pwc-archive/papers-with-abstracts huggingface dataset:
Advancing Wasserstein Convergence Analysis of Score-Based Models: Insights from Discretization and Second-Order Acceleration
Authors: Yifeng Yu, Lu Yu
Date: 2025-02-07 00:00:00

Score-based diffusion models have emerged as powerful tools in generative modeling, yet their theoretical foundations remain underexplored. In this work, we focus on the Wasserstein convergence analysis of score-based diffusion models. Specifically, we investigate the impact of various discretization schemes, including Euler discretization, exponential integrators, and midpoint randomization methods. Our analysis provides a quantitative comparison of these discrete approximations, emphasizing their influence on convergence behavior. Furthermore, we explore scenarios where Hessian information is available and propose an accelerated sampler based on the local linearization method. We demonstrate that this Hessian-based approach achieves faster convergence rates of order $\widetilde{\mathcal{O}}\left(\frac{1}{\varepsilon}\right)$ significantly improving upon the standard rate $\widetilde{\mathcal{O}}\left(\frac{1}{\varepsilon^2}\right)$ of vanilla diffusion models, where $\varepsilon$ denotes the target accuracy.
Student-t processes as infinite-width limits of posterior Bayesian neural networks
Authors: Francesco Caporali, Stefano Favaro, Dario Trevisan
Date: 2025-02-06 00:00:00
Tasks: Gaussian Processes

The asymptotic properties of Bayesian Neural Networks (BNNs) have been extensively studied, particularly regarding their approximations by Gaussian processes in the infinite-width limit. We extend these results by showing that posterior BNNs can be approximated by Student-t processes, which offer greater flexibility in modeling uncertainty. Specifically, we show that, if the parameters of a BNN follow a Gaussian prior distribution, and the variance of both the last hidden layer and the Gaussian likelihood function follows an Inverse-Gamma prior distribution, then the resulting posterior BNN converges to a Student-t process in the infinite-width limit. Our proof leverages the Wasserstein metric to establish control over the convergence rate of the Student-t process approximation.
Data denoising with self consistency, variance maximization, and the Kantorovich dominance
Authors: Joshua Zoen-Git Hiew, Tongseok Lim, Brendan Pass, Marcelo Cruz de Souza
Date: 2025-02-05 00:00:00
Tasks: Computational Efficiency, Denoising

We introduce a new framework for data denoising, partially inspired by martingale optimal transport. For a given noisy distribution (the data), our approach involves finding the closest distribution to it among all distributions which 1) have a particular prescribed structure (expressed by requiring they lie in a particular domain), and 2) are self-consistent with the data. We show that this amounts to maximizing the variance among measures in the domain which are dominated in convex order by the data. For particular choices of the domain, this problem and a relaxed version of it, in which the self-consistency condition is removed, are intimately related to various classical approaches to denoising. We prove that our general problem has certain desirable features: solutions exist under mild assumptions, have certain robustness properties, and, for very simple domains, coincide with solutions to the relaxed problem. We also introduce a novel relationship between distributions, termed Kantorovich dominance, which retains certain aspects of the convex order while being a weaker, more robust, and easier-to-verify condition. Building on this, we propose and analyze a new denoising problem by substituting the convex order in the previously described framework with Kantorovich dominance. We demonstrate that this revised problem shares some characteristics with the full convex order problem but offers enhanced stability, greater computational efficiency, and, in specific domains, more meaningful solutions. Finally, we present simple numerical examples illustrating solutions for both the full convex order problem and the Kantorovich dominance problem.
Provable Sample-Efficient Transfer Learning Conditional Diffusion Models via Representation Learning
Authors: Ziheng Cheng, Tianyu Xie, Shiyue Zhang, Cheng Zhang
Date: 2025-02-06 00:00:00
Tasks: Representation Learning, Transfer Learning

While conditional diffusion models have achieved remarkable success in various applications, they require abundant data to train from scratch, which is often infeasible in practice. To address this issue, transfer learning has emerged as an essential paradigm in small data regimes. Despite its empirical success, the theoretical underpinnings of transfer learning conditional diffusion models remain unexplored. In this paper, we take the first step towards understanding the sample efficiency of transfer learning conditional diffusion models through the lens of representation learning. Inspired by practical training procedures, we assume that there exists a low-dimensional representation of conditions shared across all tasks. Our analysis shows that with a well-learned representation from source tasks, the samplecomplexity of target tasks can be reduced substantially. In addition, we investigate the practical implications of our theoretical results in several real-world applications of conditional diffusion models. Numerical experiments are also conducted to verify our results.
Generalised Bayesian distance-based phylogenetics for the genomics era
Authors: Matthew J. Penn, Neil Scheidwasser, Mark P. Khurana, Christl A. Donnelly, David A. Duchêne, Samir Bhatt
Date: 2025-02-06 00:00:00
Tasks: Bayesian Inference

As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient, but are rarely favoured due to their inferior performance. Here, we extend distance-based phylogenetics using an entropy-based likelihood of the evolution among pairs of taxa, allowing for fast Bayesian inference in genome-scale datasets. We provide evidence of a close link between the inference criteria used in distance methods and Felsenstein's likelihood, such that the methods are expected to have comparable performance in practice. Using the entropic likelihood, we perform Bayesian inference on three phylogenetic benchmark datasets and find that estimates closely correspond with previous inferences. We also apply this rapid inference approach to a 60-million-site alignment from 363 avian taxa, covering most avian families. The method has outstanding performance and reveals substantial uncertainty in the avian diversification events immediately after the K-Pg transition event. The entropic likelihood allows for efficient Bayesian phylogenetic inference, accommodating the analysis demands of the genomic era.
Robust Label Shift Quantification
Authors: Alexandre Lecestre
Date: 2025-02-05 00:00:00

In this paper, we investigate the label shift quantification problem. We propose robust estimators of the label distribution which turn out to coincide with the Maximum Likelihood Estimator. We analyze the theoretical aspects and derive deviation bounds for the proposed method, providing optimal guarantees in the well-specified case, along with notable robustness properties against outliers and contamination. Our results provide theoretical validation for empirical observations on the robustness of Maximum Likelihood Label Shift.
Parametric Scaling Law of Tuning Bias in Conformal Prediction
Authors: Hao Zeng, Kangdao Liu, BingYi Jing, Hongxin Wei
Date: 2025-02-05 00:00:00
Tasks: Conformal Prediction, Holdout Set, Prediction, Uncertainty Quantification

Conformal prediction is a popular framework of uncertainty quantification that constructs prediction sets with coverage guarantees. To uphold the exchangeability assumption, many conformal prediction methods necessitate an additional holdout set for parameter tuning. Yet, the impact of violating this principle on coverage remains underexplored, making it ambiguous in practical applications. In this work, we empirically find that the tuning bias - the coverage gap introduced by leveraging the same dataset for tuning and calibration, is negligible for simple parameter tuning in many conformal prediction methods. In particular, we observe the scaling law of the tuning bias: this bias increases with parameter space complexity and decreases with calibration set size. Formally, we establish a theoretical framework to quantify the tuning bias and provide rigorous proof for the scaling law of the tuning bias by deriving its upper bound. In the end, we discuss how to reduce the tuning bias, guided by the theories we developed.
Sample Complexity of Bias Detection with Subsampled Point-to-Subspace Distances
Authors: German Martinez Matilla, Jakub Marecek
Date: 2025-02-04 00:00:00
Tasks: Bias Detection

Sample complexity of bias estimation is a lower bound on the runtime of any bias detection method. Many regulatory frameworks require the bias to be tested for all subgroups, whose number grows exponentially with the number of protected attributes. Unless one wishes to run a bias detection with a doubly-exponential run-time, one should like to have polynomial complexity of bias detection for a single subgroup. At the same time, the reference data may be based on surveys, and thus come with non-trivial uncertainty. Here, we reformulate bias detection as a point-to-subspace problem on the space of measures and show that, for supremum norm, it can be subsampled efficiently. In particular, our probabilistically approximately correct (PAC) results are corroborated by tests on well-known instances.
A spatially resolved and lipid-structured model for macrophage populations in early human atherosclerotic lesions
Authors: Keith L. Chambers, Mary R. Myerscough, Michael G. Watson, Helen M. Byrne
Date: 2025-02-07 00:00:00
Tasks: Sensitivity

Atherosclerosis is a chronic inflammatory disease of the artery wall. The early stages of atherosclerosis are driven by interactions between lipids and monocyte-derived-macrophages (MDMs). The mechanisms that govern the spatial distribution of lipids and MDMs in the lesion remain poorly understood. In this paper, we develop a spatially-resolved and lipid-structured model for early atherosclerosis. The model development and analysis are guided by images of human coronary lesions by Nakashima et al. 2007. Consistent with their findings, the model predicts that lipid initially accumulates deep in the intima due to a spatially non-uniform LDL retention capacity. The model also qualitatively reproduces the global internal maxima in the Nakashima images only when the MDM mobility is sufficiently sensitive to lipid content, and MDM lifespan sufficiently insensitive. Introducing lipid content-dependence to MDM mobility and mean lifespan produced minimal impact on model behaviour at early times, but strongly impacted lesion composition at steady state. Increases to the sensitivity of MDM lifespan to lipid content yield lesions with fewer MDMs, less total lesion lipid content and reduced mean MDM infiltration depth. Increases to the sensitivity of MDM mobility to lipid content also reduces the MDM infiltration depth, but increases the proportion of lipid-laden MDMs. We find that MDM lipid content increases with spatial depth, regardless of blood LDL and HDL content. These results shed light on the mechanisms that drive spatial variation in the composition of early atherosclerotic lesions, and the role of macrophage lipid content in disease progression.
Revisiting convolutive blind source separation for identifying spiking motor neuron activity: From theory to practice
Authors: Thomas Klotz, Robin Rohlén
Date: 2025-02-06 00:00:00
Tasks: blind source separation, Electromyography (EMG)

Objective: Identifying the activity of motor neurons (MNs) non-invasively is possible by decomposing signals from muscles, e.g., surface electromyography (EMG) or ultrasound. The theoretical background of MN identification is convolutive blind source separation (cBSS), and different algorithms have been developed and validated. Yet, the existence and identifiability of inverse solutions and the corresponding estimation errors are not fully understood. Further, the guidelines for selecting appropriate parameters are often built on empirical observations, limiting the translation to clinical applications and other modalities. Approach: We revisited the cBSS model for MN identification, augmented it with new theoretical insights and derived a framework that can predict the existence of inverse solutions. This framework allows the quantification of estimation errors due to the imperfect inversion of the motor unit action potentials (MUAP), noise sources, and the ill-conditioning of the inverse problem. To bridge the gap between theory and practice, we used computer simulations. Main results: (1) Increasing the similarity of MUAPs or correlation between spike trains increases the bias for detecting high amplitude MUs. (2) The optimal objective function depends on the expected spike amplitude, spike amplitude statistics and the amplitude of background spikes. (3) There is some wiggle room for MN detection given non-stationary MUAPs. (4) There is no connection between MUAP duration and extension factor, in contrast to previous guidelines. (5) Source quality metrics like the silhouette score (SIL) or the pulse-to-noise ratio (PNR) are highly correlated with a source's objective function output. (6) SIL is superior to PNR. Significance: These findings will guide cBSS algorithm developments tailored to MN identification and clinical application translation.
Controllable Sequence Editing for Biological and Clinical Trajectories
Authors: Michelle M. Li, Kevin Li, Yasha Ektefaie, Ying Jin, Yepeng Huang, Shvat Messica, Tianxi Cai, Marinka Zitnik
Date: 2025-02-05 00:00:00
Tasks: counterfactual, Counterfactual Inference, Counterfactual Reasoning

Conditional generation models for longitudinal sequences can generate new or modified trajectories given a conditioning input. While effective at generating entire sequences, these models typically lack control over the timing and scope of the edits. Most existing approaches either operate on univariate sequences or assume that the condition affects all variables and time steps. However, many scientific and clinical applications require more precise interventions, where a condition takes effect only after a specific time and influences only a subset of variables. We introduce CLEF, a controllable sequence editing model for conditional generation of immediate and delayed effects in multivariate longitudinal sequences. CLEF learns temporal concepts that encode how and when a condition alters future sequence evolution. These concepts allow CLEF to apply targeted edits to the affected time steps and variables while preserving the rest of the sequence. We evaluate CLEF on 6 datasets spanning cellular reprogramming and patient health trajectories, comparing against 9 state-of-the-art baselines. CLEF improves immediate sequence editing accuracy by up to 36.01% (MAE). Unlike prior models, CLEF enables one-step conditional generation at arbitrary future times, outperforming them in delayed sequence editing by up to 65.71% (MAE). We test CLEF under counterfactual inference assumptions and show up to 63.19% (MAE) improvement on zero-shot conditional generation of counterfactual trajectories. In a case study of patients with type 1 diabetes mellitus, CLEF identifies clinical interventions that generate realistic counterfactual trajectories shifted toward healthier outcomes.
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
Authors: Zehui Li, Vallijah Subasri, Yifei Shen, Dongsheng Li, Yiren Zhao, Guy-Bart Stan, Caihua Shan
Date: 2025-02-05 00:00:00
Tasks: Multi-Task Learning

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127
Graph Structure Learning for Tumor Microenvironment with Cell Type Annotation from non-spatial scRNA-seq data
Authors: Yu-An Huang, Yue-Chao Li, Hai-Ru You, Jie Pan, Xiyue Cao, Xinyuan Li, Zhi-An Huang, Zhu-Hong You
Date: 2025-02-04 00:00:00
Tasks: Graph Neural Network, Graph structure learning, Type prediction

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however, lack spatial context and rely on incomplete datasets of ligand-receptor interactions (LRIs), limiting accurate cell type annotation and cell-cell communication (CCC) inference. This study addresses these challenges using a novel graph neural network (GNN) model that enhances cell type prediction and cell interaction analysis. Our study utilized a dataset consisting of 49,020 cells from 19 patients across three cancer types: Leukemia, Breast Invasive Carcinoma, and Colorectal Cancer. The proposed scGSL model demonstrated robust performance, achieving an average accuracy of 84.83%, precision of 86.23%, recall of 81.51%, and an F1 score of 80.92% across all datasets. These metrics represent a significant enhancement over existing methods, which typically exhibit lower performance metrics. Additionally, by reviewing existing literature on gene interactions within the TME, the scGSL model proves to robustly identify biologically meaningful gene interactions in an unsupervised manner, validated by significant expression differences in key gene pairs across various cancers. The source code and data used in this paper can be found in https://github.com/LiYuechao1998/scGSL.
A Foundational Brain Dynamics Model via Stochastic Optimal Control
Authors: Joonhyeong Park, Byoungwoo Park, Chang-Bae Bang, JungWon Choi, Hyungjin Chung, Byung-Hoon Kim, Juho Lee
Date: 2025-02-07 00:00:00
Tasks: Prognosis, Representation Learning, Self-Supervised Learning

We introduce a foundational model for brain dynamics that utilizes stochastic optimal control (SOC) and amortized inference. Our method features a continuous-discrete state space model (SSM) that can robustly handle the intricate and noisy nature of fMRI signals. To address computational limitations, we implement an approximation strategy grounded in the SOC framework. Additionally, we present a simulation-free latent dynamics approach that employs locally linear approximations, facilitating efficient and scalable inference. For effective representation learning, we derive an Evidence Lower Bound (ELBO) from the SOC formulation, which integrates smoothly with recent advancements in self-supervised learning (SSL), thereby promoting robust and transferable representations. Pre-trained on extensive datasets such as the UKB, our model attains state-of-the-art results across a variety of downstream tasks, including demographic prediction, trait analysis, disease diagnosis, and prognosis. Moreover, evaluating on external datasets such as HCP-A, ABIDE, and ADHD200 further validates its superior abilities and resilience across different demographic and clinical distributions. Our foundational model provides a scalable and efficient approach for deciphering brain dynamics, opening up numerous applications in neuroscience.
Shifting Attention to You: Personalized Brain-Inspired AI Models
Authors: Stephen Chong Zhao, Yang Hu, Jason Lee, Andrew Bender, Trisha Mazumdar, Mark Wallace, David A. Tovar
Date: 2025-02-07 00:00:00

The integration of human and artificial intelligence offers a powerful avenue for advancing our understanding of information processing, as each system provides unique computational insights. However, despite the promise of human-AI integration, current AI models are largely trained on massive datasets, optimized for population-level performance, lacking mechanisms to align their computations with individual users' perceptual semantics and neural dynamics. Here we show that integrating human behavioral insights and millisecond scale neural data within a fine tuned CLIP based model not only captures generalized and individualized aspects of perception but also over doubles behavioral performance compared to the unmodified CLIP baseline. By embedding human inductive biases and mirroring dynamic neural processes during training, personalized neural fine tuning improves predictions of human similarity judgments and tracks the temporal evolution of individual neural responses. Our work establishes a novel, interpretable framework for designing adaptive AI systems, with broad implications for neuroscience, personalized medicine, and human-computer interaction.
How the Stroop Effect Arises from Optimal Response Times in Laterally Connected Self-Organizing Maps
Authors: Divya Prabhakaran, Uli Grasemann, Swathi Kiran, Risto Miikkulainen
Date: 2025-02-05 00:00:00

The Stroop effect refers to cognitive interference in a color-naming task: When the color and the word do not match, the response is slower and more likely to be incorrect. The Stroop task is used to assess cognitive flexibility, selective attention, and executive function. This paper implements the Stroop task with self-organizing maps (SOMs): Target color and the competing word are inputs for the semantic and lexical maps, associative connections bring color information to the lexical map, and lateral connections combine their effects over time. The model achieved an overall accuracy of 84.2%, with significantly fewer errors and faster responses in congruent compared to no-input and incongruent conditions. The model's effect is a side effect of optimizing response times, and can thus be seen as a cost associated with overall efficient performance. The model can further serve studying neurologically-inspired cognitive control and related phenomena.