Electrocardiogram (ECG) signals provide essential information about the heart's condition and are widely used for diagnosing cardiovascular diseases. The morphology of a single heartbeat over the available leads is a primary biosignal for monitoring cardiac conditions. However, analyzing heartbeat morphology can be challenging due to noise and artifacts, missing leads, and a lack of annotated data.Generative models, such as denoising diffusion generative models (DDMs), have proven successful in generating complex data. We introduce $\texttt{BeatDiff}$, a light-weight DDM tailored for the morphology of multiple leads heartbeats.We then show that many important ECG downstream tasks can be formulated as conditional generation methods in a Bayesian inverse problem framework using $\texttt{BeatDiff}$ as priors. We propose $\texttt{EM-BeatDiff}$, an Expectation-Maximization algorithm, to solve this conditional generation tasks without fine-tuning. We illustrate our results with several tasks, such as removal of ECG noise and artifacts (baseline wander, electrode motion), reconstruction of a 12-lead ECG from a single lead (useful for ECG reconstruction of smartwatch experiments), and unsupervised explainable anomaly detection. Numerical experiments show that the combination of $\texttt{BeatDiff}$ and $\texttt{EM-BeatDiff}$ outperforms SOTA methods for the problems considered in this work.
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Predicting high-fidelity 3D structures of atomic systems is a fundamental yet challenging problem in scientific domains. While recent work demonstrates the advantage of generative models in this realm, the exploration of different probability paths are still insufficient, and hallucinations during sampling are persistently occurring. To address these pitfalls, we introduce FlowDPO, a novel framework that explores various probability paths with flow matching models and further suppresses hallucinations using Direct Preference Optimization (DPO) for structure generation. Our approach begins with a pre-trained flow matching model to generate multiple candidate structures for each training sample. These structures are then evaluated and ranked based on their distance to the ground truth, resulting in an automatic preference dataset. Using this dataset, we apply DPO to optimize the original model, improving its performance in generating structures closely aligned with the desired reference distribution. As confirmed by our theoretical analysis, such paradigm and objective function are compatible with arbitrary Gaussian paths, exhibiting favorable universality. Extensive experimental results on antibodies and crystals demonstrate substantial benefits of our FlowDPO, highlighting its potential to advance the field of 3D structure prediction with generative models.
Miscellaneous Aspects of Machine Learning · General Machine Learning Techniques
We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular *low displacement rank*) for integrating tensor fields defined on weighted trees. Several applications of the resulting *fast tree-field integrators* (FTFIs) are presented, including: (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) *Topological Transformers* (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as **three** extra learnable parameters per Transformer layer, leading to **1.0-1.5\%+** accuracy gains. Importantly, most of FTFIs are **exact** methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide **5.7-13x** speedups. We also provide an extensive theoretical analysis of our methods.
Trustworthy Machine Learning
It is well known that query-based attacks tend to have relatively higher successrates in adversarial black-box attacks. While research on black-box attacks is activelybeing conducted, relatively few studies have focused on pixel attacks thattarget only a limited number of pixels. In image classification, query-based pixelattacks often rely on patches, which heavily depend on randomness and neglectthe fact that scattered pixels are more suitable for adversarial attacks. Moreover, tothe best of our knowledge, query-based pixel attacks have not been explored in thefield of object detection. To address these issues, we propose a novel pixel-basedblack-box attack called Remember and Forget Pixel Attack using ReinforcementLearning(RFPAR), consisting of two main components: the Remember and Forgetprocesses. RFPAR mitigates randomness and avoids patch dependency byleveraging rewards generated through a one-step RL algorithm to perturb pixels.RFPAR effectively creates perturbed images that minimize the confidence scoreswhile adhering to limited pixel constraints. Furthermore, we advance our proposedattack beyond image classification to object detection, where RFPAR reducesthe confidence scores of detected objects to avoid detection. Experimentson the ImageNet-1K dataset for classification show that RFPAR outperformedstate-of-the-art query-based pixel attacks. For object detection, using the MSCOCOdataset with YOLOv8 and DDQ, RFPAR demonstrates comparable mAPreduction to state-of-the-art query-based attack while requiring fewer query. Furtherexperiments on the Argoverse dataset using YOLOv8 confirm that RFPAReffectively removed objects on a larger scale dataset. Our code is available athttps://github.com/KAU-QuantumAILab/RFPAR.
Computer Vision
A proper scene representation is central to the pursuit of spatial intelligence where agents can robustly reconstruct and efficiently understand 3D scenes. A scene representation is either metric, such as landmark maps in 3D reconstruction, 3D bounding boxes in object detection, or voxel grids in occupancy prediction, or topological, such as pose graphs with loop closures in SLAM or visibility graphs in SfM. In this work, we propose to build Multiview Scene Graphs (MSG) from unposed images, representing a scene topologically with interconnected place and object nodes. The task of building MSG is challenging for existing representation learning methods since it needs to jointly address both visual place recognition, object detection, and object association from images with limited fields of view and potentially large viewpoint changes. To evaluate any method tackling this task, we developed an MSG dataset and annotation based on a public 3D dataset. We also propose an evaluation metric based on the intersection-over-union score of MSG edges. Moreover, we develop a novel baseline method built on mainstream pretrained vision models, combining visual place recognition and object association into one Transformer decoder architecture. Experiments demonstrate that our method has superior performance compared to existing relevant baselines.
We study the convergence behavior of a generalized Frank-Wolfe algorithm in constrained (stochastic) monotone variational inequality (MVI) problems. In recent years, there have been numerous efforts to design algorithms for solving constrained MVI problems due to their connections with optimization, machine learning, and equilibrium computation in games. Most work in this domain has focused on extensions of simultaneous gradient play, with particular emphasis on understanding the convergence properties of extragradient and optimistic gradient methods. In contrast, we examine the performance of an algorithm from another well-known class of optimization algorithms: Frank-Wolfe. We show that a generalized variant of this algorithm achieves a fast $\mathcal{O}(T^{-1/2})$ last-iterate convergence rate in constrained MVI problems. By drawing connections between our generalized Frank-Wolfe algorithm and the well-known smoothed fictitious play (FP) from game theory, we also derive a finite-sample convergence rate for smoothed FP in zero-sum matrix games. Furthermore, we demonstrate that a stochastic variant of the generalized Frank-Wolfe algorithm for MVI problems also converges in a last-iterate sense, albeit at a slower $\mathcal{O}(T^{-1/6})$ convergence rate.
Computer Vision
Accurate and robust 3D object detection is a critical component in autonomous vehicles and robotics. While recent radar-camera fusion methods have made significant progress by fusing information in the bird's-eye view (BEV) representation, they often struggle to effectively capture the motion of dynamic objects, leading to limited performance in real-world scenarios. In this paper, we introduce CRT-Fusion, a novel framework that integrates temporal information into radar-camera fusion to address this challenge. Our approach comprises three key modules: Multi-View Fusion (MVF), Motion Feature Estimator (MFE), and Motion Guided Temporal Fusion (MGTF). The MVF module fuses radar and image features within both the camera view and bird's-eye view, thereby generating a more precise unified BEV representation. The MFE module conducts two simultaneous tasks: estimation of pixel-wise velocity information and BEV segmentation. Based on the velocity and the occupancy score map obtained from the MFE module, the MGTF module aligns and fuses feature maps across multiple timestamps in a recurrent manner. By considering the motion of dynamic objects, CRT-Fusion can produce robust BEV feature maps, thereby improving detection accuracy and robustness. Extensive evaluations on the challenging nuScenes dataset demonstrate that CRT-Fusion achieves state-of-the-art performance for radar-camera-based 3D object detection. Our approach outperforms the previous best method in terms of NDS by +1.7%, while also surpassing the leading approach in mAP by +1.4%. These significant improvements in both metrics showcase the effectiveness of our proposed fusion strategy in enhancing the reliability and accuracy of 3D object detection.
Computational Biology
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of determining their microbial compositions. In this paper, we revisit k-mer-based representations of genomes and provide a theoretical analysis of their use in representation learning. Based on the analysis, we propose a lightweight and scalable model for performing metagenomic binning at the genome read level, relying only on the k-mer compositions of the DNA fragments. We compare the model to recent genome foundation models and demonstrate that while the models are comparable in performance, the proposed model is significantly more effective in terms of scalability, a crucial aspect for performing metagenomic binning of real-world data sets.
Optimization · Non-Convex
Adaptive methods are extremely popular in machine learning as they make learning rate tuning less expensive. This paper introduces a novel optimization algorithm named KATE, which presents a scale-invariant adaptation of the well-known AdaGrad algorithm. We prove the scale-invariance of KATE for the case of Generalized Linear Models. Moreover, for general smooth non-convex problems, we establish a convergence rate of $O((\log T)/\sqrt{T})$ for KATE, matching the best-known ones for AdaGrad and Adam. We also compare KATE to other state-of-the-art adaptive algorithms Adam and AdaGrad in numerical experiments with different problems, including complex machine learning tasks like image classification and text classification on real data. The results indicate that KATE consistently outperforms AdaGrad and matches/surpasses the performance of Adam in all considered scenarios.
The $k$-sparse parity problem is a classical problem in computational complexity and algorithmic theory, serving as a key benchmark for understanding computational classes. In this paper, we solve the $k$-sparse parity problem with sign stochastic gradient descent, a variant of stochastic gradient descent (SGD) on two-layer fully-connected neural networks. We demonstrate that this approach can efficiently solve the $k$-sparse parity problem on a $d$-dimensional hypercube ($k\le O(\sqrt{d})$) with a sample complexity of $\tilde{O}(d^{k-1})$ using $2^{\Theta(k)}$ neurons, matching the established $\Omega(d^{k})$ lower bounds of Statistical Query (SQ) models. Our theoretical analysis begins by constructing a good neural network capable of correctly solving the $k$-parity problem. We then demonstrate how a trained neural network with sign SGD can effectively approximate this good network, solving the $k$-parity problem with small statistical errors. To the best of our knowledge, this is the first result that matches the SQ lower bound for solving $k$-sparse parity problem using gradient-based methods.
Trustworthy Machine Learning
Out-of-Distribution (OoD) detection is vital for the reliability of Deep Neural Networks (DNNs).Existing works have shown the insufficiency of Principal Component Analysis (PCA) straightforwardly applied on the features of DNNs in detecting OoD data from In-Distribution (InD) data.The failure of PCA suggests that the network features residing in OoD and InD are not well separated by simply proceeding in a linear subspace, which instead can be resolved through proper non-linear mappings.In this work, we leverage the framework of Kernel PCA (KPCA) for OoD detection, and seek suitable non-linear kernels that advocate the separability between InD and OoD data in the subspace spanned by the principal components.Besides, explicit feature mappings induced from the devoted task-specific kernels are adopted so that the KPCA reconstruction error for new test samples can be efficiently obtained with large-scale data.Extensive theoretical and empirical results on multiple OoD data sets and network structures verify the superiority of our KPCA detector in efficiency and efficacy with state-of-the-art detection performance.
Time Series
Time series forecasting has played a pivotal role across various industries, including finance, transportation, energy, healthcare, and climate. Due to the abundant seasonal information they contain, timestamps possess the potential to offer robust global guidance for forecasting techniques. However, existing works primarily focus on local observations, with timestamps being treated merely as an optional supplement that remains underutilized. When data gathered from the real world is polluted, the absence of global information will damage the robust prediction capability of these algorithms. To address these problems, we propose a novel framework named GLAFF. Within this framework, the timestamps are modeled individually to capture the global dependencies. Working as a plugin, GLAFF adaptively adjusts the combined weights for global and local information, enabling seamless collaboration with any time series forecasting backbone. Extensive experiments conducted on nine real-world datasets demonstrate that GLAFF significantly enhances the average performance of widely used mainstream forecasting models by 12.5\%, surpassing the previous state-of-the-art method by 5.5\%.
Privacy
Federated learning (FL) is inherently susceptible to privacy breaches and poisoning attacks. To tackle these challenges, researchers have separately devised secure aggregation mechanisms to protect data privacy and robust aggregation methods that withstand poisoning attacks. However, simultaneously addressing both concerns is challenging; secure aggregation facilitates poisoning attacks as most anomaly detection techniques require access to unencrypted local model updates, which are obscured by secure aggregation. Few recent efforts to simultaneously tackle both challenges offen depend on impractical assumption of non-colluding two-server setups that disrupt FL's topology, or three-party computation which introduces scalability issues, complicating deployment and application. To overcome this dilemma, this paper introduce a Dual Defense Federated learning (DDFed) framework. DDFed simultaneously boosts privacy protection and mitigates poisoning attacks, without introducing new participant roles or disrupting the existing FL topology. DDFed initially leverages cutting-edge fully homomorphic encryption (FHE) to securely aggregate model updates, without the impractical requirement for non-colluding two-server setups and ensures strong privacy protection. Additionally, we proposes a unique two-phase anomaly detection mechanism for encrypted model updates, featuring secure similarity computation and feedback-driven collaborative selection, with additional measures to prevent potential privacy breaches from Byzantine clients incorporated into the detection process. We conducted extensive experiments on various model poisoning attacks and FL scenarios, including both cross-device and cross-silo FL. Experiments on publicly available datasets demonstrate that DDFed successfully protects model privacy and effectively defends against model poisoning threats.
Learning Theory
We develop and analyze data subsampling techniques for Poisson regression, the standard model for count data $y\in\mathbb{N}$. In particular, we consider the Poisson generalized linear model with ID- and square root-link functions. We consider the method of \emph{coresets}, which are small weighted subsets that approximate the loss function of Poisson regression up to a factor of $1\pm\varepsilon$. We show $\Omega(n)$ lower bounds against coresets for Poisson regression that continue to hold against arbitrary data reduction techniques up to logarithmic factors. By introducing a novel complexity parameter and a domain shifting approach, we show that sublinear coresets with $1\pm\varepsilon$ approximation guarantee exist when the complexity parameter is small. In particular, the dependence on the number of input points can be reduced to polylogarithmic. We show that the dependence on other input parameters can also be bounded sublinearly, though not always logarithmically. In particular, we show that the square root-link admits an $O(\log(y_{\max}))$ dependence, where $y_{\max}$ denotes the largest count presented in the data, while the ID-link requires a $\Theta(\sqrt{y_{\max}/\log(y_{\max})})$ dependence. As an auxiliary result for proving the tightness of the bound with respect to $y_{\max}$ in the case of the ID-link, we show an improved bound on the principal branch of the Lambert $W_0$ function, which may be of independent interest. We further show the limitations of our analysis when $p$th degree root-link functions for $p\geq 3$ are considered, which indicate that other analytical or computational methods would be required if such a generalization is even possible.
Computer Vision
3D object detection is fundamentally important for various emerging applications, including autonomous driving and robotics. A key requirement for training an accurate 3D object detector is the availability of a large amount of LiDAR-based point cloud data. Unfortunately, labeling point cloud data is extremely challenging, as accurate 3D bounding boxes and semantic labels are required for each potential object. This paper proposes a unified active 3D object detection framework, for greatly reducing the labeling cost of training 3D object detectors. Our framework is based on a novel formulation of submodular optimization, specifically tailored to the problem of active 3D object detection. In particular, we address two fundamental challenges associated with active 3D object detection: data imbalance and the need to cover the distribution of the data, including LiDAR-based point cloud data of varying difficulty levels. Extensive experiments demonstrate that our method achieves state-of-the-art performance with high computational efficiency compared to existing active learning methods. The code is available at [https://github.com/RuiyuM/STONE](https://github.com/RuiyuM/STONE)
Deep Learning · Everything Else
Pre-trained foundation models, particularly large language models, have achieved remarkable success and led to massive fine-tuned variants. These models are commonly fine-tuned locally and then uploaded by users to cloud platforms such as HuggingFace for secure storage. However, the huge model number and their billion-level parameters impose heavy storage overhead for cloud with limited resources. Our empirical and theoretical analysis reveals that most fine-tuned models in cloud have a small difference (delta) from their pre-trained models. To this end, we propose a novel lossless compression scheme FM-Delta specifically for storing massive fine-tuned models in cloud. FM-Delta maps fine-tuned and pre-trained model parameters into integers with the same bits, and entropy codes their integer delta. In this way, cloud only needs to store one uncompressed pre-trained model and other compressed fine-tuned models. Extensive experiments have demonstrated that FM-Delta efficiently reduces cloud storage consumption for massive fine-tuned models by an average of around 50% with only negligible additional time in most end-to-end cases. For example, on up to 10 fine-tuned models in the GPT-NeoX-20B family, FM-Delta reduces the original storage requirement from 423GB to 205GB, significantly saving cloud storage costs.
Learning Theory
In this paper, we study the contextual multinomial logit (MNL) bandit problem in which a learning agent sequentially selects an assortment based on contextual information, and user feedback follows an MNL choice model.There has been a significant discrepancy between lower and upper regret bounds, particularly regarding the maximum assortment size $K$. Additionally, the variation in reward structures between these bounds complicates the quest for optimality. Under uniform rewards, where all items have the same expected reward, we establish a regret lower bound of $\Omega(d\sqrt{\smash[b]{T/K}})$ and propose a constant-time algorithm, OFU-MNL+, that achieves a matching upper bound of $\tilde{\mathcal{O}}(d\sqrt{\smash[b]{T/K}})$. We also provide instance-dependent minimax regret bounds under uniform rewards.Under non-uniform rewards, we prove a lower bound of $\Omega(d\sqrt{T})$ and an upper bound of $\tilde{\mathcal{O}}(d\sqrt{T})$, also achievable by OFU-MNL+. Our empirical studies support these theoretical findings. To the best of our knowledge, this is the first work in the contextual MNL bandit literature to prove minimax optimality --- for either uniform or non-uniform reward setting --- and to propose a computationally efficient algorithm that achieves this optimality up to logarithmic factors.
Data-centric AI · Data-centric AI methods and tools
The pretraining data of today's strongest language models remains opaque, even when their parameters are open-sourced.In particular, little is known about the proportions of different domains, languages, or code represented in the data. While a long line of membership inference attacks aim to identify training examples on an instance level, they do not extend easily to *global* statistics about the corpus. In this work, we tackle a task which we call *data mixture inference*, which aims to uncover the distributional make-up of the pretraining data. We introduce a novel attack based on a previously overlooked source of information — byte-pair encoding (BPE) tokenizers, used by the vast majority of modern language models. Our key insight is that the ordered vocabulary learned by a BPE tokenizer naturally reveals information about the token frequencies in its training data: the first token is the most common byte pair, the second is the most common pair after merging the first token, and so on. Given a tokenizer's merge list along with data samples for each category of interest (e.g., different natural languages), we formulate a linear program that solves for the relative proportion of each category in the tokenizer's training set. Importantly, to the extent to which tokenizer training data is representative of the pretraining data, we indirectly learn about the pretraining data. In controlled experiments, we show that our attack can recover mixture ratios with high precision for tokenizers trained on known mixtures of natural languages, programming languages, and data sources. We then apply our approach to off-the-shelf tokenizers released alongside recent LMs. We confirm much publicly disclosed information about these models, and also make several new inferences: GPT-4o is much more multilingual than its predecessors, training on 10x more non-English data than GPT-3.5, Llama 3 and Claude are trained on predominantly code, and many recent models are trained on 7-16% books. We hope our work sheds light on current design practices for pretraining data, and inspires continued research into data mixture inference for LMs.
Probabilistic Methods · Monte Carlo and Sampling Methods
Given a graph $G$ and a positive integer $k$, the Graphlet Sampling problem asks to sample a connected induced $k$-vertex subgraph of $G$ uniformly at random.Graphlet sampling enhances machine learning applications by transforming graph structures into feature vectors for tasks such as graph classification and subgraph identification, boosting neural network performance, and supporting clustered federated learning by capturing local structures and relationships.A recent work has shown that the problem admits an algorithm that preprocesses $G$ in time $O(nk^2 \log k + m)$, and draws one sample in expected time $k^{O(k)} \log n$, where $n=|V(G)|$ and $m=|E(G)|$. Such an algorithm relies on the assumption that the input graph fits into main memory and it does not seem to be straightforward to adapt it to very large graphs. We consider Graphlet Sampling in the semi-streaming setting, where we have a memory of $M = \Omega(n \log n)$ words, and $G$ can be only read through sequential passes over the edge list. We develop a semi-streaming algorithm that preprocesses $G$ in $p={O}(\log n)$ passes and samples $\Theta(M k^{-O(k)})$ independent uniform $k$-graphlets in $O(k)$ passes. For constant $k$, both phases run in time $O((n+m)\log n)$. We also show that the tradeoff between memory and number of passes of our algorithms is near-optimal. Our extensive evaluation on very large graphs shows the effectiveness of our algorithms.
Online Learning
We provide a full characterization of the concept classes that are optimistically universally online learnable with {0, 1} labels. The notion of optimistically universal online learning was defined in [Hanneke, 2021] in order to understand learnability under minimal assumptions. In this paper, following the philosophy behind that work, we investigate two questions, namely, for every concept class: (1) What are the minimal assumptions on the data process admitting online learnability? (2) Is there a learning algorithm which succeeds under every data process satisfying the minimal assumptions? Such an algorithm is said to be optimistically universal for the given concept class. We resolve both of these questions for all concept classes, and moreover, as part of our solution we design general learning algorithms for each case. Finally, we extend these algorithms and results to the agnostic case, showing an equivalence between the minimal assumptions on the data process for learnability in the agnostic and realizable cases, for every concept class, as well as the equivalence of optimistically universal learnability.