Haris Vikalo

Professor, Electrical and Computer Engineering

The University of Texas at Austin

hvikalo [AT] ece.utexas.edu  ·  Google Scholar

Publications

Submitted
  • H. Zhang, S. Cha, H. B. Beytur, K. Chan, G. de Veciana, and H. Vikalo
    Online Learning for Multi-Layer Hierarchical Inference under Partial and Policy-Dependent Feedback
    submitted, 2026
  • S. Cha, H. Chen, D. Kim, H. Zhang, K. Chan, G. de Veciana, and H. Vikalo
    CoreQ: Learning-Free Mismatch Correction and Successive Rounding for Quantization
    submitted, 2026
  • D. Kim, A. de Wynter, H. Chen, H. Kim, and H. Vikalo
    Foundation-Preserving Adaptation via Generalized Rayleigh-Quotient Optimization
    submitted, 2026
  • J. Zhu, Y. Ro, J. Robertson, K. Wang, J. Li, H. Vikalo, A. Akella, and Z. Wang
    Long-Lived AI Agents Age Too: They Quietly Decay After Deployment
    submitted, 2026
  • D. Kim, H. Zhang, C. Wang, and H. Vikalo
    Class-Incremental Learning with Zero-Shot Unlearning via Activation Disentanglement
    submitted, 2026
  • J. Robertson, J. Zhu, H. Vikalo, and Z. Wang
    When Is Rank-1 Steering Cheap? Geometry, Granularity, and Budgeted Search
    submitted, 2026
  • U. Akram, F. Zhang, Y. Li, and H. Vikalo
    Diffusion-Based Channel Inpainting for Robust SRS-Based CSI Acquisition
    IEEE Communication Letters, submitted, 2026
  • S. Ahn, H. Chen, and H. Vikalo
    FedProTIP: Task-Agnostic Federated Continual Learning via Replay-Free Gradient Projection
    Transactions on Machine Learning Research, submitted, 2026
2026
  • H. Zhang, D. Kim, S. Cha, and H. Vikalo
    FedRot-LoRA: Mitigating Rotational Misalignment in Federated LoRA
    ICML 2026
  • H. Chen, J. Li, W. Zhuang, H. Vikalo, and L. Lyu
    Training-Free Layout-to-Image Generation with Marginal Attention Constraints
    CVPR Workshop on Efficient and On-Device Generation (EDGE), 2026
  • U. Akram, M. Graham, and H. Vikalo
    PRISM-AMC: Replay-Free Continual Learning for Automatic Modulation Classification
    FLICS 2026
  • Y. Chen, U. Akram, C. Wang, and H. Vikalo
    Adaptive Evolutionary Clustering for Federated Learning under Nonstationary Client Distributions
    FLICS 2026
  • H. B. Beytur, G. de Veciana, H. Vikalo, and K. Chan
    Optimal Resource Allocation for ML Model Training and Deployment under Concept Drift
    IEEE ICMLCN 2026
  • S. Cha, K. Chan, G. de Veciana, and H. Vikalo
    Joint Model Onloading and Offloading for Hierarchical Multi-Task Inference
    IEEE ICMLCN 2026
  • D. Kim, S. Cha, H. Chen, C. Wang, and H. Vikalo
    Quantized Gradient Projection for Memory-Efficient Continual Learning
    ICLR 2026
  • U. Akram and H. Vikalo
    Transformers as Implicit State Estimators: In-Context Learning in Dynamical Systems
    Transactions on Machine Learning Research, 2026
  • A. Aydin, A. G. Aydin, C. Turhan, and H. Vikalo
    Managing task offloading in viewport prediction via reinforcement learning
    IEEE Access, vol. 14, 2026
2025
  • U. Akram, Y. Chen, and H. Vikalo
    Federated self-supervised learning for automatic modulation classification in heterogeneous settings
    SPAWC 2025
  • U. Akram, F. Zhang, S. Ma, Y. Li, and H. Vikalo
    Super capacity SRS design for 5G and beyond using channel in-painting
    ICASSP 2025
  • J. Robertson, S. Consul, and H. Vikalo
    NextVir: Enabling classification of tumor-causing viruses with genomic foundation models
    PLoS Computational Biology, 21(8), 2025
  • S. Consul, J. Robertson, and H. Vikalo
    XVir: A transformer-based architecture for identifying viral reads from cancer samples
    Journal of Computational Biology, vol. 32, no. 7, 2025
  • Y. Chen, A. Hashemi, and H. Vikalo
    Accelerated distributed stochastic non-convex optimization over time-varying directed networks
    IEEE Transactions on Automatic Control, vol. 70, no. 4, 2025
  • A. G. Aydin and H. Vikalo
    Viewport prediction via adaptive edge offloading
    IEEE Networking Letters, vol. 7, no. 1, 2025
  • M. Ribero, H. Vikalo, and G. de Veciana
    Federated Learning at Scale: Addressing Client Intermittency and Resource Constraints
    IEEE Journal of Selected Topics in Signal Processing, vol. 19, no. 1, 2025
  • S. Consul, J. Robertson, and H. Vikalo
    XVir: A transformer-based architecture for identifying viral reads from cancer samples
    Journal of Computational Biology, vol. 32, no. 7, 2025
  • Y. Chen, A. Hashemi, and H. Vikalo
    Accelerated distributed stochastic non-convex optimization over time-varying directed networks
    IEEE Transactions on Automatic Control, vol. 70, no. 4, 2025
2024
  • H. Chen and H. Vikalo
    Heterogeneity-guided client sampling: Towards fast and efficient non-IID federated learning
    NeurIPS 2024
  • H. Chen and H. Vikalo
    Recovering labels from local updates in federated learning
    ICML 2024
  • H. Chen and H. Vikalo
    Mixed-precision quantization for federated learning on resource-constrained heterogeneous devices
    CVPR 2024
  • H. B. Beytur, A. Aydin, G. de Veciana, and H. Vikalo
    Optimization of offloading policies for accuracy-delay tradeoffs in hierarchical inference
    INFOCOM 2024
  • Y. Chen, C. Wang, and H. Vikalo
    Fed-QSSL: A framework for personalized federated learning under bitwidth and data heterogeneity
    AAAI 2024
  • M. Ribero and H. Vikalo
    Reducing communication in federated learning via efficient client sampling
    Pattern Recognition, vol. 148, 2024
2023
  • H. Chen and H. Vikalo
    Federated learning in non-IID settings aided by differentially private synthetic data
    CVPR Workshops 2023
  • H. Chen, C. Wang, and H. Vikalo
    The best of both worlds: Accurate global and personalized models through federated learning with data-free hyper-knowledge distillation
    ICLR 2023
  • S. Consul, Z. Ke, and H. Vikalo
    XHap: Haplotype assembly using long-distance read correlations learned by transformers
    Bioinformatics Advances, vol. 3, no. 1, 2023
  • M. Sakthi, M. Arvinte, and H. Vikalo
    Automotive RADAR sub-sampling via object detection networks: Leveraging prior signal information
    IEEE Open Journal of Intelligent Transportation Systems, vol. 4, 2023
  • Z. Ke and H. Vikalo
    Graph-based reconstruction and analysis of disease transmission networks using viral genomic data
    Journal of Computational Biology, 30(7), 2023
  • M. Ribeiro, H. Vikalo, and G. de Veciana
    Federated learning under intermittent client availability and time-varying communication constraints
    IEEE Journal of Selected Topics in Signal Processing, vol. 17, no. 1, 2023
  • Z. Ke and H. Vikalo
    Graph-based reconstruction and analysis of disease transmission networks using viral genomic data
    Journal of Computational Biology, 30(7), 2023
2022
  • S. Consul, H. B. Beytur, G. de Veciana, H. Vikalo, Z. Shamsi, A. Liu, and J. Boksiner
    RF-based Network Inference: Learning from Channel Usage and Activity Dynamics Data
    IEEE MILCOM 2022
  • M. Sakthi, A. Tewfik, M. Arvinte, and H. Vikalo
    End-to-end system for object detection from sub-sampled radar data
    EUSIPCO 2022
  • Z. Ke and H. Vikalo
    Deep learning for assembly of haplotypes and viral quasispecies from short and long sequencing reads
    ACM BCB 2022
  • S. Bibikar, H. Vikalo, Z. Wang, and X. Chen
    Federated dynamic sparse training: Computing less, communicating less, yet learning better
    AAAI 2022
  • A. Hashemi, A. Acharya, R. Das, H. Vikalo, S. Sanghavi, and I. Dhillon
    On the benefits of multiple gossip steps in communication-constrained decentralized federated learning
    IEEE Transactions on Parallel and Distributed Systems, vol. 33, no. 11, 2022
  • M. Ribero, J. Henderson, S. Williamson, and H. Vikalo
    Federated recommendations using differentially private prototypes
    Pattern Recognition, vol. 129, 2022
  • A. Hashemi, H. Vikalo, and G. de Veciana
    On the benefits of progressively increasing sampling sizes in stochastic greedy weak submodular maximization
    IEEE Transactions on Signal Processing, vol. 70, 2022
  • A. Hashemi, R. Shafipour, H. Vikalo, and G. Mateos
    Towards accelerated greedy sampling and reconstruction of bandlimited graph signals
    Signal Processing, vol. 195, 2022
  • Z. Ke and H. Vikalo
    Real-Time Radio Technology and Modulation Classification via an LSTM Auto-Encoder
    IEEE Transactions on Wireless Communications, vol. 21, no. 1, 2022
  • Y. Chen, A. Hashemi, and H. Vikalo
    Communication-efficient variance-reduced decentralized stochastic optimization over time-varying directed graphs
    IEEE Transactions on Automatic Control, vol. 67, no. 12, 2022
2021
  • S. Consul, H. Beytur, G. de Veciana, and H. Vikalo
    RF-based network inference: Theoretical foundations
    IEEE MILCOM, 2021
  • M. Ghasemi, A. Hashemi, H. Vikalo, and U. Topcu
    No-regret learning with high-probability in adversarial Markov decision processes
    UAI 2021
  • M. Stecklein, H. Beytur, H. Vikalo, and G. de Veciana
    Optimizing resource constrained distributed collaborative sensing
    IEEE ICC Workshop 2021
  • Y. Chen, A. Hashemi, and H. Vikalo
    Decentralized optimization on time-varying directed graphs under communication constraints
    ICASSP 2021
  • A. Hashemi, H. Vikalo, and G. de Veciana
    On the performance-complexity tradeoff in stochastic greedy weak submodular optimization
    ICASSP 2021
  • Z. Ke and H. Vikalo
    Real-time radio modulation classification with an LSTM auto-encoder
    ICASSP 2021
  • M. Ghasemi, A. Hashemi, U. Topcu, and H. Vikalo
    Online learning with implicit exploration in episodic Markov decision processes
    ACC 2021
  • S. Lee, X. Zheng, J. Hua, H. Vikalo, and C. Julien
    Opportunistic federated learning: An exploration of egocentric collaboration for pervasive computing applications
    IEEE PerCom 2021
  • N. M. Arzeno and H. Vikalo
    Evolutionary clustering via message passing
    IEEE Transactions on Knowledge and Data Engineering, vol. 33, no. 6, 2021
  • A. Hashemi, M. Ghasemi, H. Vikalo, and U. Topcu
    Randomized greedy sensor selection: Leveraging weak submodularity
    IEEE Transactions on Automatic Control, vol. 66, no. 1, 2021
  • A. Hashemi, M. Ghasemi, H. Vikalo, and U. Topcu
    Greedy sensor selection: Leveraging submodularity
    IEEE Transactions on Automatic Control, vol. 66, no. 1, 2021
2020
  • Z. Ke and H. Vikalo
    A convolutional auto-encoder for haplotype assembly and viral quasispecies reconstruction
    NeurIPS 2020
  • M. Ghasemi, A. Hashemi, H. Vikalo, and U. Topcu
    Identifying low-dimensional structures in Markov Chains: A nonnegative matrix factorization approach
    ACC 2020
  • M. Usman, W. Wang, M. Vasic, K. Wang, H. Vikalo, and S. Khurshid
    A study of the learnability of relational properties
    PLDI 2020
  • Z. Ke and H. Vikalo
    A graph auto-encoder for haplotype assembly and viral quasispecies reconstruction
    AAAI 2020
  • A. Sankararaman, H. Vikalo, and F. Baccelli
    ComHapDet: A spatial community detection algorithm for haplotype assembly
    BMC Genomics, 21:586, 2020
2019
  • S. Consul and H. Vikalo
    Reconstructing intra-tumor heterogeneity via convex optimization and branch-and-bound search
    ACM BCB 2019
  • S. Mourad, A. Tewfik, and H. Vikalo
    Weighted subset selection for fast SVM training
    EUSIPCO 2019
  • M. Ghasemi, A. Hashemi, U. Topcu, and H. Vikalo
    On submodularity of quadratic observation selection in constrained networked sensing systems
    ACC 2019
  • R. Shafipour, A. Hashemi, G. Mateos, and H. Vikalo
    Online topology inference from streaming stationary graph signals
    IEEE Data Science Workshop 2019
  • S. Mourad, H. Vikalo, and A. Tewfik
    Online selective training for faster neural network learning
    IEEE Data Science Workshop 2019
  • A. Hashemi, M. Ghasemi, H. Vikalo, and U. Topcu
    Submodular observation selection and information gathering for quadratic models
    ICML 2019
  • M. Ribero, D. Chizhik, R. A. Valenzuela, R. W. Heath Jr., and H. Vikalo
    Deep learning propagation models over irregular terrain
    ICASSP 2019
  • A. Hashemi and H. Vikalo
    Evolutionary subspace clustering: Discovering structure in self-expressive time-series data
    ICASSP 2019
  • S. Consul, A. Hashemi, and H. Vikalo
    A MAP framework for support recovery of sparse signals using orthogonal least squares
    ICASSP 2019
  • S. Barik and H. Vikalo
    Matrix completion and performance guarantees for single individual haplotyping
    IEEE Transactions on Signal Processing, vol. 67, no. 18, 2019
  • S. Barik and H. Vikalo
    Binary matrix completion with performance guarantees for single individual haplotyping
    IEEE Transactions on Signal Processing, vol. 67, no. 18, 2019
2018
  • A. Hashemi, O. F. Kilic, and H. Vikalo
    Near-optimal distributed estimation for a network of sensing units operating under communication constraints
    57th IEEE Conference on Decision and Control (CDC), 2018
  • A. Hashemi, R. Shafipour, H. Vikalo and G. Mateos
    A novel scheme for support identification and iterative sampling of bandlimited graph signals
    2018 IEEE Global Conference on Signal and Information Processing (GlobalSIP)
  • A. Hashemi, M. Ghasemi, H. Vikalo and U. Topcu
    A randomized greedy algorithm for near-optimal sensor scheduling in large-scale sensor networks
    The 2018 American Control Conference (ACC)
  • A. Hashemi, R. Shafipour, H. Vikalo and G. Mateos
    Sampling and reconstruction of graph signal via weak submodularity and semidefinite relaxation
    IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2018
  • A. Hashemi and H. Vikalo
    Evolutionary self-expressive models for subspace clustering
    IEEE Journal of Selected Topics in Signal Processing, vol. 12, no. 6, 2018
  • A. Hashemi and H. Vikalo
    Accelerated orthogonal least-squares for large-scale sparse reconstruction
    Digital Signal Processing, vol. 82, 2018
  • S. Ahn, Z. Ke, and H. Vikalo
    Viral quasispecies reconstruction via tensor factorization with successive removal
    Bioinformatics (ISMB Special Issue), vol. 34, no. 13, 2018
  • A. Hassibi et al. and H. Vikalo
    Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip
    Nature Biotechnology, 36, 2018
  • H. Yang, J. Chun, and H. Vikalo
    Cyclic block coordinate minimization algorithms for DOA estimation in co-prime arrays
    Signal Processing, vol. 145, 2018
  • A. Hashemi, B. Zhu, and H. Vikalo
    Sparse tensor decomposition for haplotype assembly of diploids and polyploids
    BMC Genomics, 19(Suppl 4):191, 2018
  • S. Ahn and H. Vikalo
    aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity
    Journal of Computational Biology, 2018
  • S. Ahn, Z. Ke, and H. Vikalo
    Viral quasispecies reconstruction via tensor factorization
    Bioinformatics (ISMB Special Issue), vol. 34, no. 13, 2018
  • A. Hashemi, B. Zhu, and H. Vikalo
    Sparse tensor decomposition for haplotype assembly of diploids and polyploids
    BMC Genomics, 19(Suppl 4):191, 2018
  • S. Ahn and H. Vikalo
    aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity
    Journal of Computational Biology, 2018
2017
  • S. Mourad, A. Tewfik and H. Vikalo
    Data subset selection for efficient SVM training
    The 25th European Signal Processing Conference (EUSIPCO), 2017
  • X. Zheng, H. Vikalo, S. Song, L. K. John and A. Gerstlauer
    Sampling-based binary-level cross-platform performance estimation
    Design, Estimation and Test in Europe (DATE), 2017
  • A. Hashemi and H. Vikalo
    Recovery of sparse signals via Branch-and-Bound least-squares
    IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2017
  • N. M. Arzeno and H. Vikalo
    Evolutionary affinity propagation
    IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2017
  • S. Barik and H. Vikalo
    QSdpR: Viral quasispecies reconstruction via correlation clustering
    Genomics, 2017
  • H. Si, H. Vikalo, and S. Vishwanath
    Information-theoretic analysis of haplotype assembly
    IEEE Transactions on Information Theory, vol. 63, no. 6, 2017
  • S. Das and H. Vikalo
    Optimal haplotype assembly via a branch-and-bound algorithm
    IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, vol. 3, no. 1, 2017
2016
  • A. Hashemi and H. Vikalo
    Sparse linear regression via generalized orthogonal least-squares
    IEEE GlobalSIP Symposium on Signal Processing of Big Data, 2016
  • H. Yang, J. Chun, and H. Vikalo
    Nonnegative gridless compressive sensing for co-prime arrays
    IEEE GlobalSIP Symposium on Sparse Signal Processing for Communications, 2016
  • V. Va, H. Vikalo, and R. W. Heath
    Beam tracking for mobile millimeter wave communication systems
    IEEE GlobalSIP Symposium on Transceivers and Signal Processing for 5G Wireless and mm-Wave Systems, 2016
  • C. Cai, S. Sanghavi, and H. Vikalo
    Structurally-constrained gradient descent for matrix factorization in haplotype assembly problems
    IEEE International Conference on Acoustic, Speech and Signal Processing (ICASSP), 2016
  • E. O'Reilly, F. Baccelli, G. de Veciana, and H. Vikalo
    End-to-end optimization of high-throughput DNA sequencing
    Journal of Computational Biology, 23(10), 2016
  • C. Cao, S. Sanghavi, and H. Vikalo
    Structured low-rank matrix factorization for haplotype assembly
    IEEE Journal of Selected Topics in Signal Processing, vol. 10, no. 4, 2016
  • Z. Puljiz and H. Vikalo
    Decoding genetic variations: Communications-inspired haplotype assembly
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 13, no. 3, 2016
2015
  • T. Goodall, A. C. Bovik, H. Vikalo, and N. G. Paulter Jr.
    Non-uniformity correction of IR images using natural scene statistics
    IEEE Global Conference on Signal and Information Processing (GlobalSIP), 2015
  • A. K. Gupta, S. Barik and H. Vikalo
    Distributed self localization of sensors with poisson deployment using extended Kalman filter
    IEEE Wireless Communications and Networks Conference (WCNC), 2015
  • N. M. Arzeno, K. A. Lawson, S. V. Duzinski, and H. Vikalo
    Designing optimal mortality risk prediction scores that preserve clinical knowledge
    Journal of Biomedical Informatics, vol. 56, 2015
  • S. Ahn and H. Vikalo
    Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm
    BMC Bioinformatics, 16:223, 2015
  • N. M. Arzeno and H. Vikalo
    Semi-supervised affinity propagation with soft instance-level constraints
    IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, 2015
  • S. Das and H. Vikalo
    SDhaP: Haplotype assembly for diploids and polyploids via semi-definite programming
    BMC Genomics, 16:260, 2015
2014
  • S. Das and H. Vikalo
    Optimal haplotype assembly with statistical pruning
    IEEE Workshop Conference on Signal and Information Processing (GlobalSIP), 2014
  • S. Das and H. Vikalo
    Single individual haplotyping with low rank semidefinite programming
    NIPS 2014 Workshop on Machine Learning in Computational Biology (MLCB)
  • H. Si, H. Vikalo and S. Vishwanath
    Haplotype assembly: An information-theoretic view
    IEEE Information Theory Workshop, 2014
  • Z. Puljiz and H. Vikalo
    Iterative learning of single individual haplotypes from high-throughput DNA sequencing data
    8th International Symposium on Turbo Codes and Iterative Information Processing (ISTC), 2014
  • X. Shen, M. Shamaiah, and H. Vikalo
    Iterative learning for reference-guided DNA sequence assembly from short reads: Algorithms and limits of performance
    IEEE Transactions on Signal Processing, vol. 62, no. 17, 2014
  • S. Barik and H. Vikalo
    Sparsity-aware sphere decoding: Algorithms and complexity analysis
    IEEE Transactions on Signal Processing, vol. 62, no. 9, 2014
2013
  • S. Ahn and H. Vikalo
    Deterministic sequential Monte Carlo for haplotype inference
    IEEE Global Conference on Signal and Information Processing, 2013
  • Z. Puljiz and H. Vikalo
    A message passing algorithm for haplotype assembly
    Asilomar Conference on Systems, Signals & Computers, Asilomar, pp. 1726-1729, November 3-6, 2013 (invited)
  • X. Shen, M. Shamaiah, and H. Vikalo
    Message passing algorithm for inferring consensus sequence from next-generation sequencing data
    IEEE International Symposium on Information Theory, 2013
  • N. Arzeno-Gonzalez and H. Vikalo
    Exploiting time series properties for mortality prediction in pediatric brain injury
    Workshop on Role of Machine Learning in Transforming Healthcare, 2013
  • S. Barik and H. Vikalo
    Expected complexity of sphere decoding for sparse integer least-square problems
    IEEE International Conf. on Acoustic, Signal, 2013
  • M. Park, M. Nassar, and H. Vikalo
    Bayesian active learning for drug combinations
    IEEE Transactions on Biomedical Engineering, vol. 60, no. 11, 2013
  • S. Das and H. Vikalo
    Base calling for high-throughput short-read sequencing: Dynamic programming solutions
    BMC Bioinformatics, 14:129, 2013
  • S.-H. Lee, M. Shamaiah, H. Vikalo, and S. Vishwanath
    Message-passing algorithms for coordinated spectrum sensing in cognitive radio networks
    IEEE Communications Letters, vol. 17, no. 4, 2013
2012
  • X. Shen and H. Vikalo
    A message passing algorithm for reference-guided sequence assembly from high-throughput sequencing data
    IEEE Workshop on Genomic Signal Processing and Statistics, 2012
  • C. H. Lee, N. M. Arzeno-Gonzales, J. C. Ho, H. Vikalo, and J. Ghosh
    An imputation-enhanced algorithm for ICU mortality prediction
    Computing in Cardiology (CinC), 2012
  • M. Shamaiah and H. Vikalo
    Base calling error rates in next-generation DNA sequencing
    IEEE Workshop on Statistical Signal Processing, 2012
  • M. Park, M. Nassar, B. L. Evans, and H. Vikalo
    Adaptive experimental design for drug combinations
    IEEE Workshop on Statistical Signal Processing, 2012
  • M. Shamaiah, S.-H. Lee, S. Vishwanath, and H. Vikalo
    Distributed algorithms for spectrum access in cognitive radio relay networks
    IEEE Journal on Selected Areas in Communications, vol. 30, no. 10, 2012
  • T. Wu and H. Vikalo
    Joint parameter estimation and base-calling for pyrosequencing systems
    IEEE Transactions on Signal Processing, vol. 60, no. 8, 2012
  • M. Shamaiah, S. Banerjee, and H. Vikalo
    Greedy sensor selection under channel uncertainty
    IEEE Wireless Communications Letters, vol. 1, no. 4, 2012
  • X. Shen and H. Vikalo
    ParticleCall: A particle filter for base calling in next-generation sequencing systems
    BMC Bioinformatics, 13:160, 2012
  • S. Das and H. Vikalo
    OnlineCall: Fast online parameter estimation and base calling for Illumina’s next-generation sequencing
    Bioinformatics, vol. 28, no. 13, 2012
  • M. Shamaiah, X. Shen, and H. Vikalo
    Estimating parameters of sampled diffusion processes in affinity biosensors
    IEEE Transactions on Signal Processing, vol. 60, no. 6, 2012
  • M. Shamaiah, S.-H. Lee, and H. Vikalo
    Graphical models and inference on graphs in genomics: Challenges of high-throughput data analysis
    IEEE Signal Processing Magazine, vol. 29, no. 1, 2012
2011
  • X. Shen and H. Vikalo
    A sequential Monte Carlo base-calling method for next-generation DNA sequencing
    2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)
  • T. Wu, H. Vikalo, and M. Shamaiah
    An MCMC Algorithm for base calling in sequencing-by-synthesis
    Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, pp. 1017-1020, November 2011 (invited)
  • S.-H. Lee, M. Shamaiah, S. Vishwanath, and H. Vikalo
    A message-passing algorithm for spectrum access in cognitive radio relay networks
    Asilomar Conference on Signals, Systems, 2011
  • S. Das and H. Vikalo
    Base-calling for Illumina’s next-generation DNA sequencing systems via Viterbi algorithm
    49th Annual Allerton Conference on Communication, 2011
  • M. Shamaiah and H. Vikalo
    A dual Kalman filter for parameter-state estimation in real-time DNA microarrays
    IEEE Annual International Conference of the Engineering in Medicine and Biology Society (EMBC), 2011
  • S.-H. Lee, M. Shamaiah, and H. Vikalo
    Message-passing for base-calling in sequencing-by-synthesis systems
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2011
  • M. Shamaiah, S.-H. Lee, S. Vishwanath, and H. Vikalo
    Distributed routing in networks using affinity propagation
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2011
  • M. Shamaiah, X. Shen, and H. Vikalo
    Sequential Monte Carlo method for parameter estimation in diffusion models of affinity-based biosensors
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2011
  • M. Shamaiah and H. Vikalo
    Estimating time-varying sparse signals under communication constraints
    IEEE Transactions on Signal Processing, vol. 59, no. 6, 2011
2010
  • M. Shamaiah, S.-H. Lee, and H. Vikalo
    Inference of gene-regulatory networks using message-passing algorithms
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2010
  • S. Das, H. Vikalo, and A. Hassibi
    Model-based sequential base calling for Illumina sequencing
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2010
  • M. Shamaiah, X. Shen, and H. Vikalo
    On parameter estimation for diffusion processes in real-time biosensors
    IEEE Asilomar Conference on Signals, Systems, 2010
  • S.-H. Lee, M. Shamaiah, and H. Vikalo
    Optimal estimation in DNA Microarrays via global optimization
    IEEE Asilomar Conference on Signals, Systems, 2010
  • T. Wu and H. Vikalo
    Maximum likelihood DNA sequence detection via sphere decoding
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2010
  • X. Shen and H. Vikalo
    Inferring parameters of gene regulatory networks via particle filtering
    EURASIP Journal on Advances in Signal Processing, 2010
  • S.-H. Lee, H. Vikalo, and S. Vishwanath
    Further results on message-passing algorithms for motif finding
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2010
  • M. Shamaiah and H. Vikalo
    Rao-Blackwellized unscented Kalman filter for nonlinear systems with bandwidth constrains
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2010
  • M. Shamaiah and H. Vikalo
    Compressed sensing for bandwidth constrained systems
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2010
  • H. Vikalo and M. Gokdemir
    An MCMC algorithm for target estimation in real-time DNA microarrays
    EURASIP Journal on Advances in Signal Processing, 2010
  • X. Shen and H. Vikalo
    Inferring parameters of gene regulatory networks via particle filtering
    EURASIP Journal on Advances in Signal Processing, 2010
  • H. Vikalo, B. Hassibi, and A. Hassibi
    Limits of performance of quantitative polymerase chain reaction systems
    IEEE Transactions on Information Theory, vol. 56, no. 2, 2010
2009
  • H. Vikalo and B. Hassibi
    Limits of performance of real-time DNA microarrays
    Allerton Conference on Communications, Control, 2009
  • M. Gokdemir and H. Vikalo
    An MCMC algorithm for parameter estimation in stochastically modeled real-time biosensor arrays
    IEEE Workshop on Statistical Signal Processing, 2009
  • S.-H. Lee, H. Vikalo, and S. Vishwanath
    Message-passing for motif finding
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009
  • S. Das, H. Vikalo, and A. Hassibi
    Stochastic modeling of reaction kinetics in biosensors using the Fokker-Planck equation
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009
  • M. Gokdemir and H. Vikalo
    A particle filtering algorithm for parameter estimation in real-time biosensor arrays
    IEEE Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009
  • A. Miduthuri, T. Wu, and H. Vikalo
    Target estimation in real-time polymerase chain reaction using sequential Monte Carlo
    IEEE Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009
  • M. El-Khamy, H. Vikalo, B. Hassibi, and R. J. McEliece
    Performance of sphere decoding of block codes
    IEEE Transactions on Communications, vol. 57, no. 10, 2009
  • A. Hassibi, H. Vikalo, J.-L. Reichmann, and B. Hassibi
    Real-time DNA microarray analysis
    Nucleic Acids Research, vol. 37, no. 20, 2009
  • S. Das, H. Vikalo, and A. Hassibi
    On scaling laws of biosensors: A stochastic approach
    Journal of Applied Physics, vol. 105, no. 10, 2009
  • M. El-Khamy, H. Vikalo, B. Hassibi, and R. J. McEliece
    On the performance of sphere decoding of block codes
    IEEE Transactions on Communications, vol. 57, no. 10, 2009
2008
  • H. Vikalo and A. Hassibi
    Estimation in real-time affinity-based biosensors
    IEEE Asilomar Conference on Signals, Systems, 2008
  • H. Vikalo, F. Parvaresh, S. Misra, and B. Hassibi
    Sparse measurements, compressed sampling, and DNA microarrays
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2008
  • H. Vikalo, B. Hassibi, and A. Hassibi
    On estimation in real-time microarrays
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2008
  • H. Vikalo, B. Hassibi, and A. Hassibi
    Modeling and estimation for real-time microarrays
    IEEE Journal of Selected Topics in Signal Processing, vol. 2, no. 3, 2008
  • F. Parvaresh, H. Vikalo, S. Misra, and B. Hassibi
    Recovering sparse signals using sparse measurement matrices in compressed DNA microarrays
    IEEE Journal of Selected Topics in Signal Processing, vol. 2, no. 3, 2008
  • M. Stojnic, H. Vikalo, and B. Hassibi
    Speeding up the sphere decoder with H-infinity and SDP inspired lower bounds
    IEEE Transactions on Signal Processing, vol. 56, no. 2, 2008
2007
  • H. Vikalo, B. Hassibi, and A. Hassibi
    Signal processing aspects of real-time DNA microarrays
    Computational Advances in Multi-Sensor Adaptive Processing, 2007
  • H. Vikalo, A. Hassibi, and B. Hassibi
    Signal processing for real-time DNA microarrays
    IEEE Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, pp. 170-174, November 2007 (invited)
  • H. Vikalo, F. Parvaresh, and B. Hassibi
    On recovery of sparse signals in compressed DNA microarrays
    IEEE Asilomar Conference on Signals, Systems, 2007
  • H. Vikalo, B. Hassibi, M. Stojnic, and A. Hassibi
    Modeling the kinetics of hybridization in microarrays
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2007
  • M. Stojnic, B. Hassibi, and H. Vikalo
    PEP analysis of SDP-based non-coherent signal detection
    IEEE International Symposium on Information Theory (ISIT), 2007
  • H. Vikalo, B. Hassibi, and A. Hassibi
    ML estimation of DNA initial copy number in polymerase chain reaction processes
    IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP), 2007
  • M. Stojnic, B. Hassibi, and H. Vikalo
    PEP analysis of the SDP based joint channel estimation and signal detection
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2007
  • A. Hassibi, H. Vikalo, and A. Hajimiri
    On noise processes and limits of performance in biosensors
    Journal of Applied Physics, vol. 102, no. 1, 2007
2006
  • H. Vikalo, B. Hassibi, and A. Hassibi
    On limits of performance of DNA microarrays
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2006
  • H. Vikalo, B. Hassibi, and A. Hassibi
    On joint maximum-likelihood estimation of PCR efficiency and initial amount of target
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2006
  • M. Stojnic, H. Vikalo, and B. Hassibi
    Further results on speeding up the sphere decoder
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2006
  • M. Stojnic, H. Vikalo, and B. Hassibi
    Asymptotic analysis of the Gaussian broadcast channel with perturbation preprocessing
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2006
  • H. Vikalo and B. Hassibi
    On joint detection and decoding of linear block codes on Gaussian vector channels
    IEEE Transactions on Signal Processing, vol. 54, no. 9, 2006
  • M. Stojnic, H. Vikalo, and B. Hassibi
    Rate maximization in multi-antenna broadcast channels with linear preprocessing
    IEEE Transactions on Wireless Communications, vol. 5, no. 9, 2006
  • H. Vikalo, B. Hassibi, and P. Stoica
    Efficient joint maximum-likelihood channel estimation and signal detection
    IEEE Transactions on Wireless Communications, vol. 5, no. 7, 2006
  • H. Vikalo, B. Hassibi, and U. Mitra
    Sphere-constrained ML detection for frequency-selective channels
    IEEE Transactions on Communications, vol. 54, no. 7, 2006
  • H. Vikalo, B. Hassibi, and A. Hassibi
    A statistical model for microarrays, optimal estimation algorithms, and limits of performance
    IEEE Transactions on Signal Processing, vol. 54, no. 6, 2006
  • M. Stojnic, H. Vikalo, and B. Hassibi
    Rate maximization in multi-antenna broadcast channels with linear preprocessing
    IEEE Transactions on Wireless Communications, vol. 5, no. 9, 2006
  • H. Vikalo, B. Hassibi, and U. Mitra
    Sphere-constrained ML detection for frequency-selective channels
    IEEE Transactions on Communications, vol. 54, no. 7, 2006
2005
  • M. El-Khamy, H. Vikalo, and B. Hassibi
    Bounds on the performance of sphere decoding of linear block codes
    IEEE-ITSOC Information Theory Workshop on Coding and Complexity (ITW), 2005
  • M. Stojnic, H. Vikalo, and B. Hassibi
    An efficient H-infinity estimation approach to speed up the sphere decoder
    International Conference on Wireless Networks, Communications, and Mobile Computing (WirelessCom), 2005
  • M. Stojnic, H. Vikalo, and B. Hassibi
    An H-infinity based lower bound to speed up sphere decoder
    6th IEEE International Workshop on Signal Processing Advances in Wireless Communications (SPAWC), 2005
  • H. Vikalo, A. Hassibi, and B. Hassibi
    Optimal estimation of gene expression levels in microarrays
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2005
  • A. Hassibi and H. Vikalo
    A probabilistic model for inherent noise and systematic errors of microarrays
    IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2005
  • M. Stojnic, H. Vikalo, and B. Hassibi
    A branch and bound approach to speed up the sphere decoder
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2005
  • H. Vikalo and B. Hassibi
    On sphere-decoding algorithm II. Generalizations, second-order statistics, and applications to communications
    IEEE Transactions on Signal Processing, vol. 53, no. 8, 2005
  • B. Hassibi and H. Vikalo
    On sphere-decoding algorithm I. Expected complexity
    IEEE Transactions on Signal Processing, vol. 53, no. 8, 2005
  • H. Vikalo, B. Hassibi, A. Erdogan, and T. Kailath
    On robust signal reconstruction in noisy filter banks
    Signal Processing, vol. 85, no. 1, 2005
2004
  • H. Vikalo and B. Hassibi
    Statistical approach to ML decoding of linear block codes on symmetric channels
    IEEE International Symposium on Information Theory (ISIT), 2004
  • H. Vikalo, A. Hassibi, and B. Hassibi
    Nucleic acid detection using bioluminescence regenerative cycle and statistical signal processing
    IEEE International Workshop on Genomics Signal Processing and Statistics (GENSIPS), 2004
  • H. Vikalo, B. Hassibi, and T. Kailath
    Iterative decoding for MIMO channels via modified sphere decoding
    IEEE Transactions on Wireless Communications, vol. 3, no. 6, 2004
  • H. Vikalo, B. Hassibi, B. Hochwald, and T. Kailath
    On the capacity of frequency-selective channels in training-based transmission schemes
    IEEE Transactions on Signal Processing, vol. 52, no. 9, 2004
2003
  • H. Vikalo, B. Hassibi, and U. Mitra
    Sphere-constrained ML detection for channels with memory
    37th Asilomar Conference on Signals, Systems, 2003
  • H. Vikalo and B. Hassibi
    On joint ML detection and decoding
    IEEE International Symposium on Information Theory (ISIT), 2003
  • P. Stoica, H. Vikalo, and B. Hassibi
    Joint ML channel estimation and signal detection for SIMO channels
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2003
2002
  • H. Vikalo and B. Hassibi
    Low-complexity iterative detection and decoding of multi-antenna systems employing channel and space-time codes
    36th Asilomar Conference on Signals, Systems, 2002
  • H. Vikalo and B. Hassibi
    On the expected complexity of sphere decoding for frequency-selective channels
    Allerton Conference on Communications, Control, 2002
  • H. Vikalo and B. Hassibi
    Modified Fincke-Pohst algorithm for low-complexity iterative decoding over multiple antenna channels
    IEEE International Symposium on Information Theory (ISIT), 2002
  • H. Vikalo and B. Hassibi
    Towards closing the capacity gap on multiple antenna channels
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2002
  • B. Hassibi and H. Vikalo
    On the expected complexity of integer least-squares problems
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2002
  • H. Vikalo and B. Hassibi
    Maximum-likelihood sequence detection of multiple antenna systems over dispersive channels via sphere decoding
    EURASIP Journal of Applied Signal Processing, vol. 5, 2002
2001
  • H. Vikalo and B. Hassibi
    Low-complexity iterative decoding over multiple antenna channels via a modified sphere decoder
    Allerton Conference on Communications, Control, 2001
  • B. Hassibi and H. Vikalo
    On the expected complexity of sphere decoding
    35th Asilomar Conference on Signals, Systems, 2001
  • H. Vikalo, B. Hassibi, B. Hochwald, and T. Kailath
    Optimal training for frequency-selective fading channels
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2001
2000
  • H. Vikalo, B. Hassibi, and T. Kailath
    On robust multiuser detection
    34th Asilomar Conference on Signals, Systems, 2000
  • S. Mudulodu, H. Vikalo, A. Paulraj, and T. Kailath
    CDMA multiuser detection based on state-space estimation techniques
    34th Asilomar Conference on Signals, Systems, 2000
  • H. Vikalo, A. T Erdogan, B. Hassibi, and T. Kailath
    Exponential-quadratic optimal signal reconstruction in noisy filter banks
    SPIE International Symposium on Optical Science and Technology, 2000
  • T. Simunic, H. Vikalo, P. Glynn, and G. De Micheli
    Energy efficient design of portable wireless systems
    IEEE International Symposium on Low Power Electronics and Design, 2000
  • H. Vikalo, B. Hassibi, and T. Kailath
    Mixed H2/H-infinity optimal signal reconstruction in noisy filter banks
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2000
1999
  • H. Vikalo, B. Hassibi, and T. Kailath
    On H-infinity optimal signal reconstruction in noisy filter banks
    IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 1999
1997
  • H. Vikalo and R. S. Blum
    Distributed detection in dependent nonGaussian noise
    IEEE International Symposium on Information Theory (ISIT), 1997
  • H. Vikalo and R. S. Blum
    Distributed detection of known signals in Gaussian mixture noise which is dependent from sensor to sensor
    International Conference on Telecommunications (ICT), 1997
1995
  • Z. Kovacic, S. Bogdan, and H. Vikalo
    Design and parameter adaptation of a fuzzy servo controller
    6th International Fuzzy Systems Association World Congress, 1995