arXiv:2512.15116v3 Announce Type: replace-cross
Abstract: Multivariate time series imputation is fundamental in applications such as healthcare, traffic forecasting, and biological modeling, where sensor failures and irregular sampling lead to pervasive missing values. Existing Transformer- and diffusion-based imputers achieve strong performance, but they often rely mainly on time-domain modeling and lack adaptive spectral bias for recovering structured temporal gaps. We propose FADTI, a Fourier- and attention-driven diffusion framework for multivariate time series imputation. FADTI introduces a Fourier Bias Projection (FBP) module that injects learnable frequency-aware bias into intermediate hidden states during denoising. It projects intermediate hidden states onto Fourier bases, avoiding direct spectral estimation from masked or zero-filled inputs. With DFT, STFT, and FSST instantiations, FBP captures global periodicity, localized time–frequency variations, and non-stationary oscillatory patterns. By coupling FBP with self-attention and gated convolution, FADTI integrates frequency-domain guidance, temporal dependency modeling, and probabilistic denoising in a unified framework. Experiments on multiple benchmarks, including a new biological imputation benchmark, show that FADTI improves accuracy, uncertainty estimation, and sampling efficiency, especially under high missing rates and structured missing patterns. Code is available at https://github.com/RazeenLI/FADTI
Abstract: Multivariate time series imputation is fundamental in applications such as healthcare, traffic forecasting, and biological modeling, where sensor failures and irregular sampling lead to pervasive missing values. Existing Transformer- and diffusion-based imputers achieve strong performance, but they often rely mainly on time-domain modeling and lack adaptive spectral bias for recovering structured temporal gaps. We propose FADTI, a Fourier- and attention-driven diffusion framework for multivariate time series imputation. FADTI introduces a Fourier Bias Projection (FBP) module that injects learnable frequency-aware bias into intermediate hidden states during denoising. It projects intermediate hidden states onto Fourier bases, avoiding direct spectral estimation from masked or zero-filled inputs. With DFT, STFT, and FSST instantiations, FBP captures global periodicity, localized time–frequency variations, and non-stationary oscillatory patterns. By coupling FBP with self-attention and gated convolution, FADTI integrates frequency-domain guidance, temporal dependency modeling, and probabilistic denoising in a unified framework. Experiments on multiple benchmarks, including a new biological imputation benchmark, show that FADTI improves accuracy, uncertainty estimation, and sampling efficiency, especially under high missing rates and structured missing patterns. Code is available at https://github.com/RazeenLI/FADTI
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