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Anthony Nguyen

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Published work

7 published item(s)

preprint2026arXiv

Bridging the Version Gap: Multi-version Training Improves ICD Code Prediction, Especially for Rare Codes

Clinical coding maps clinical documentation to standardized medical codes, an essential yet time-consuming administrative task that could benefit from automation. Current models on ICD coding are typically optimized for codes from a specific ICD version. However, in reality, ICD systems evolve continuously, and different versions are adopted across time periods and regions. Moreover, ICD coding suffers from the long-tail problem, and rare code performance can be a bottleneck for developing implementable models. We examine whether it is viable to train version-independent models by combining data annotated in different ICD versions, which may help address these challenges. We add ICD-9 data to the training of a modified label-wise attention model for ICD-10 prediction, and find that despite the version mismatch, adding ICD-9 yields a 27% increase in micro F1 for 18K rare ICD codes compared to training on ICD-10 alone. On 8K frequent ICD-10 codes, the multi-version training also substantially improves macro metrics, with far fewer model parameters.

preprint2026arXiv

Systematic Evaluation of the Quality of Synthetic Clinical Notes Rephrased by LLMs at Million-Note Scale

Large language models (LLMs) can generate or synthesize clinical text for a wide range of applications, from improving clinical documentation to augmenting clinical text analytics. Yet evaluations typically focus on a narrow aspect -- such as similarity or utility comparisons -- even though these aspects are complementary and best viewed in parallel. In this study, we aim to conduct a systematic evaluation of LLM-generated clinical text, which includes intrinsic, extrinsic, and factuality evaluations of synthetic clinical notes rephrased from MIMIC databases at million-note scale. Our analysis demonstrates that synthetic notes preserve core clinical information and predictive utility for coarse-grained tasks despite substantial linguistic changes, but lose fine-grained details for task like ICD coding. We show this loss of detail can be substantially mitigated by rephrasing notes by chunks rather than by the whole note, but at the cost of reduced factual precision under incomplete context. Through fact-checking and error analysis, we further find that synthesis errors are dominated by misinterpretation of clinical context, alongside temporal confusion, measurement errors, and fabricated claims. Finally, we show that the synthetic notes -- despite their task-agnostic nature -- can effectively augment task-specific training for rare ICD codes.

preprint2022arXiv

Applying data technologies to combat AMR: current status, challenges, and opportunities on the way forward

Antimicrobial resistance (AMR) is a growing public health threat, estimated to cause over 10 million deaths per year and cost the global economy 100 trillion USD by 2050 under status quo projections. These losses would mainly result from an increase in the morbidity and mortality from treatment failure, AMR infections during medical procedures, and a loss of quality of life attributed to AMR. Numerous interventions have been proposed to control the development of AMR and mitigate the risks posed by its spread. This paper reviews key aspects of bacterial AMR management and control which make essential use of data technologies such as artificial intelligence, machine learning, and mathematical and statistical modelling, fields that have seen rapid developments in this century. Although data technologies have become an integral part of biomedical research, their impact on AMR management has remained modest. We outline the use of data technologies to combat AMR, detailing recent advancements in four complementary categories: surveillance, prevention, diagnosis, and treatment. We provide an overview on current AMR control approaches using data technologies within biomedical research, clinical practice, and in the "One Health" context. We discuss the potential impact and challenges wider implementation of data technologies is facing in high-income as well as in low- and middle-income countries, and recommend concrete actions needed to allow these technologies to be more readily integrated within the healthcare and public health sectors.

preprint2022arXiv

Readout of a quantum processor with high dynamic range Josephson parametric amplifiers

We demonstrate a high dynamic range Josephson parametric amplifier (JPA) in which the active nonlinear element is implemented using an array of rf-SQUIDs. The device is matched to the 50 $Ω$ environment with a Klopfenstein-taper impedance transformer and achieves a bandwidth of 250-300 MHz, with input saturation powers up to -95 dBm at 20 dB gain. A 54-qubit Sycamore processor was used to benchmark these devices, providing a calibration for readout power, an estimate of amplifier added noise, and a platform for comparison against standard impedance matched parametric amplifiers with a single dc-SQUID. We find that the high power rf-SQUID array design has no adverse effect on system noise, readout fidelity, or qubit dephasing, and we estimate an upper bound on amplifier added noise at 1.6 times the quantum limit. Lastly, amplifiers with this design show no degradation in readout fidelity due to gain compression, which can occur in multi-tone multiplexed readout with traditional JPAs.

preprint2022arXiv

Stochastic Multi-level Composition Optimization Algorithms with Level-Independent Convergence Rates

In this paper, we study smooth stochastic multi-level composition optimization problems, where the objective function is a nested composition of $T$ functions. We assume access to noisy evaluations of the functions and their gradients, through a stochastic first-order oracle. For solving this class of problems, we propose two algorithms using moving-average stochastic estimates, and analyze their convergence to an $ε$-stationary point of the problem. We show that the first algorithm, which is a generalization of \cite{GhaRuswan20} to the $T$ level case, can achieve a sample complexity of $\mathcal{O}(1/ε^6)$ by using mini-batches of samples in each iteration. By modifying this algorithm using linearized stochastic estimates of the function values, we improve the sample complexity to $\mathcal{O}(1/ε^4)$. {\color{black}This modification not only removes the requirement of having a mini-batch of samples in each iteration, but also makes the algorithm parameter-free and easy to implement}. To the best of our knowledge, this is the first time that such an online algorithm designed for the (un)constrained multi-level setting, obtains the same sample complexity of the smooth single-level setting, under standard assumptions (unbiasedness and boundedness of the second moments) on the stochastic first-order oracle.

preprint2020arXiv

A Label Attention Model for ICD Coding from Clinical Text

ICD coding is a process of assigning the International Classification of Disease diagnosis codes to clinical/medical notes documented by health professionals (e.g. clinicians). This process requires significant human resources, and thus is costly and prone to error. To handle the problem, machine learning has been utilized for automatic ICD coding. Previous state-of-the-art models were based on convolutional neural networks, using a single/several fixed window sizes. However, the lengths and interdependence between text fragments related to ICD codes in clinical text vary significantly, leading to the difficulty of deciding what the best window sizes are. In this paper, we propose a new label attention model for automatic ICD coding, which can handle both the various lengths and the interdependence of the ICD code related text fragments. Furthermore, as the majority of ICD codes are not frequently used, leading to the extremely imbalanced data issue, we additionally propose a hierarchical joint learning mechanism extending our label attention model to handle the issue, using the hierarchical relationships among the codes. Our label attention model achieves new state-of-the-art results on three benchmark MIMIC datasets, and the joint learning mechanism helps improve the performances for infrequent codes.

preprint2016arXiv

The Benefits of Word Embeddings Features for Active Learning in Clinical Information Extraction

This study investigates the use of unsupervised word embeddings and sequence features for sample representation in an active learning framework built to extract clinical concepts from clinical free text. The objective is to further reduce the manual annotation effort while achieving higher effectiveness compared to a set of baseline features. Unsupervised features are derived from skip-gram word embeddings and a sequence representation approach. The comparative performance of unsupervised features and baseline hand-crafted features in an active learning framework are investigated using a wide range of selection criteria including least confidence, information diversity, information density and diversity, and domain knowledge informativeness. Two clinical datasets are used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Our results demonstrate significant improvements in terms of effectiveness as well as annotation effort savings across both datasets. Using unsupervised features along with baseline features for sample representation lead to further savings of up to 9% and 10% of the token and concept annotation rates, respectively.