Xihao Piao

Xihao Piao, Pei Gao, Zheng Chen et al.

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}

Ziwei Yang, Rikuto Kotoge, Xihao Piao et al.

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals, including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. In this paper, we introduce MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

Xihao Piao, Zheng Chen, Taichi Murayama et al.

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