An increasing amount of research is being devoted to applying machine learning methods to electronic health record (EHR) data for various clinical purposes. This growing area of research has exposed the challenges of the accessibility of EHRs. MIMIC is a popular, public, and free EHR dataset in a raw format that has been used in numerous studies. The absence of standardized pre-processing steps can be, however, a significant barrier to the wider adoption of this rare resource. Additionally, this absence can reduce the reproducibility of the developed tools and limit the ability to compare the results among similar studies. In this work, we provide a greatly customizable pipeline to extract, clean, and pre-process the data available in the fourth version of the MIMIC dataset (MIMIC-IV). The pipeline also presents an end-to-end wizard-like package supporting predictive model creations and evaluations. The pipeline covers a range of clinical prediction tasks which can be broadly classified into four categories - readmission, length of stay, mortality, and phenotype prediction.

The development of deep neural networks has improved representation learning in various domains, including textual, graph structural, and relational triple representations. This development opened the door to new relation extraction beyond the traditional text-oriented relation extraction. However, research on the effectiveness of considering multiple heterogeneous domain information simultaneously is still under exploration, and if a model can take an advantage of integrating heterogeneous information, it is expected to exhibit a significant contribution to many problems in the world. This thesis works on Drug-Drug Interactions (DDIs) from the literature as a case study and realizes relation extraction utilizing heterogeneous domain information. First, a deep neural relation extraction model is prepared and its attention mechanism is analyzed. Next, a method to combine the drug molecular structure information and drug description information to the input sentence information is proposed, and the effectiveness of utilizing drug molecular structures and drug descriptions for the relation extraction task is shown. Then, in order to further exploit the heterogeneous information, drug-related items, such as protein entries, medical terms and pathways are collected from multiple existing databases and a new data set in the form of a knowledge graph (KG) is constructed. A link prediction task on the constructed data set is conducted to obtain embedding representations of drugs that contain the heterogeneous domain information. Finally, a method that integrates the input sentence information and the heterogeneous KG information is proposed. The proposed model is trained and evaluated on a widely used data set, and as a result, it is shown that utilizing heterogeneous domain information significantly improves the performance of relation extraction from the literature.

Past work has shown that large language models are susceptible to privacy attacks, where adversaries generate sequences from a trained model and detect which sequences are memorized from the training set. In this work, we show that the success of these attacks is largely due to duplication in commonly used web-scraped training sets. We first show that the rate at which language models regenerate training sequences is superlinearly related to a sequence's count in the training set. For instance, a sequence that is present 10 times in the training data is on average generated ~1000 times more often than a sequence that is present only once. We next show that existing methods for detecting memorized sequences have near-chance accuracy on non-duplicated training sequences. Finally, we find that after applying methods to deduplicate training data, language models are considerably more secure against these types of privacy attacks. Taken together, our results motivate an increased focus on deduplication in privacy-sensitive applications and a reevaluation of the practicality of existing privacy attacks.

With the development of a series of Galaxy sky surveys in recent years, the observations increased rapidly, which makes the research of machine learning methods for galaxy image recognition a hot topic. Available automatic galaxy image recognition researches are plagued by the large differences in similarity between categories, the imbalance of data between different classes, and the discrepancy between the discrete representation of Galaxy classes and the essentially gradual changes from one morphological class to the adjacent class (DDRGC). These limitations have motivated several astronomers and machine learning experts to design projects with improved galaxy image recognition capabilities. Therefore, this paper proposes a novel learning method, ``Hierarchical Imbalanced data learning with Weighted sampling and Label smoothing" (HIWL). The HIWL consists of three key techniques respectively dealing with the above-mentioned three problems: (1) Designed a hierarchical galaxy classification model based on an efficient backbone network; (2) Utilized a weighted sampling scheme to deal with the imbalance problem; (3) Adopted a label smoothing technique to alleviate the DDRGC problem. We applied this method to galaxy photometric images from the Galaxy Zoo-The Galaxy Challenge, exploring the recognition of completely round smooth, in between smooth, cigar-shaped, edge-on and spiral. The overall classification accuracy is 96.32\%, and some superiorities of the HIWL are shown based on recall, precision, and F1-Score in comparing with some related works. In addition, we also explored the visualization of the galaxy image features and model attention to understand the foundations of the proposed scheme.

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Cancer is one of the most challenging diseases because of its complexity, variability, and diversity of causes. It has been one of the major research topics over the past decades, yet it is still poorly understood. To this end, multifaceted therapeutic frameworks are indispensable. \emph{Anticancer peptides} (ACPs) are the most promising treatment option, but their large-scale identification and synthesis require reliable prediction methods, which is still a problem. In this paper, we present an intuitive classification strategy that differs from the traditional \emph{black box} method and is based on the well-known statistical theory of \emph{sparse-representation classification} (SRC). Specifically, we create over-complete dictionary matrices by embedding the \emph{composition of the K-spaced amino acid pairs} (CKSAAP). Unlike the traditional SRC frameworks, we use an efficient \emph{matching pursuit} solver instead of the computationally expensive \emph{basis pursuit} solver in this strategy. Furthermore, the \emph{kernel principal component analysis} (KPCA) is employed to cope with non-linearity and dimension reduction of the feature space whereas the \emph{synthetic minority oversampling technique} (SMOTE) is used to balance the dictionary. The proposed method is evaluated on two benchmark datasets for well-known statistical parameters and is found to outperform the existing methods. The results show the highest sensitivity with the most balanced accuracy, which might be beneficial in understanding structural and chemical aspects and developing new ACPs. The Google-Colab implementation of the proposed method is available at the author's GitHub page (\href{https://github.com/ehtisham-Fazal/ACP-Kernel-SRC}{https://github.com/ehtisham-fazal/ACP-Kernel-SRC}).

Annotating the dataset with high-quality labels is crucial for performance of deep network, but in real world scenarios, the labels are often contaminated by noise. To address this, some methods were proposed to automatically split clean and noisy labels, and learn a semi-supervised learner in a Learning with Noisy Labels (LNL) framework. However, they leverage a handcrafted module for clean-noisy label splitting, which induces a confirmation bias in the semi-supervised learning phase and limits the performance. In this paper, we for the first time present a learnable module for clean-noisy label splitting, dubbed SplitNet, and a novel LNL framework which complementarily trains the SplitNet and main network for the LNL task. We propose to use a dynamic threshold based on a split confidence by SplitNet to better optimize semi-supervised learner. To enhance SplitNet training, we also present a risk hedging method. Our proposed method performs at a state-of-the-art level especially in high noise ratio settings on various LNL benchmarks.

This paper concerns with statistical estimation and inference for the ranking problems based on pairwise comparisons with additional covariate information such as the attributes of the compared items. Despite extensive studies, few prior literatures investigate this problem under the more realistic setting where covariate information exists. To tackle this issue, we propose a novel model, Covariate-Assisted Ranking Estimation (CARE) model, that extends the well-known Bradley-Terry-Luce (BTL) model, by incorporating the covariate information. Specifically, instead of assuming every compared item has a fixed latent score $\{\theta_i^*\}_{i=1}^n$, we assume the underlying scores are given by $\{\alpha_i^*+{x}_i^\top\beta^*\}_{i=1}^n$, where $\alpha_i^*$ and ${x}_i^\top\beta^*$ represent latent baseline and covariate score of the $i$-th item, respectively. We impose natural identifiability conditions and derive the $\ell_{\infty}$- and $\ell_2$-optimal rates for the maximum likelihood estimator of $\{\alpha_i^*\}_{i=1}^{n}$ and $\beta^*$ under a sparse comparison graph, using a novel `leave-one-out' technique (Chen et al., 2019) . To conduct statistical inferences, we further derive asymptotic distributions for the MLE of $\{\alpha_i^*\}_{i=1}^n$ and $\beta^*$ with minimal sample complexity. This allows us to answer the question whether some covariates have any explanation power for latent scores and to threshold some sparse parameters to improve the ranking performance. We improve the approximation method used in (Gao et al., 2021) for the BLT model and generalize it to the CARE model. Moreover, we validate our theoretical results through large-scale numerical studies and an application to the mutual fund stock holding dataset.

In recommender systems, a common problem is the presence of various biases in the collected data, which deteriorates the generalization ability of the recommendation models and leads to inaccurate predictions. Doubly robust (DR) learning has been studied in many tasks in RS, with the advantage that unbiased learning can be achieved when either a single imputation or a single propensity model is accurate. In this paper, we propose a multiple robust (MR) estimator that can take the advantage of multiple candidate imputation and propensity models to achieve unbiasedness. Specifically, the MR estimator is unbiased when any of the imputation or propensity models, or a linear combination of these models is accurate. Theoretical analysis shows that the proposed MR is an enhanced version of DR when only having a single imputation and propensity model, and has a smaller bias. Inspired by the generalization error bound of MR, we further propose a novel multiple robust learning approach with stabilization. We conduct extensive experiments on real-world and semi-synthetic datasets, which demonstrates the superiority of the proposed approach over state-of-the-art methods.

Automated slicing aims to identify subsets of evaluation data where a trained model performs anomalously. This is an important problem for machine learning pipelines in production since it plays a key role in model debugging and comparison, as well as the diagnosis of fairness issues. Scalability has become a critical requirement for any automated slicing system due to the large search space of possible slices and the growing scale of data. We present AutoSlicer, a scalable system that searches for problematic slices through distributed metric computation and hypothesis testing. We develop an efficient strategy that reduces the search space through pruning and prioritization. In the experiments, we show that our search strategy finds most of the anomalous slices by inspecting a small portion of the search space.