This work has been submitted to the IEEE for possible publication. Abstract --Gas Chromatography coupled with Ion Mobility Spectrometry (GC-IMS) is a dual-separation analytical technique widely used for identifying components in gaseous samples by separating and analysing the arrival times of their constituent species. Data generated by GC-IMS is typically represented as two-dimensional spectra, providing rich information but posing challenges for data-driven analysis due to limited labelled datasets. This study introduces a novel method for generating synthetic 2D spectra using a deep learning framework based on Autoencoders. Although applied here to GC-IMS data, the approach is broadly applicable to any two-dimensional spectral measurements where labelled data are scarce. While performing component classification over a labelled dataset of GC-IMS records, the addition of synthesized records significantly has improved the classification performance, demonstrating the method's potential for overcoming dataset limitations in machine learning frameworks. I NTRODUCTION Gas Chromatography coupled with Ion Mobility Spectrometry (GC-IMS) is a technique used to identify chemical components within a sample [1]. Initially, the sample, carried by a carrier gas, is introduced into the GC column, where interactions between the sample components and the column affect their transit speeds, leading to an initial separation.

The prevalent fully-connected tensor network (FCTN) has achieved excellent success to compress data. However, the FCTN decomposition suffers from slow computational speed when facing higher-order and large-scale data. Naturally, there arises an interesting question: can a new model be proposed that decomposes the tensor into smaller ones and speeds up the computation of the algorithm? This work gives a positive answer by formulating a novel higher-order tensor decomposition model that utilizes latent matrices based on the tensor network structure, which can decompose a tensor into smaller-scale data than the FCTN decomposition, hence we named it Latent Matrices for Tensor Network Decomposition (LMTN). Furthermore, three optimization algorithms, LMTN-PAM, LMTN-SVD and LMTN-AR, have been developed and applied to the tensor-completion task. In addition, we provide proofs of theoretical convergence and complexity analysis for these algorithms. Experimental results show that our algorithm has the effectiveness in both deep learning dataset compression and higher-order tensor completion, and that our LMTN-SVD algorithm is 3-6 times faster than the FCTN-PAM algorithm and only a 1.8 points accuracy drop.

Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose a method called Sparse Tropical Matrix Factorization (STMF) for the estimation of missing (unknown) values. We evaluate the efficiency of the STMF method on both synthetic data and biological data in the form of gene expression measurements downloaded from The Cancer Genome Atlas (TCGA) database. Tests on unique synthetic data showed that STMF approximation achieves a higher correlation than non-negative matrix factorization (NMF), which is unable to recover patterns effectively. On real data, STMF outperforms NMF on six out of nine gene expression datasets. While NMF assumes normal distribution and tends toward the mean value, STMF can better fit to extreme values and distributions. STMF is the first work that uses tropical semiring on sparse data. We show that in certain cases semirings are useful because they consider the structure, which is different and simpler to understand than it is with standard linear algebra.

Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of various types of cancers better. Tri-matrix factorization is an efficient tool to learn associations between two different entities (e.g., cancer types and pathways in our case) from data. To successfully apply tri-matrix factorization methods to biomedical problems, biological prior knowledge such as pathway databases or protein-protein interaction (PPI) networks, should be taken into account in the factorization model. However, it is not straightforward in the Bayesian setting even though Bayesian methods are more appealing than point estimate methods, such as a maximum likelihood or a maximum posterior method, in the sense that they calculate distributions over variables and are robust against overfitting. We propose a Bayesian (semi-)nonnegative matrix factorization model for human cancer genomic data, where the biological prior knowledge represented by a pathway database and a PPI network is taken into account in the factorization model through a finite dependent Beta-Bernoulli prior. We tested our method on The Cancer Genome Atlas (TCGA) dataset and found that the pathways identified by our method can be used as a prognostic biomarkers for patient subgroup identification.

The vast majority of current machine learning algorithms are designed to predict single responses or a vector of responses, yet many types of response are more naturally organized as matrices or higher-order tensor objects where characteristics are shared across modes. We present a new machine learning algorithm BaTFLED (Bayesian Tensor Factorization Linked to External Data) that predicts values in a three-dimensional response tensor using input features for each of the dimensions. BaTFLED uses a probabilistic Bayesian framework to learn projection matrices mapping input features for each mode into latent representations that multiply to form the response tensor. By utilizing a Tucker decomposition, the model can capture weights for interactions between latent factors for each mode in a small core tensor. Priors that encourage sparsity in the projection matrices and core tensor allow for feature selection and model regularization. This method is shown to far outperform elastic net and neural net models on 'cold start' tasks from data simulated in a three-mode structure. Additionally, we apply the model to predict dose-response curves in a panel of breast cancer cell lines treated with drug compounds that was used as a Dialogue for Reverse Engineering Assessments and Methods (DREAM) challenge.

Data sparsity is an emerging real-world problem observed in a various domains ranging from sensor networks to medical diagnosis. Consecutively, numerous machine learning methods were modeled to treat missing values. Nevertheless, sparsity, defined as missing segments, has not been thoroughly investigated in the context of time series classification. We propose a novel principle for classifying time series, which in contrast to existing approaches, avoids reconstructing the missing segments in time series and operates solely on the observed ones. Based on the proposed principle, we develop a method that prevents adding noise that incurs during the reconstruction of the original time series. Ourmethod adapts supervised matrix factorization by projecting time series in a latent space through stochasticlearning. Furthermore the projected data is built in a supervised fashion via a logistic regression. Abundant experiments on a large collection of 37 data sets demonstrate the superiority of our method, which in the majority of cases outperforms a set of baselines that do not follow our proposed principle.