Modeling Time-evolving Causality over Data Streams

Given an extensive, semi-infinite collection of multivariate coevolving data sequences (e.g., sensor/web activity streams) whose observations influence each other, how can we discover the time-changing cause-and-effect relationships in co-evolving data streams? How efficiently can we reveal dynamical patterns that allow us to forecast future values? In this paper, we present a novel streaming method, ModePlait, which is designed for modeling such causal relationships (i.e., time-evolving causality) in multivariate co-evolving data streams and forecasting their future values. The solution relies on characteristics of the causal relationships that evolve over time in accordance with the dynamic changes of exogenous variables. ModePlait has the following properties: (a) Effective: it discovers the time-evolving causality in multivariate co-evolving data streams by detecting the transitions of distinct dynamical patterns adaptively. (b) Accurate: it enables both the discovery of time-evolving causality and the forecasting of future values in a streaming fashion. (c) Scalable: our algorithm does not depend on data stream length and thus is applicable to very large sequences. Extensive experiments on both synthetic and real-world datasets demonstrate that our proposed model outperforms state-of-the-art methods in terms of discovering the time-evolving causality as well as forecasting.

SODor: Long-Term EEG Partitioning for Seizure Onset Detection

Deep learning models have recently shown great success in classifying epileptic patients using EEG recordings. Unfortunately, classification-based methods lack a sound mechanism to detect the onset of seizure events. In this work, we propose a two-stage framework, \method, that explicitly models seizure onset through a novel task formulation of subsequence clustering. Given an EEG sequence, the framework first learns a set of second-level embeddings with label supervision. It then employs model-based clustering to explicitly capture long-term temporal dependencies in EEG sequences and identify meaningful subsequences. Epochs within a subsequence share a common cluster assignment (normal or seizure), with cluster or state transitions representing successful onset detections. Extensive experiments on three datasets demonstrate that our method can correct misclassifications, achieving 5%-11% classification improvements over other baselines and accurately detecting seizure onsets.

Modeling Latent Non-Linear Dynamical System over Time Series

We study the problem of modeling a non-linear dynamical system when given a time series by deriving equations directly from the data. Despite the fact that time series data are given as input, models for dynamics and estimation algorithms that incorporate long-term temporal dependencies are largely absent from existing studies. In this paper, we introduce a latent state to allow time-dependent modeling and formulate this problem as a dynamics estimation problem in latent states. We face multiple technical challenges, including (1) modeling latent non-linear dynamics and (2) solving circular dependencies caused by the presence of latent states. To tackle these challenging problems, we propose a new method, Latent Non-Linear equation modeling (LaNoLem), that can model a latent non-linear dynamical system and a novel alternating minimization algorithm for effectively estimating latent states and model parameters. In addition, we introduce criteria to control model complexity without human intervention. Compared with the state-of-the-art model, LaNoLem achieves competitive performance for estimating dynamics while outperforming other methods in prediction.

GeSubNet: Gene Interaction Inference for Disease Subtype Network Generation

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts. The GeSubNet resource is available: https://anonymous.4open.science/r/GeSubNet/

SplitSEE: A Splittable Self-supervised Framework for Single-Channel EEG Representation Learning

While end-to-end multi-channel electroencephalography (EEG) learning approaches have shown significant promise, their applicability is often constrained in neurological diagnostics, such as intracranial EEG resources. When provided with a single-channel EEG, how can we learn representations that are robust to multi-channels and scalable across varied tasks, such as seizure prediction? In this paper, we present SplitSEE, a structurally splittable framework designed for effective temporal-frequency representation learning in single-channel EEG. The key concept of SplitSEE is a self-supervised framework incorporating a deep clustering task. Given an EEG, we argue that the time and frequency domains are two distinct perspectives, and hence, learned representations should share the same cluster assignment. To this end, we first propose two domain-specific modules that independently learn domain-specific representation and address the temporal-frequency tradeoff issue in conventional spectrogram-based methods. Then, we introduce a novel clustering loss to measure the information similarity. This encourages representations from both domains to coherently describe the same input by assigning them a consistent cluster. SplitSEE leverages a pre-training-to-fine-tuning framework within a splittable architecture and has following properties: (a) Effectiveness: it learns representations solely from single-channel EEG but has even outperformed multi-channel baselines. (b) Robustness: it shows the capacity to adapt across different channels with low performance variance. Superior performance is also achieved with our collected clinical dataset. (c) Scalability: With just one fine-tuning epoch, SplitSEE achieves high and stable performance using partial model layers.

FredNormer: Frequency Domain Normalization for Non-stationary Time Series Forecasting

Recent normalization-based methods have shown great success in tackling the distribution shift issue, facilitating non-stationary time series forecasting. Since these methods operate in the time domain, they may fail to fully capture the dynamic patterns that are more apparent in the frequency domain, leading to suboptimal results. This paper first theoretically analyzes how normalization methods affect frequency components. We prove that the current normalization methods that operate in the time domain uniformly scale non-zero frequencies, and thus, they struggle to determine components that contribute to more robust forecasting. Therefore, we propose FredNormer, which observes datasets from a frequency perspective and adaptively up-weights the key frequency components. To this end, FredNormer consists of two components: a statistical metric that normalizes the input samples based on their frequency stability and a learnable weighting layer that adjusts stability and introduces sample-specific variations. Notably, FredNormer is a plug-and-play module, which does not compromise the efficiency compared to existing normalization methods. Extensive experiments show that FredNormer improves the averaged MSE of backbone forecasting models by 33.3% and 55.3% on the ETTm2 dataset. Compared to the baseline normalization methods, FredNormer achieves 18 top-1 results and 6 top-2 results out of 28 settings.

Mining of Switching Sparse Networks for Missing Value Imputation in Multivariate Time Series

Multivariate time series data suffer from the problem of missing values, which hinders the application of many analytical methods. To achieve the accurate imputation of these missing values, exploiting inter-correlation by employing the relationships between sequences (i.e., a network) is as important as the use of temporal dependency, since a sequence normally correlates with other sequences. Moreover, exploiting an adequate network depending on time is also necessary since the network varies over time. However, in real-world scenarios, we normally know neither the network structure nor when the network changes beforehand. Here, we propose a missing value imputation method for multivariate time series, namely MissNet, that is designed to exploit temporal dependency with a state-space model and inter-correlation by switching sparse networks. The network encodes conditional independence between features, which helps us understand the important relationships for imputation visually. Our algorithm, which scales linearly with reference to the length of the data, alternatively infers networks and fills in missing values using the networks while discovering the switching of the networks. Extensive experiments demonstrate that MissNet outperforms the state-of-the-art algorithms for multivariate time series imputation and provides interpretable results.

CMOB: Large-Scale Cancer Multi-Omics Benchmark with Open Datasets, Tasks, and Baselines

Machine learning has shown great potential in the field of cancer multi-omics studies, offering incredible opportunities for advancing precision medicine. However, the challenges associated with dataset curation and task formulation pose significant hurdles, especially for researchers lacking a biomedical background. Here, we introduce the CMOB, the first large-scale cancer multi-omics benchmark integrates the TCGA platform, making data resources accessible and usable for machine learning researchers without significant preparation and expertise.To date, CMOB includes a collection of 20 cancer multi-omics datasets covering 32 cancers, accompanied by a systematic data processing pipeline. CMOB provides well-processed dataset versions to support 20 meaningful tasks in four studies, with a collection of benchmarks. We also integrate CMOB with two complementary resources and various biological tools to explore broader research avenues.All resources are open-accessible with user-friendly and compatible integration scripts that enable non-experts to easily incorporate this complementary information for various tasks. We conduct extensive experiments on selected datasets to offer recommendations on suitable machine learning baselines for specific applications. Through CMOB, we aim to facilitate algorithmic advances and hasten the development, validation, and clinical translation of machine-learning models for personalized cancer treatments. CMOB is available on GitHub (\url{https://github.com/chenzRG/Cancer-Multi-Omics-Benchmark}).

$\mathbb{BEHR}$NOULLI: A Binary EHR Data-Oriented Medication Recommendation System

The medical community believes binary medical event outcomes in EHR data contain sufficient information for making a sensible recommendation. However, there are two challenges to effectively utilizing such data: (1) modeling the relationship between massive 0,1 event outcomes is difficult, even with expert knowledge; (2) in practice, learning can be stalled by the binary values since the equally important 0 entries propagate no learning signals. Currently, there is a large gap between the assumed sufficient information and the reality that no promising results have been shown by utilizing solely the binary data: visiting or secondary information is often necessary to reach acceptable performance. In this paper, we attempt to build the first successful binary EHR data-oriented drug recommendation system by tackling the two difficulties, making sensible drug recommendations solely using the binary EHR medical records. To this end, we take a statistical perspective to view the EHR data as a sample from its cohorts and transform them into continuous Bernoulli probabilities. The transformed entries not only model a deterministic binary event with a distribution but also allow reflecting \emph{event-event} relationship by conditional probability. A graph neural network is learned on top of the transformation. It captures event-event correlations while emphasizing \emph{event-to-patient} features. Extensive results demonstrate that the proposed method achieves state-of-the-art performance on large-scale databases, outperforming baseline methods that use secondary information by a large margin. The source code is available at \url{https://github.com/chenzRG/BEHRMecom}

Fredformer: Frequency Debiased Transformer for Time Series Forecasting

The Transformer model has shown leading performance in time series forecasting. Nevertheless, in some complex scenarios, it tends to learn low-frequency features in the data and overlook high-frequency features, showing a frequency bias. This bias prevents the model from accurately capturing important high-frequency data features. In this paper, we undertook empirical analyses to understand this bias and discovered that frequency bias results from the model disproportionately focusing on frequency features with higher energy. Based on our analysis, we formulate this bias and propose Fredformer, a Transformer-based framework designed to mitigate frequency bias by learning features equally across different frequency bands. This approach prevents the model from overlooking lower amplitude features important for accurate forecasting. Extensive experiments show the effectiveness of our proposed approach, which can outperform other baselines in different real-world time-series datasets. Furthermore, we introduce a lightweight variant of the Fredformer with an attention matrix approximation, which achieves comparable performance but with much fewer parameters and lower computation costs. The code is available at: https://github.com/chenzRG/Fredformer