Missing data is a common concern in health datasets, and its impact on good decision-making processes is well documented. Our study's contribution is a methodology for tackling missing data problems using a combination of synthetic dataset generation, missing data imputation and deep learning methods to resolve missing data challenges. Specifically, we conducted a series of experiments with these objectives; $a)$ generating a realistic synthetic dataset, $b)$ simulating data missingness, $c)$ recovering the missing data, and $d)$ analyzing imputation performance. Our methodology used a gaussian mixture model whose parameters were learned from a cleaned subset of a real demographic and health dataset to generate the synthetic data. We simulated various missingness degrees ranging from $10 \%$, $20 \%$, $30 \%$, and $40\%$ under the missing completely at random scheme MCAR. We used an integrated performance analysis framework involving clustering, classification and direct imputation analysis. Our results show that models trained on synthetic and imputed datasets could make predictions with an accuracy of $83 \%$ and $80 \%$ on $a) $ an unseen real dataset and $b)$ an unseen reserved synthetic test dataset, respectively. Moreover, the models that used the DAE method for imputed yielded the lowest log loss an indication of good performance, even though the accuracy measures were slightly lower. In conclusion, our work demonstrates that using our methodology, one can reverse engineer a solution to resolve missingness on an unseen dataset with missingness. Moreover, though we used a health dataset, our methodology can be utilized in other contexts.

Semiconductor lasers, one of the key components for optical communication systems, have been rapidly evolving to meet the requirements of next generation optical networks with respect to high speed, low power consumption, small form factor etc. However, these demands have brought severe challenges to the semiconductor laser reliability. Therefore, a great deal of attention has been devoted to improving it and thereby ensuring reliable transmission. In this paper, a predictive maintenance framework using machine learning techniques is proposed for real-time heath monitoring and prognosis of semiconductor laser and thus enhancing its reliability. The proposed approach is composed of three stages: i) real-time performance degradation prediction, ii) degradation detection, and iii) remaining useful life (RUL) prediction. First of all, an attention based gated recurrent unit (GRU) model is adopted for real-time prediction of performance degradation. Then, a convolutional autoencoder is used to detect the degradation or abnormal behavior of a laser, given the predicted degradation performance values. Once an abnormal state is detected, a RUL prediction model based on attention-based deep learning is utilized. Afterwards, the estimated RUL is input for decision making and maintenance planning. The proposed framework is validated using experimental data derived from accelerated aging tests conducted for semiconductor tunable lasers. The proposed approach achieves a very good degradation performance prediction capability with a small root mean square error (RMSE) of 0.01, a good anomaly detection accuracy of 94.24% and a better RUL estimation capability compared to the existing ML-based laser RUL prediction models.

Single-cell RNA-seq datasets are growing in size and complexity, enabling the study of cellular composition changes in various biological/clinical contexts. Scalable dimensionality reduction techniques are in need to disentangle biological variation in them, while accounting for technical and biological confounders. In this work, we extend a popular approach for probabilistic non-linear dimensionality reduction, the Gaussian process latent variable model (Lawrence, 2004), to scale to massive single-cell datasets while explicitly accounting for technical and biological confounders. The key idea is to use an augmented kernel which preserves the factorisability of the lower bound allowing for fast stochastic variational inference. We demonstrate its ability to reconstruct latent signatures of innate immunity recovered in Kumasaka et al. (2021) with 9x speed-up on training time. We further analyse a dataset of blood cells from COVID-19 patients and demonstrate that this framework enables to capture interpretable signatures of infection, while integrating data across individuals and technical batches. Specifically, we explore COVID-19 severity as a latent dimension to refine patient stratification and capture disease-specific gene expression signatures.

Time Series Forecasting has been an active area of research due to its many applications ranging from network usage prediction, resource allocation, anomaly detection, and predictive maintenance. Numerous publications published in the last five years have proposed diverse sets of objective loss functions to address cases such as biased data, long-term forecasting, multicollinear features, etc. In this paper, we have summarized 14 well-known regression loss functions commonly used for time series forecasting and listed out the circumstances where their application can aid in faster and better model convergence. We have also demonstrated how certain categories of loss functions perform well across all data sets and can be considered as a baseline objective function in circumstances where the distribution of the data is unknown. Our code is available at GitHub: https://github.com/aryan-jadon/Regression-Loss-Functions-in-Time-Series-Forecasting-Tensorflow.

Natural laws are often described through differential equations yet finding a differential equation that describes the governing law underlying observed data is a challenging and still mostly manual task. In this paper we make a step towards the automation of this process: we propose a transformer-based sequence-to-sequence model that recovers scalar autonomous ordinary differential equations (ODEs) in symbolic form from time-series data of a single observed solution of the ODE. Our method is efficiently scalable: after one-time pretraining on a large set of ODEs, we can infer the governing laws of a new observed solution in a few forward passes of the model. Then we show that our model performs better or on par with existing methods in various test cases in terms of accurate symbolic recovery of the ODE, especially for more complex expressions.

Volatile organic compounds (VOCs) are chemicals emitted by various groups, such as foods, bacteria, and plants. While there are specific pathways and biological features significantly related to such VOCs, detection of these is achieved mostly by human odor testing or high-end methods such as gas chromatography–mass spectrometry that can analyze the gaseous component. However, odor characterization can be quite helpful in the rapid classification of some samples in sufficient concentrations. Lower-cost metal-oxide gas sensors have the potential to allow the same type of detection with less training required. Here, we report a portable, battery-powered electronic nose system that utilizes multiple metal-oxide gas sensors and machine learning algorithms to detect and classify VOCs. An in-house circuit was designed with ten metal-oxide sensors and voltage dividers; an STM32 microcontroller was used for data acquisition with 12-bit analog-to-digital conversion. For classification of target samples, a supervised machine learning algorithm such as support vector machine (SVM) was applied to classify the VOCs based on the measurement results. The coefficient of variation (standard deviation divided by mean) of 8 of the 10 sensors stayed below 10%, indicating the excellent repeatability of these sensors. As a proof of concept, four different types of wine samples and three different oil samples were classified, and the training model reported 100% and 98% accuracy based on the confusion matrix analysis, respectively. When the trained model was challenged against new sets of data, sensitivity and specificity of 98.5% and 98.6% were achieved for the wine test and 96.3% and 93.3% for the oil test, respectively, when the SVM classifier was used. These results suggest that the metal-oxide sensors are suitable for usage in food authentication applications.

Bayesian optimization (BO) is increasingly employed in critical applications such as materials design and drug discovery. An increasingly popular strategy in BO is to forgo the sole reliance on high-fidelity data and instead use an ensemble of information sources which provide inexpensive low-fidelity data. The overall premise of this strategy is to reduce the overall sampling costs by querying inexpensive low-fidelity sources whose data are correlated with high-fidelity samples. Here, we propose a multi-fidelity cost-aware BO framework that dramatically outperforms the state-of-the-art technologies in terms of efficiency, consistency, and robustness. We demonstrate the advantages of our framework on analytic and engineering problems and argue that these benefits stem from our two main contributions: (1) we develop a novel acquisition function for multi-fidelity cost-aware BO that safeguards the convergence against the biases of low-fidelity data, and (2) we tailor a newly developed emulator for multi-fidelity BO which enables us to not only simultaneously learn from an ensemble of multi-fidelity datasets, but also identify the severely biased low-fidelity sources that should be excluded from BO.

Survival modeling in healthcare relies on explainable statistical models; yet, their underlying assumptions are often simplistic and, thus, unrealistic. Machine learning models can estimate more complex relationships and lead to more accurate predictions, but are non-interpretable. This study shows it is possible to estimate hospitalization for congestive heart failure by a 30 seconds single-lead electrocardiogram signal. Using a machine learning approach not only results in greater predictive power but also provides clinically meaningful interpretations. We train an eXtreme Gradient Boosting accelerated failure time model and exploit SHapley Additive exPlanations values to explain the effect of each feature on predictions. Our model achieved a concordance index of 0.828 and an area under the curve of 0.853 at one year and 0.858 at two years on a held-out test set of 6,573 patients. These results show that a rapid test based on an electrocardiogram could be crucial in targeting and treating high-risk individuals.

Learning expressive molecular representations is crucial to facilitate the accurate prediction of molecular properties. Despite the significant advancement of graph neural networks (GNNs) in molecular representation learning, they generally face limitations such as neighbors-explosion, under-reaching, over-smoothing, and over-squashing. Also, GNNs usually have high computational costs because of the large-scale number of parameters. Typically, such limitations emerge or increase when facing relatively large-size graphs or using a deeper GNN model architecture. An idea to overcome these problems is to simplify a molecular graph into a small, rich, and informative one, which is more efficient and less challenging to train GNNs. To this end, we propose a novel molecular graph coarsening framework named FunQG utilizing Functional groups, as influential building blocks of a molecule to determine its properties, based on a graph-theoretic concept called Quotient Graph. By experiments, we show that the resulting informative graphs are much smaller than the molecular graphs and thus are good candidates for training GNNs. We apply the FunQG on popular molecular property prediction benchmarks and then compare the performance of some popular baseline GNNs on the obtained datasets with the performance of several state-of-the-art baselines on the original datasets. By experiments, this method significantly outperforms previous baselines on various datasets, besides its dramatic reduction in the number of parameters and low computational costs. Therefore, the FunQG can be used as a simple, cost-effective, and robust method for solving the molecular representation learning problem.

Continual learning (CL) learns a sequence of tasks incrementally. There are two popular CL settings, class incremental learning (CIL) and task incremental learning (TIL). A major challenge of CL is catastrophic forgetting (CF). While a number of techniques are already available to effectively overcome CF for TIL, CIL remains to be highly challenging. So far, little theoretical study has been done to provide a principled guidance on how to solve the CIL problem. This paper performs such a study. It first shows that probabilistically, the CIL problem can be decomposed into two sub-problems: Within-task Prediction (WP) and Task-id Prediction (TP). It further proves that TP is correlated with out-of-distribution (OOD) detection, which connects CIL and OOD detection. The key conclusion of this study is that regardless of whether WP and TP or OOD detection are defined explicitly or implicitly by a CIL algorithm, good WP and good TP or OOD detection are necessary and sufficient for good CIL performances. Additionally, TIL is simply WP. Based on the theoretical result, new CIL methods are also designed, which outperform strong baselines in both CIL and TIL settings by a large margin.