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Haris Vikalo

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10 papers

2 author rows

TMLR Journal 2026 Journal Article

Transformers as Implicit State Estimators: In-Context Learning in Dynamical Systems

Usman Akram
Haris Vikalo

Predicting the behavior of a dynamical system from noisy observations of its past outputs is a classical problem encountered across engineering and science. For linear systems with Gaussian inputs, the Kalman filter -- the best linear minimum mean-square error estimator of the state trajectory -- is optimal in the Bayesian sense. For nonlinear systems, Bayesian filtering is typically approached using suboptimal heuristics such as the Extended Kalman Filter (EKF), or numerical methods such as particle filtering (PF). In this work, we show that transformers, employed in an in-context learning (ICL) setting, can implicitly infer hidden states in order to predict the outputs of a wide family of dynamical systems, without test-time gradient updates or explicit knowledge of the system model. Specifically, when provided with a short context of past input–output pairs and, optionally, system parameters, a frozen transformer accurately predicts the current output. In linear-Gaussian regimes, its predictions closely match those of the Kalman filter; in nonlinear regimes, its performance approaches that of EKF and PF. Moreover, prediction accuracy degrades gracefully when key parameters, such as the state-transition matrix, are withheld from the context, demonstrating robustness and implicit parameter inference. These findings suggest that transformer in-context learning provides a flexible, non-parametric alternative for output prediction in dynamical systems, grounded in implicit latent-state estimation.

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AAAI Conference 2024 Conference Paper

Fed-QSSL: A Framework for Personalized Federated Learning under Bitwidth and Data Heterogeneity

Yiyue Chen
Haris Vikalo
Chianing Wang

Motivated by high resource costs of centralized machine learning schemes as well as data privacy concerns, federated learning (FL) emerged as an efficient alternative that relies on aggregating locally trained models rather than collecting clients' potentially private data. In practice, available resources and data distributions vary from one client to another, creating an inherent system heterogeneity that leads to deterioration of the performance of conventional FL algorithms. In this work, we present a federated quantization-based self-supervised learning scheme (Fed-QSSL) designed to address heterogeneity in FL systems. At clients' side, to tackle data heterogeneity we leverage distributed self-supervised learning while utilizing low-bit quantization to satisfy constraints imposed by local infrastructure and limited communication resources. At server's side, Fed-QSSL deploys de-quantization, weighted aggregation and re-quantization, ultimately creating models personalized to both data distribution as well as specific infrastructure of each client's device. We validated the proposed algorithm on real world datasets, demonstrating its efficacy, and theoretically analyzed impact of low-bit training on the convergence and robustness of the learned models.

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NeurIPS Conference 2024 Conference Paper

Heterogeneity-Guided Client Sampling: Towards Fast and Efficient Non-IID Federated Learning

Huancheng Chen
Haris Vikalo

Statistical heterogeneity of data present at client devices in a federated learning (FL) system renders the training of a global model in such systems difficult. Particularly challenging are the settings where due to communication resource constraints only a small fraction of clients can participate in any given round of FL. Recent approaches to training a global model in FL systems with non-IID data have focused on developing client selection methods that aim to sample clients with more informative updates of the model. However, existing client selection techniques either introduce significant computation overhead or perform well only in the scenarios where clients have data with similar heterogeneity profiles. In this paper, we propose HiCS-FL (Federated Learning via Hierarchical Clustered Sampling), a novel client selection method in which the server estimates statistical heterogeneity of a client's data using the client’s update of the network’s output layer and relies on this information to cluster and sample the clients. We analyze the ability of the proposed techniques to compare heterogeneity of different datasets, and characterize convergence of the training process that deploys the introduced client selection method. Extensive experimental results demonstrate that in non-IID settings HiCS-FL achieves faster convergence than state-of-the-art FL client selection schemes. Notably, HiCS-FL drastically reduces computation cost compared to existing selection schemes and is adaptable to different heterogeneity scenarios.

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ICML Conference 2024 Conference Paper

Recovering Labels from Local Updates in Federated Learning

Huancheng Chen
Haris Vikalo

Gradient inversion (GI) attacks present a threat to the privacy of clients in federated learning (FL) by aiming to enable reconstruction of the clients’ data from communicated model updates. A number of such techniques attempts to accelerate data recovery by first reconstructing labels of the samples used in local training. However, existing label extraction methods make strong assumptions that typically do not hold in realistic FL settings. In this paper we present a novel label recovery scheme, Recovering Labels from Local Updates (RLU), which provides near-perfect accuracy when attacking untrained (most vulnerable) models. More significantly, RLU achieves high performance even in realistic real-world settings where the clients in an FL system run multiple local epochs, train on heterogeneous data, and deploy various optimizers to minimize different objective functions. Specifically, RLU estimates labels by solving a least-square problem that emerges from the analysis of the correlation between labels of the data points used in a training round and the resulting update of the output layer. The experimental results on several datasets, architectures, and data heterogeneity scenarios demonstrate that the proposed method consistently outperforms existing baselines, and helps improve quality of the reconstructed images in GI attacks in terms of both PSNR and LPIPS.

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ICLR Conference 2023 Conference Paper

The Best of Both Worlds: Accurate Global and Personalized Models through Federated Learning with Data-Free Hyper-Knowledge Distillation

Huancheng Chen
Chianing Wang
Haris Vikalo

Heterogeneity of data distributed across clients limits the performance of global models trained through federated learning, especially in the settings with highly imbalanced class distributions of local datasets. In recent years, personalized federated learning (pFL) has emerged as a potential solution to the challenges presented by heterogeneous data. However, existing pFL methods typically enhance performance of local models at the expense of the global model's accuracy. We propose FedHKD (Federated Hyper-Knowledge Distillation), a novel FL algorithm in which clients rely on knowledge distillation (KD) to train local models. In particular, each client extracts and sends to the server the means of local data representations and the corresponding soft predictions -- information that we refer to as ``hyper-knowledge". The server aggregates this information and broadcasts it to the clients in support of local training. Notably, unlike other KD-based pFL methods, FedHKD does not rely on a public dataset nor it deploys a generative model at the server. We analyze convergence of FedHKD and conduct extensive experiments on visual datasets in a variety of scenarios, demonstrating that FedHKD provides significant improvement in both personalized as well as global model performance compared to state-of-the-art FL methods designed for heterogeneous data settings.

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AAAI Conference 2022 Conference Paper

Federated Dynamic Sparse Training: Computing Less, Communicating Less, Yet Learning Better

Sameer Bibikar
Haris Vikalo
Zhangyang Wang
Xiaohan Chen

Federated learning (FL) enables distribution of machine learning workloads from the cloud to resource-limited edge devices. Unfortunately, current deep networks remain not only too compute-heavy for inference and training on edge devices, but also too large for communicating updates over bandwidth-constrained networks. In this paper, we develop, implement, and experimentally validate a novel FL framework termed Federated Dynamic Sparse Training (FedDST) by which complex neural networks can be deployed and trained with substantially improved efficiency in both ondevice computation and in-network communication. At the core of FedDST is a dynamic process that extracts and trains sparse sub-networks from the target full network. With this scheme, “two birds are killed with one stone: ” instead of full models, each client performs efficient training of its own sparse networks, and only sparse networks are transmitted between devices and the cloud. Furthermore, our results reveal that the dynamic sparsity during FL training more flexibly accommodates local heterogeneity in FL agents than the fixed, shared sparse masks. Moreover, dynamic sparsity naturally introduces an “in-time self-ensembling effect” into the training dynamics, and improves the FL performance even over dense training. In a realistic and challenging non i. i. d. FL setting, FedDST consistently outperforms competing algorithms in our experiments: for instance, at any fixed upload data cap on non-iid CIFAR-10, it gains an impressive accuracy advantage of 10% over FedAvgM when given the same upload data cap; the accuracy gap remains 3% even when FedAvgM is given 2× the upload data cap, further demonstrating efficacy of FedDST. Code is available at: https: //github. com/bibikar/feddst.

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UAI Conference 2021 Conference Paper

No-regret learning with high-probability in adversarial Markov decision processes

Mahsa Ghasemi
Abolfazl Hashemi
Haris Vikalo
Ufuk Topcu

In a variety of problems, a decision-maker is unaware of the loss function associated with a task, yet it has to minimize this unknown loss in order to accomplish the task. Furthermore, the decision-maker’s task may evolve, resulting in a varying loss function. In this setting, we explore sequential decision-making problems modeled by adversarial Markov decision processes, where the loss function may arbitrarily change at every time step. We consider the bandit feedback scenario, where the agent observes only the loss corresponding to its actions. We propose an algorithm, called online relative-entropy policy search with implicit exploration, that achieves a sublinear regret not only in expectation but, more importantly, with high probability. In particular, we prove that by employing an optimistically biased loss estimator, the proposed algorithm achieves a regret of $\tilde{\mathcal{O}}((T|\act||\st|)^{\pp} \sqrt{\tau})$, where $|\st|$ is the number of states, $|\act|$ is the number of actions, $\tau$ is the mixing time, and $T$ is the time horizon. To our knowledge, the proposed algorithm is the first scheme that enjoys such high-probability regret bounds for general adversarial Markov decision processes under the presence of bandit feedback.

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NeurIPS Conference 2020 Conference Paper

A Convolutional Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction

Ziqi Ke
Haris Vikalo

Haplotype assembly and viral quasispecies reconstruction are challenging tasks concerned with analysis of genomic mixtures using sequencing data. High-throughput sequencing technologies generate enormous amounts of short fragments (reads) which essentially oversample components of a mixture; the representation redundancy enables reconstruction of the components (haplotypes, viral strains). The reconstruction problem, known to be NP-hard, boils down to grouping together reads originating from the same component in a mixture. Existing methods struggle to solve this problem with required level of accuracy and low runtimes; the problem is becoming increasingly more challenging as the number and length of the components increase. This paper proposes a read clustering method based on a convolutional auto-encoder designed to first project sequenced fragments to a low-dimensional space and then estimate the probability of the read origin using learned embedded features. The components are reconstructed by finding consensus sequences that agglomerate reads from the same origin. Mini-batch stochastic gradient descent and dimension reduction of reads allow the proposed method to efficiently deal with massive numbers of long reads. Experiments on simulated, semi-experimental and experimental data demonstrate the ability of the proposed method to accurately reconstruct haplotypes and viral quasispecies, often demonstrating superior performance compared to state-of-the-art methods. Source codes are available at https: //github. com/WuLoli/CAECseq.

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AAAI Conference 2020 Conference Paper

A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction

Ziqi Ke
Haris Vikalo

Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities. Highthroughput DNA sequencing platforms oversample mixture components to provide massive amounts of reads whose relative positions can be determined by mapping the reads to a known reference genome; assembly of the components, however, requires discovery of the reads’ origin – an NP-hard problem that the existing methods struggle to solve with the required level of accuracy. In this paper, we present a learning framework based on a graph auto-encoder designed to exploit structural properties of sequencing data. The algorithm is a neural network which essentially trains to ignore sequencing errors and infers the posterior probabilities of the origin of sequencing reads. Mixture components are then reconstructed by ﬁnding consensus of the reads determined to originate from the same genomic component. Results on realistic synthetic as well as experimental data demonstrate that the proposed framework reliably assembles haplotypes and reconstructs viral communities, often signiﬁcantly outperforming state-ofthe-art techniques. Source codes, datasets and supplementary document are available at https: //github. com/WuLoli/GAEseq.

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ICML Conference 2019 Conference Paper

Submodular Observation Selection and Information Gathering for Quadratic Models

Abolfazl Hashemi
Mahsa Ghasemi
Haris Vikalo
Ufuk Topcu

We study the problem of selecting most informative subset of a large observation set to enable accurate estimation of unknown parameters. This problem arises in a variety of settings in machine learning and signal processing including feature selection, phase retrieval, and target localization. Since for quadratic measurement models the moment matrix of the optimal estimator is generally unknown, majority of prior work resorts to approximation techniques such as linearization of the observation model to optimize the alphabetical optimality criteria of an approximate moment matrix. Conversely, by exploiting a connection to the classical Van Trees’ inequality, we derive new alphabetical optimality criteria without distorting the relational structure of the observation model. We further show that under certain conditions on parameters of the problem these optimality criteria are monotone and (weak) submodular set functions. These results enable us to develop an efficient greedy observation selection algorithm uniquely tailored for quadratic models, and provide theoretical bounds on its achievable utility.

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