Thai-Hoang Pham

Thai-Hoang Pham, Xueru Zhang, Ping Zhang

As machine learning (ML) algorithms are increasingly used in high-stakes applications, concerns have arisen that they may be biased against certain social groups. Although many approaches have been proposed to make ML models fair, they typically rely on the assumption that data distributions in training and deployment are identical. Unfortunately, this is commonly violated in practice and a model that is fair during training may lead to an unexpected outcome during its deployment. Although the problem of designing robust ML models under dataset shifts has been widely studied, most existing works focus only on the transfer of accuracy. In this paper, we study the transfer of both fairness and accuracy under domain generalization where the data at test time may be sampled from never-before-seen domains. We first develop theoretical bounds on the unfairness and expected loss at deployment, and then derive sufficient conditions under which fairness and accuracy can be perfectly transferred via invariant representation learning. Guided by this, we design a learning algorithm such that fair ML models learned with training data still have high fairness and accuracy when deployment environments change. Experiments on real-world data validate the proposed algorithm. Model implementation is available at https://github.com/pth1993/FATDM.

Thai-Hoang Pham, Yuanlong Wang, Changchang Yin et al.

Domain adaptation (DA) tackles the issue of distribution shift by learning a model from a source domain that generalizes to a target domain. However, most existing DA methods are designed for scenarios where the source and target domain data lie within the same feature space, which limits their applicability in real-world situations. Recently, heterogeneous DA (HeDA) methods have been introduced to address the challenges posed by heterogeneous feature space between source and target domains. Despite their successes, current HeDA techniques fall short when there is a mismatch in both feature and label spaces. To address this, this paper explores a new DA scenario called open-set HeDA (OSHeDA). In OSHeDA, the model must not only handle heterogeneity in feature space but also identify samples belonging to novel classes. To tackle this challenge, we first develop a novel theoretical framework that constructs learning bounds for prediction error on target domain. Guided by this framework, we propose a new DA method called Representation Learning for OSHeDA (RL-OSHeDA). This method is designed to simultaneously transfer knowledge between heterogeneous data sources and identify novel classes. Experiments across text, image, and clinical data demonstrate the effectiveness of our algorithm. Model implementation is available at \url{https://github.com/pth1993/OSHeDA}.

Biplob Biswas, Thai-Hoang Pham, Ping Zhang

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

Thai-Hoang Pham, Xuan-Khoai Pham, Phuong Le-Hong

Semantic role labelling (SRL) is a task in natural language processing which detects and classifies the semantic arguments associated with the predicates of a sentence. It is an important step towards understanding the meaning of a natural language. There exists SRL systems for well-studied languages like English, Chinese or Japanese but there is not any such system for the Vietnamese language. In this paper, we present the first SRL system for Vietnamese with encouraging accuracy. We first demonstrate that a simple application of SRL techniques developed for English could not give a good accuracy for Vietnamese. We then introduce a new algorithm for extracting candidate syntactic constituents, which is much more accurate than the common node-mapping algorithm usually used in the identification step. Finally, in the classification step, in addition to the common linguistic features, we propose novel and useful features for use in SRL. Our SRL system achieves an $F_1$ score of 73.53\% on the Vietnamese PropBank corpus. This system, including software and corpus, is available as an open source project and we believe that it is a good baseline for the development of future Vietnamese SRL systems.

Xuwei Tan, Yuanlong Wang, Thai-Hoang Pham et al.

As machine learning systems become increasingly integrated into human-centered domains such as healthcare, ensuring fairness while maintaining high predictive performance is critical. Existing bias mitigation techniques often impose a trade-off between fairness and accuracy, inadvertently degrading performance for certain demographic groups. In high-stakes domains like clinical diagnosis, such trade-offs are ethically and practically unacceptable. In this study, we propose a fairness-without-harm approach by learning distinct representations for different demographic groups and selectively applying demographic experts consisting of group-specific representations and personalized classifiers through a no-harm constrained selection. We evaluate our approach on three real-world medical datasets -- covering eye disease, skin cancer, and X-ray diagnosis -- as well as two face datasets. Extensive empirical results demonstrate the effectiveness of our approach in achieving fairness without harm.

Thai-Hoang Pham, Xueru Zhang, Ping Zhang

Although recent advances in machine learning have shown its success to learn from independent and identically distributed (IID) data, it is vulnerable to out-of-distribution (OOD) data in an open world. Domain generalization (DG) deals with such an issue and it aims to learn a model from multiple source domains that can be generalized to unseen target domains. Existing studies on DG have largely focused on stationary settings with homogeneous source domains. However, in many applications, domains may evolve along a specific direction (e.g., time, space). Without accounting for such non-stationary patterns, models trained with existing methods may fail to generalize on OOD data. In this paper, we study domain generalization in non-stationary environment. We first examine the impact of environmental non-stationarity on model performance and establish the theoretical upper bounds for the model error at target domains. Then, we propose a novel algorithm based on adaptive invariant representation learning, which leverages the non-stationary pattern to train a model that attains good performance on target domains. Experiments on both synthetic and real data validate the proposed algorithm.

Changchang Yin, Shihan Fu, Bingsheng Yao et al.

Sepsis is an organ dysfunction caused by a deregulated immune response to an infection. Early sepsis prediction and identification allow for timely intervention, leading to improved clinical outcomes. Clinical calculators (e.g., the six-organ dysfunction assessment of SOFA) play a vital role in sepsis identification within clinicians' workflow, providing evidence-based risk assessments essential for sepsis diagnosis. However, artificial intelligence (AI) sepsis prediction models typically generate a single sepsis risk score without incorporating clinical calculators for assessing organ dysfunctions, making the models less convincing and transparent to clinicians. To bridge the gap, we propose to mimic clinicians' workflow with a novel framework SepsisCalc to integrate clinical calculators into the predictive model, yielding a clinically transparent and precise model for utilization in clinical settings. Practically, clinical calculators usually combine information from multiple component variables in Electronic Health Records (EHR), and might not be applicable when the variables are (partially) missing. We mitigate this issue by representing EHRs as temporal graphs and integrating a learning module to dynamically add the accurately estimated calculator to the graphs. Experimental results on real-world datasets show that the proposed model outperforms state-of-the-art methods on sepsis prediction tasks. Moreover, we developed a system to identify organ dysfunctions and potential sepsis risks, providing a human-AI interaction tool for deployment, which can help clinicians understand the prediction outputs and prepare timely interventions for the corresponding dysfunctions, paving the way for actionable clinical decision-making support for early intervention.

Thai-Hoang Pham, Jiayuan Chen, Seungyeon Lee et al.

As machine learning (ML) algorithms are increasingly used in medical image analysis, concerns have emerged about their potential biases against certain social groups. Although many approaches have been proposed to ensure the fairness of ML models, most existing works focus only on medical image diagnosis tasks, such as image classification and segmentation, and overlooked prognosis scenarios, which involve predicting the likely outcome or progression of a medical condition over time. To address this gap, we introduce FairTTE, the first comprehensive framework for assessing fairness in time-to-event (TTE) prediction in medical imaging. FairTTE encompasses a diverse range of imaging modalities and TTE outcomes, integrating cutting-edge TTE prediction and fairness algorithms to enable systematic and fine-grained analysis of fairness in medical image prognosis. Leveraging causal analysis techniques, FairTTE uncovers and quantifies distinct sources of bias embedded within medical imaging datasets. Our large-scale evaluation reveals that bias is pervasive across different imaging modalities and that current fairness methods offer limited mitigation. We further demonstrate a strong association between underlying bias sources and model disparities, emphasizing the need for holistic approaches that target all forms of bias. Notably, we find that fairness becomes increasingly difficult to maintain under distribution shifts, underscoring the limitations of existing solutions and the pressing need for more robust, equitable prognostic models.

Jiayuan Chen, Thai-Hoang Pham, Yuanlong Wang et al.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for \textit{de novo} cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to \textit{de novo} cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for \textit{de novo} cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

Seungyeon Lee, Thai-Hoang Pham, Zhao Cheng et al.

Sleep staging has become a critical task in diagnosing and treating sleep disorders to prevent sleep related diseases. With growing large scale sleep databases, significant progress has been made toward automatic sleep staging. However, previous studies face critical problems in sleep studies; the heterogeneity of subjects' physiological signals, the inability to extract meaningful information from unlabeled data to improve predictive performances, the difficulty in modeling correlations between sleep stages, and the lack of an effective mechanism to quantify predictive uncertainty. In this study, we propose a neural network based sleep staging model, DREAM, to learn domain generalized representations from physiological signals and models sleep dynamics. DREAM learns sleep related and subject invariant representations from diverse subjects' sleep signals and models sleep dynamics by capturing interactions between sequential signal segments and between sleep stages. We conducted a comprehensive empirical study to demonstrate the superiority of DREAM, including sleep stage prediction experiments, a case study, the usage of unlabeled data, and uncertainty. Notably, the case study validates DREAM's ability to learn generalized decision function for new subjects, especially in case there are differences between testing and training subjects. Uncertainty quantification shows that DREAM provides prediction uncertainty, making the model reliable and helping sleep experts in real world applications.

Thai-Hoang Pham, Changchang Yin, Laxmi Mehta et al.

Complication risk profiling is a key challenge in the healthcare domain due to the complex interaction between heterogeneous entities (e.g., visit, disease, medication) in clinical data. With the availability of real-world clinical data such as electronic health records and insurance claims, many deep learning methods are proposed for complication risk profiling. However, these existing methods face two open challenges. First, data heterogeneity relates to those methods leveraging clinical data from a single view only while the data can be considered from multiple views (e.g., sequence of clinical visits, set of clinical features). Second, generalized prediction relates to most of those methods focusing on single-task learning, whereas each complication onset is predicted independently, leading to suboptimal models. We propose a multi-view multi-task network (MuViTaNet) for predicting the onset of multiple complications to tackle these issues. In particular, MuViTaNet complements patient representation by using a multi-view encoder to effectively extract information by considering clinical data as both sequences of clinical visits and sets of clinical features. In addition, it leverages additional information from both related labeled and unlabeled datasets to generate more generalized representations by using a new multi-task learning scheme for making more accurate predictions. The experimental results show that MuViTaNet outperforms existing methods for profiling the development of cardiac complications in breast cancer survivors. Furthermore, thanks to its multi-view multi-task architecture, MuViTaNet also provides an effective mechanism for interpreting its predictions in multiple perspectives, thereby helping clinicians discover the underlying mechanism triggering the onset and for making better clinical treatments in real-world scenarios.

Thai-Hoang Pham, Khai Mai, Nguyen Minh Trung et al.

Fine-Grained Named Entity Recognition (FG-NER) is critical for many NLP applications. While classical named entity recognition (NER) has attracted a substantial amount of research, FG-NER is still an open research domain. The current state-of-the-art (SOTA) model for FG-NER relies heavily on manual efforts for building a dictionary and designing hand-crafted features. The end-to-end framework which achieved the SOTA result for NER did not get the competitive result compared to SOTA model for FG-NER. In this paper, we investigate how effective multi-task learning approaches are in an end-to-end framework for FG-NER in different aspects. Our experiments show that using multi-task learning approaches with contextualized word representation can help an end-to-end neural network model achieve SOTA results without using any additional manual effort for creating data and designing features.

Thai-Hoang Pham, Xuan-Khoai Pham, Phuong Le-Hong

This paper presents an empirical study of two machine translation-based approaches for Vietnamese diacritic restoration problem, including phrase-based and neural-based machine translation models. This is the first work that applies neural-based machine translation method to this problem and gives a thorough comparison to the phrase-based machine translation method which is the current state-of-the-art method for this problem. On a large dataset, the phrase-based approach has an accuracy of 97.32% while that of the neural-based approach is 96.15%. While the neural-based method has a slightly lower accuracy, it is about twice faster than the phrase-based method in terms of inference speed. Moreover, neural-based machine translation method has much room for future improvement such as incorporating pre-trained word embeddings and collecting more training data.

Phuong Le-Hong, Minh Pham Quang Nhat, Thai-Hoang Pham et al.

This paper presents an empirical study of two widely-used sequence prediction models, Conditional Random Fields (CRFs) and Long Short-Term Memory Networks (LSTMs), on two fundamental tasks for Vietnamese text processing, including part-of-speech tagging and named entity recognition. We show that a strong lower bound for labeling accuracy can be obtained by relying only on simple word-based features with minimal hand-crafted feature engineering, of 90.65\% and 86.03\% performance scores on the standard test sets for the two tasks respectively. In particular, we demonstrate empirically the surprising efficiency of word embeddings in both of the two tasks, with both of the two models. We point out that the state-of-the-art LSTMs model does not always outperform significantly the traditional CRFs model, especially on moderate-sized data sets. Finally, we give some suggestions and discussions for efficient use of sequence labeling models in practical applications.

Thai-Hoang Pham, Xuan-Khoai Pham, Tuan-Anh Nguyen et al.

This paper demonstrates neural network-based toolkit namely NNVLP for essential Vietnamese language processing tasks including part-of-speech (POS) tagging, chunking, named entity recognition (NER). Our toolkit is a combination of bidirectional Long Short-Term Memory (Bi-LSTM), Convolutional Neural Network (CNN), Conditional Random Field (CRF), using pre-trained word embeddings as input, which achieves state-of-the-art results on these three tasks. We provide both API and web demo for this toolkit.

Thai-Hoang Pham, Phuong Le-Hong

This paper presents a state-of-the-art system for Vietnamese Named Entity Recognition (NER). By incorporating automatic syntactic features with word embeddings as input for bidirectional Long Short-Term Memory (Bi-LSTM), our system, although simpler than some deep learning architectures, achieves a much better result for Vietnamese NER. The proposed method achieves an overall F1 score of 92.05% on the test set of an evaluation campaign, organized in late 2016 by the Vietnamese Language and Speech Processing (VLSP) community. Our named entity recognition system outperforms the best previous systems for Vietnamese NER by a large margin.

Thai-Hoang Pham, Phuong Le-Hong

This paper demonstrates end-to-end neural network architectures for Vietnamese named entity recognition. Our best model is a combination of bidirectional Long Short-Term Memory (Bi-LSTM), Convolutional Neural Network (CNN), Conditional Random Field (CRF), using pre-trained word embeddings as input, which achieves an F1 score of 88.59% on a standard test set. Our system is able to achieve a comparable performance to the first-rank system of the VLSP campaign without using any syntactic or hand-crafted features. We also give an extensive empirical study on using common deep learning models for Vietnamese NER, at both word and character level.

Thai-Hoang Pham, Phuong Le-Hong

Short Message Service (SMS) spam is a serious problem in Vietnam because of the availability of very cheap pre-paid SMS packages. There are some systems to detect and filter spam messages for English, most of which use machine learning techniques to analyze the content of messages and classify them. For Vietnamese, there is some research on spam email filtering but none focused on SMS. In this work, we propose the first system for filtering Vietnamese spam SMS. We first propose an appropriate preprocessing method since existing tools for Vietnamese preprocessing cannot give good accuracy on our dataset. We then experiment with vector representations and classifiers to find the best model for this problem. Our system achieves an accuracy of 94% when labelling spam messages while the misclassification rate of legitimate messages is relatively small, about only 0.4%. This is an encouraging result compared to that of English and can be served as a strong baseline for future development of Vietnamese SMS spam prevention systems.