Manar D. Samad

Maksims Kazijevs, Manar D. Samad

The imputation of missing values in multivariate time series (MTS) data is critical in ensuring data quality and producing reliable data-driven predictive models. Apart from many statistical approaches, a few recent studies have proposed state-of-the-art deep learning methods to impute missing values in MTS data. However, the evaluation of these deep methods is limited to one or two data sets, low missing rates, and completely random missing value types. This survey performs six data-centric experiments to benchmark state-of-the-art deep imputation methods on five time series health data sets. Our extensive analysis reveals that no single imputation method outperforms the others on all five data sets. The imputation performance depends on data types, individual variable statistics, missing value rates, and types. Deep learning methods that jointly perform cross-sectional (across variables) and longitudinal (across time) imputations of missing values in time series data yield statistically better data quality than traditional imputation methods. Although computationally expensive, deep learning methods are practical given the current availability of high-performance computing resources, especially when data quality and sample size are highly important in healthcare informatics. Our findings highlight the importance of data-centric selection of imputation methods to optimize data-driven predictive models.

Megan A. Witherow, Manar D. Samad, Norou Diawara et al.

Imaging of facial affects may be used to measure psychophysiological attributes of children through their adulthood for applications in education, healthcare, and entertainment, among others. Deep convolutional neural networks show promising results in classifying facial expressions of adults. However, classifier models trained with adult benchmark data are unsuitable for learning child expressions due to discrepancies in psychophysical development. Similarly, models trained with child data perform poorly in adult expression classification. We propose domain adaptation to concurrently align distributions of adult and child expressions in a shared latent space for robust classification of either domain. Furthermore, age variations in facial images are studied in age-invariant face recognition yet remain unleveraged in adult-child expression classification. We take inspiration from multiple fields and propose deep adaptive FACial Expressions fusing BEtaMix SElected Landmark Features (FACE-BE-SELF) for adult-child expression classification. For the first time in the literature, a mixture of Beta distributions is used to decompose and select facial features based on correlations with expression, domain, and identity factors. We evaluate FACE-BE-SELF using 5-fold cross validation for two pairs of adult-child data sets. Our proposed FACE-BE-SELF approach outperforms transfer learning and other baseline domain adaptation methods in aligning latent representations of adult and child expressions.

Shourav B. Rabbani, Ivan V. Medri, Manar D. Samad

Deep learning methods are primarily proposed for supervised learning of images or text with limited applications to clustering problems. In contrast, tabular data with heterogeneous features pose unique challenges in representation learning, where deep learning has yet to replace traditional machine learning. This paper addresses these challenges in developing one of the first deep clustering methods for tabular data: Gaussian Cluster Embedding in Autoencoder Latent Space (G-CEALS). G-CEALS is an unsupervised deep clustering framework for learning the parameters of multivariate Gaussian cluster distributions by iteratively updating individual cluster weights. The G-CEALS method presents average rank orderings of 2.9(1.7) and 2.8(1.7) based on clustering accuracy and adjusted Rand index (ARI) scores on sixteen tabular data sets, respectively, and outperforms nine state-of-the-art clustering methods. G-CEALS substantially improves clustering performance compared to traditional K-means and GMM, which are still de facto methods for clustering tabular data. Similar computationally efficient and high-performing deep clustering frameworks are imperative to reap the myriad benefits of deep learning on tabular data over traditional machine learning.

Sakib Abrar, Ali Sekmen, Manar D. Samad

Deep learning methods in the literature are commonly benchmarked on image data sets, which may not be suitable or effective baselines for non-image tabular data. In this paper, we take a data-centric view to perform one of the first studies on deep embedding clustering of tabular data. Eight clustering and state-of-the-art embedding clustering methods proposed for image data sets are tested on seven tabular data sets. Our results reveal that a traditional clustering method ranks second out of eight methods and is superior to most deep embedding clustering baselines. Our observation aligns with the literature that conventional machine learning of tabular data is still a robust approach against deep learning. Therefore, state-of-the-art embedding clustering methods should consider data-centric customization of learning architectures to become competitive baselines for tabular data.

Shourav B. Rabbani, Manar D. Samad

Traditional machine learning assumes samples in tabular data to be independent and identically distributed (i.i.d). This assumption may miss useful information within and between sample relationships in representation learning. This paper relaxes the i.i.d assumption to learn tabular data representations by incorporating between-sample relationships for the first time using graph neural networks (GNN). We investigate our hypothesis using several GNNs and state-of-the-art (SOTA) deep attention models to learn the between-sample relationship on ten tabular data sets by comparing them to traditional machine learning methods. GNN methods show the best performance on tabular data with large feature-to-sample ratios. Our results reveal that attention-based GNN methods outperform traditional machine learning on five data sets and SOTA deep tabular learning methods on three data sets. Between-sample learning via GNN and deep attention methods yield the best classification accuracy on seven of the ten data sets. This suggests that the i.i.d assumption may not always hold for most tabular data sets.

Karla N. Robles, Manar D. Samad

Polymer-based long-acting injectables (LAIs) have transformed the treatment of chronic diseases by enabling controlled drug delivery, thus reducing dosing frequency and extending therapeutic duration. Achieving controlled drug release from LAIs requires extensive optimization of the complex underlying physicochemical properties. Machine learning (ML) can accelerate LAI development by modeling the complex relationships between LAI properties and drug release. However, recent ML studies have provided limited information on key properties that modulate drug release, due to the lack of custom modeling and analysis tailored to LAI data. This paper presents a novel data transformation and explainable ML approach to synthesize actionable information from 321 LAI formulations by predicting early drug release at 24, 48, and 72 hours, classification of release profile types, and prediction of complete release profiles. These three experiments investigate the contribution and control of LAI material characteristics in early and complete drug release profiles. A strong correlation (>0.65) is observed between the true and predicted drug release in 72 hours, while a 0.87 F1-score is obtained in classifying release profile types. A time-independent ML framework predicts delayed biphasic and triphasic curves with better performance than current time-dependent approaches. Shapley additive explanations reveal the relative influence of material characteristics during early and for complete release which fill several gaps in previous in-vitro and ML-based studies. The novel approach and findings can provide a quantitative strategy and recommendations for scientists to optimize the drug-release dynamics of LAI. The source code for the model implementation is publicly available.

Ibna Kowsar, Kazi F. Akhter, Manar D. Samad

Transfer learning of tabular data is non-trivial due to heterogeneity in the feature space across disparate domains. The limited success of traditional deep learning in tabular knowledge transfer can be advanced by leveraging large language models (LLMs). However, the efficacy of LLMs often stagnates for mixed data types structured in tables due to the limitations of text prompts and in-context learning. We propose a lightweight transfer learning framework that fine-tunes an LLM using source tabular data and transplants the LLM's selective $key$ and $value$ projection weights into a gated feature tokenized transformer (gFTT) built for tabular data. The gFTT model with cross-domain attention is fine-tuned using target tabular data for transfer learning, eliminating the need for shared features, LLM prompt engineering, and large-scale pretrained models. Our experiments using ten pairs of source-target data sets and 12 baselines demonstrate the superiority of the proposed LLM-attention transplant for transfer learning (LATTLE) method over traditional ML models, state-of-the-art deep tabular architectures, and transfer learning models trained on thousands to billions of tabular samples. The proposed attention transfer demonstrates an effective solution to learning relationships between data tables using an LLM in a low-resource learning environment. The source code for the proposed method is publicly available.

Shourav B. Rabbani, Ivan V. Medri, Manar D. Samad

Despite groundbreaking success in image and text learning, deep learning has not achieved significant improvements against traditional machine learning (ML) when it comes to tabular data. This performance gap underscores the need for data-centric treatment and benchmarking of learning algorithms. Recently, attention and contrastive learning breakthroughs have shifted computer vision and natural language processing paradigms. However, the effectiveness of these advanced deep models on tabular data is sparsely studied using a few data sets with very large sample sizes, reporting mixed findings after benchmarking against a limited number of baselines. We argue that the heterogeneity of tabular data sets and selective baselines in the literature can bias the benchmarking outcomes. This article extensively evaluates state-of-the-art attention and contrastive learning methods on a wide selection of 28 tabular data sets (14 easy and 14 hard-to-classify) against traditional deep and machine learning. Our data-centric benchmarking demonstrates when traditional ML is preferred over deep learning and vice versa because no best learning method exists for all tabular data sets. Combining between-sample and between-feature attentions conquers the invincible traditional ML on tabular data sets by a significant margin but fails on high dimensional data, where contrastive learning takes a robust lead. While a hybrid attention-contrastive learning strategy mostly wins on hard-to-classify data sets, traditional methods are frequently superior on easy-to-classify data sets with presumably simpler decision boundaries. To the best of our knowledge, this is the first benchmarking paper with statistical analyses of attention and contrastive learning performances on a diverse selection of tabular data sets against traditional deep and machine learning baselines to facilitate further advances in this field.

Shourav B. Rabbani, Ibna Kowsar, Manar D. Samad

Despite the artificial intelligence (AI) revolution, deep learning has yet to achieve much success with tabular data due to heterogeneous feature space and limited sample sizes without viable transfer learning. The new era of generative AI, powered by large language models (LLM), brings unprecedented learning opportunities to diverse data and domains. This paper investigates the effectiveness of an LLM application programming interface (API) and transfer learning of LLM in tabular data classification. LLM APIs respond to input text prompts with tokenized data and instructions, whereas transfer learning finetunes an LLM for a target classification task. This paper proposes an end-to-end finetuning of LLM to demonstrate cross-data transfer learning on ten benchmark data sets when large pre-trained tabular data models do not exist to facilitate transfer learning. The proposed LLM finetuning method outperforms state-of-the-art machine and deep learning methods on tabular data with less than ten features - a standard feature size for tabular data sets. The transfer learning approach uses a fraction of the computational cost of other deep learning or API-based solutions while ensuring competitive or superior classification performance.

Manar D. Samad, Yina Hou, Shrabani Ghosh

In electronic health records (EHRs), clustering patients and distinguishing disease subtypes are key tasks to elucidate pathophysiology and aid clinical decision-making. However, clustering in healthcare informatics is still based on traditional methods, especially K-means, and has achieved limited success when applied to embedding representations learned by autoencoders as hybrid methods. This paper investigates the effectiveness of traditional, hybrid, and deep learning methods in heart failure patient cohorts using real EHR data from the All of Us Research Program. Traditional clustering methods perform robustly because deep learning approaches are specifically designed for image clustering, a task that differs substantially from the tabular EHR data setting. To address the shortcomings of deep clustering, we introduce an ensemble-based deep clustering approach that aggregates cluster assignments obtained from multiple embedding dimensions, rather than relying on a single fixed embedding space. When combined with traditional clustering in a novel ensemble framework, the proposed ensemble embedding for deep clustering delivers the best overall performance ranking across 14 diverse clustering methods and multiple patient cohorts. This paper underscores the importance of biological sex-specific clustering of EHR data and the advantages of combining traditional and deep clustering approaches over a single method.

Ibna Kowsar, Shourav B. Rabbani, Yina Hou et al.

Missing values of varying patterns and rates in real-world tabular data pose a significant challenge in developing reliable data-driven models. The most commonly used statistical and machine learning methods for missing value imputation may be ineffective when the missing rate is high and not random. This paper explores row and column attention in tabular data as between-feature and between-sample attention in a novel framework to reconstruct missing values. The proposed method uses CutMix data augmentation within a contrastive learning framework to improve the uncertainty of missing value estimation. The performance and generalizability of trained imputation models are evaluated in set-aside test data folds with missing values. The proposed framework is compared with 11 state-of-the-art statistical, machine learning, and deep imputation methods using 12 diverse tabular data sets. The average performance rank of our proposed method demonstrates its superiority over the state-of-the-art methods for missing rates between 10% and 90% and three missing value types, especially when the missing values are not random. The quality of the imputed data using our proposed method is compared in a downstream patient classification task using real-world electronic health records. This paper highlights the heterogeneity of tabular data sets to recommend imputation methods based on missing value types and data characteristics.

Yina Hou, Shourav B. Rabbani, Liang Hong et al.

The importance of clinical variables in the prognosis of the disease is explained using statistical correlation or machine learning (ML). However, the predictive importance of these variables may not represent their causal relationships with diseases. This paper uses clinical variables from a heart failure (HF) patient cohort to investigate the causal explainability of important variables obtained in statistical and ML contexts. Due to inherent regression modeling, popular causal discovery methods strictly assume that the cause and effect variables are numerical and continuous. This paper proposes a new computational framework to enable causal structure discovery (CSD) and score the causal strength of mixed-type (categorical, numerical, binary) clinical variables for binary disease outcomes. In HF classification, we investigate the association between the importance rank order of three feature types: correlated features, features important for ML predictions, and causal features. Our results demonstrate that CSD modeling for nonlinear causal relationships is more meaningful than its linear counterparts. Feature importance obtained from nonlinear classifiers (e.g., gradient-boosting trees) strongly correlates with the causal strength of variables without differentiating cause and effect variables. Correlated variables can be causal for HF, but they are rarely identified as effect variables. These results can be used to add the causal explanation of variables important for ML-based prediction modeling.

Manar D. Samad, Kazi Fuad B. Akhter, Shourav B. Rabbani et al.

Tabular data sets with varying missing values are prepared for machine learning using an arbitrary imputation strategy. Synthetic values generated by imputation models often raise concerns about data quality and the reliability of data-driven outcomes. To address these concerns, this article proposes an imputation-free incremental attention learning (IFIAL) method for tabular data. A pair of attention masks is derived and retrofitted to a transformer to directly streamline tabular data without imputing or initializing missing values. The proposed method incrementally learns partitions of overlapping and fixed-size feature sets to enhance the efficiency and performance of the transformer. The average classification performance rank order across 17 diverse tabular data sets highlights the superiority of IFIAL over 11 state-of-the-art learning methods with or without missing value imputations. Further experiments substantiate the robustness of IFIAL against varying missing value types and rates compared to methods involving missing value imputation. Our analysis reveals that a feature partition size of half the original feature space is, both computationally and in terms of accuracy, the best choice for the proposed incremental learning. The proposed method is one of the first solutions to enable deep attention learning of tabular data without requiring missing-value imputation. The source code for this paper is publicly available.

Riadul Islam, Maloy K. Devnath, Manar D. Samad et al.

The national highway traffic safety administration (NHTSA) identified cybersecurity of the automobile systems are more critical than the security of other information systems. Researchers already demonstrated remote attacks on critical vehicular electronic control units (ECUs) using controller area network (CAN). Besides, existing intrusion detection systems (IDSs) often propose to tackle a specific type of attack, which may leave a system vulnerable to numerous other types of attacks. A generalizable IDS that can identify a wide range of attacks within the shortest possible time has more practical value than attack-specific IDSs, which is not a trivial task to accomplish. In this paper we propose a novel {\textbf g}raph-based {\textbf G}aussian {\textbf n}aive {\textbf B}ayes (GGNB) intrusion detection algorithm by leveraging graph properties and PageRank-related features. The GGNB on the real rawCAN data set~\cite{Lee:2017} yields 99.61\%, 99.83\%, 96.79\%, and 96.20\% detection accuracy for denial of service (DoS), fuzzy, spoofing, replay, mixed attacks, respectively. Also, using OpelAstra data set~\cite{Guillaume:2019}, the proposed methodology has 100\%, 99.85\%, 99.92\%, 100\%, 99.92\%, 97.75\% and 99.57\% detection accuracy considering DoS, diagnostic, fuzzing CAN ID, fuzzing payload, replay, suspension, and mixed attacks, respectively. The GGNB-based methodology requires about $239\times$ and $135\times$ lower training and tests times, respectively, compared to the SVM classifier used in the same application. Using Xilinx Zybo Z7 field-programmable gate array (FPGA) board, the proposed GGNB requires $5.7 \times$, $5.9 \times$, $5.1 \times$, and $3.6 \times$ fewer slices, LUTs, flip-flops, and DSP units, respectively, than conventional NN architecture.

Manar D. Samad, Nalin D. Khounviengxay, Megan A. Witherow

Processing of raw text is the crucial first step in text classification and sentiment analysis. However, text processing steps are often performed using off-the-shelf routines and pre-built word dictionaries without optimizing for domain, application, and context. This paper investigates the effect of seven text processing scenarios on a particular text domain (Twitter) and application (sentiment classification). Skip gram-based word embeddings are developed to include Twitter colloquial words, emojis, and hashtag keywords that are often removed for being unavailable in conventional literature corpora. Our experiments reveal negative effects on sentiment classification of two common text processing steps: 1) stop word removal and 2) averaging of word vectors to represent individual tweets. New effective steps for 1) including non-ASCII emoji characters, 2) measuring word importance from word embedding, 3) aggregating word vectors into a tweet embedding, and 4) developing linearly separable feature space have been proposed to optimize the sentiment classification pipeline. The best combination of text processing steps yields the highest average area under the curve (AUC) of 88.4 (+/-0.4) in classifying 14,640 tweets with three sentiment labels. Word selection from context-driven word embedding reveals that only the ten most important words in Tweets cumulatively yield over 98% of the maximum accuracy. Results demonstrate a means for data-driven selection of important words in tweet classification as opposed to using pre-built word dictionaries. The proposed tweet embedding is robust to and alleviates the need for several text processing steps.

Mahbubul Alam, Manar D. Samad, Lasitha Vidyaratne et al.

This survey presents a review of state-of-the-art deep neural network architectures, algorithms, and systems in vision and speech applications. Recent advances in deep artificial neural network algorithms and architectures have spurred rapid innovation and development of intelligent vision and speech systems. With availability of vast amounts of sensor data and cloud computing for processing and training of deep neural networks, and with increased sophistication in mobile and embedded technology, the next-generation intelligent systems are poised to revolutionize personal and commercial computing. This survey begins by providing background and evolution of some of the most successful deep learning models for intelligent vision and speech systems to date. An overview of large-scale industrial research and development efforts is provided to emphasize future trends and prospects of intelligent vision and speech systems. Robust and efficient intelligent systems demand low-latency and high fidelity in resource-constrained hardware platforms such as mobile devices, robots, and automobiles. Therefore, this survey also provides a summary of key challenges and recent successes in running deep neural networks on hardware-restricted platforms, i.e. within limited memory, battery life, and processing capabilities. Finally, emerging applications of vision and speech across disciplines such as affective computing, intelligent transportation, and precision medicine are discussed. To our knowledge, this paper provides one of the most comprehensive surveys on the latest developments in intelligent vision and speech applications from the perspectives of both software and hardware systems. Many of these emerging technologies using deep neural networks show tremendous promise to revolutionize research and development for future vision and speech systems.