SVGD dynamics is proven to converge linearly to the Gaussian distribution closest to the target in KL divergence. In the finite-particle setting, there is both uniform in time convergence to the mean-field limit and linear convergence in time to the equilibrium if the target is Gaussian. In the general case, we propose a density-based and a particle-based implementation of the Gaussian-SVGD, and show that several recent algorithms for GVI, proposed from different perspectives, emerge as special cases of our unified framework. Interestingly, one of the new particle-based instance from this framework empirically outperforms existing approaches. Our results make concrete contributions towards obtaining a deeper understanding of both SVGD and GVI.

Nabarun Deb, Promit Ghosal, Bodhisattva Sen

Optimal transport maps between two probability distributions $μ$ and $ν$ on $\mathbb{R}^d$ have found extensive applications in both machine learning and statistics. In practice, these maps need to be estimated from data sampled according to $μ$ and $ν$. Plug-in estimators are perhaps most popular in estimating transport maps in the field of computational optimal transport. In this paper, we provide a comprehensive analysis of the rates of convergences for general plug-in estimators defined via barycentric projections. Our main contribution is a new stability estimate for barycentric projections which proceeds under minimal smoothness assumptions and can be used to analyze general plug-in estimators. We illustrate the usefulness of this stability estimate by first providing rates of convergence for the natural discrete-discrete and semi-discrete estimators of optimal transport maps. We then use the same stability estimate to show that, under additional smoothness assumptions of Besov type or Sobolev type, wavelet based or kernel smoothed plug-in estimators respectively speed up the rates of convergence and significantly mitigate the curse of dimensionality suffered by the natural discrete-discrete/semi-discrete estimators. As a by-product of our analysis, we also obtain faster rates of convergence for plug-in estimators of $W_2(μ,ν)$, the Wasserstein distance between $μ$ and $ν$, under the aforementioned smoothness assumptions, thereby complementing recent results in Chizat et al. (2020). Finally, we illustrate the applicability of our results in obtaining rates of convergence for Wasserstein barycenters between two probability distributions and obtaining asymptotic detection thresholds for some recent optimal-transport based tests of independence.