High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at //github.com/uhlerlab/InfoCORE.
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To cope with the growing prevalence of colorectal cancer (CRC), screening programs for polyp detection and removal have proven their usefulness. Colonoscopy is considered the best-performing procedure for CRC screening. To ease the examination, deep learning based methods for automatic polyp detection have been developed for conventional white-light imaging (WLI). Compared with WLI, narrow-band imaging (NBI) can improve polyp classification during colonoscopy but requires special equipment. We propose a CycleGAN-based framework to convert images captured with regular WLI to synthetic NBI (SNBI) as a pre-processing method for improving object detection on WLI when NBI is unavailable. This paper first shows that better results for polyp detection can be achieved on NBI compared to a relatively similar dataset of WLI. Secondly, experimental results demonstrate that our proposed modality translation can achieve improved polyp detection on SNBI images generated from WLI compared to the original WLI. This is because our WLI-to-SNBI translation model can enhance the observation of polyp surface patterns in the generated SNBI images.
Adaptive Local Neighborhood-based Neural Networks for MR Image Reconstruction from Undersampled Data
Recent medical image reconstruction techniques focus on generating high-quality medical images suitable for clinical use at the lowest possible cost and with the fewest possible adverse effects on patients. Recent works have shown significant promise for reconstructing MR images from sparsely sampled k-space data using deep learning. In this work, we propose a technique that rapidly estimates deep neural networks directly at reconstruction time by fitting them on small adaptively estimated neighborhoods of a training set. In brief, our algorithm alternates between searching for neighbors in a data set that are similar to the test reconstruction, and training a local network on these neighbors followed by updating the test reconstruction. Because our reconstruction model is learned on a dataset that is in some sense similar to the image being reconstructed rather than being fit on a large, diverse training set, it is more adaptive to new scans. It can also handle changes in training sets and flexible scan settings, while being relatively fast. Our approach, dubbed LONDN-MRI, was validated on multiple data sets using deep unrolled reconstruction networks. Reconstructions were performed at four fold and eight fold undersampling of k-space with 1D variable-density random phase-encode undersampling masks. Our results demonstrate that our proposed locally-trained method produces higher-quality reconstructions compared to models trained globally on larger datasets as well as other scan-adaptive methods.
Electrophysiological nature of neuronal networks allows to reveal various interactions between different cell units at a very short time-scales. One of the many challenges in analyzing these signals is to retrieve the morphology and functionality of a given network. In this work we developed a computational model, based on Reservoir Computing Network (RCN) architecture, which decodes the spatio-temporal data from electro-physiological measurements of neuronal cultures and reconstructs the network structure on a macroscopic domain, representing the connectivity between neuronal units. We demonstrate that the model can predict the connectivity map of the network with higher accuracy than the common methods such as Cross-Correlation and Transfer-Entropy. In addition, we experimentally demonstrate the ability of the model to predict a network response to a specific input, such as localized stimulus.
To investigate causal mechanisms, causal mediation analysis decomposes the total treatment effect into the natural direct and indirect effects. This paper examines the estimation of the direct and indirect effects in a general treatment effect model, where the treatment can be binary, multi-valued, continuous, or a mixture. We propose generalized weighting estimators with weights estimated by solving an expanding set of equations. Under some sufficient conditions, we show that the proposed estimators are consistent and asymptotically normal. Specifically, when the treatment is discrete, the proposed estimators attain the semiparametric efficiency bounds. Meanwhile, when the treatment is continuous, the convergence rates of the proposed estimators are slower than $N^{-1/2}$; however, they are still more efficient than that constructed from the true weighting function. A simulation study reveals that our estimators exhibit a satisfactory finite-sample performance, while an application shows their practical value
Knowledge distillation has emerged as a highly effective method for bridging the representation discrepancy between large-scale models and lightweight models. Prevalent approaches involve leveraging appropriate metrics to minimize the divergence or distance between the knowledge extracted from the teacher model and the knowledge learned by the student model. Centered Kernel Alignment (CKA) is widely used to measure representation similarity and has been applied in several knowledge distillation methods. However, these methods are complex and fail to uncover the essence of CKA, thus not answering the question of how to use CKA to achieve simple and effective distillation properly. This paper first provides a theoretical perspective to illustrate the effectiveness of CKA, which decouples CKA to the upper bound of Maximum Mean Discrepancy~(MMD) and a constant term. Drawing from this, we propose a novel Relation-Centered Kernel Alignment~(RCKA) framework, which practically establishes a connection between CKA and MMD. Furthermore, we dynamically customize the application of CKA based on the characteristics of each task, with less computational source yet comparable performance than the previous methods. The extensive experiments on the CIFAR-100, ImageNet-1k, and MS-COCO demonstrate that our method achieves state-of-the-art performance on almost all teacher-student pairs for image classification and object detection, validating the effectiveness of our approaches.
Medication recommendation is a fundamental yet crucial branch of healthcare, which provides opportunities to support clinical physicians with more accurate medication prescriptions for patients with complex health conditions. Learning from electronic health records (EHR) to recommend medications is the most common way in previous studies. However, most of them neglect incorporating domain knowledge according to the clinical manifestations in the EHR of the patient. To address these issues, we propose a novel \textbf{D}omain \textbf{K}nowledge \textbf{I}nformed \textbf{Net}work (DKINet) to integrate domain knowledge with observable clinical manifestations of the patient, which is the first dynamic domain knowledge informed framework toward medication recommendation. In particular, we first design a knowledge-driven encoder to capture the domain information and then develop a data-driven encoder to integrate domain knowledge into the observable EHR. To endow the model with the capability of temporal decision, we design an explicit medication encoder for learning the longitudinal dependence of the patient. Extensive experiments on three publicly available datasets verify the superiority of our method. The code will be public upon acceptance.
Objective: Social media-based public health research is crucial for epidemic surveillance, but most studies identify relevant corpora with keyword matching. This study develops a system to streamline the process of curating colloquial medical dictionaries. We demonstrate the pipeline by curating a UMLS-colloquial symptom dictionary from COVID-19-related tweets as proof of concept. Methods: COVID-19-related tweets from February 1, 2020, to April 30, 2022 were used. The pipeline includes three modules: a named entity recognition module to detect symptoms in tweets; an entity normalization module to aggregate detected entities; and a mapping module that iteratively maps entities to Unified Medical Language System concepts. A random 500 entity sample were drawn from the final dictionary for accuracy validation. Additionally, we conducted a symptom frequency distribution analysis to compare our dictionary to a pre-defined lexicon from previous research. Results: We identified 498,480 unique symptom entity expressions from the tweets. Pre-processing reduces the number to 18,226. The final dictionary contains 38,175 unique expressions of symptoms that can be mapped to 966 UMLS concepts (accuracy = 95%). Symptom distribution analysis found that our dictionary detects more symptoms and is effective at identifying psychiatric disorders like anxiety and depression, often missed by pre-defined lexicons. Conclusion: This study advances public health research by implementing a novel, systematic pipeline for curating symptom lexicons from social media data. The final lexicon's high accuracy, validated by medical professionals, underscores the potential of this methodology to reliably interpret and categorize vast amounts of unstructured social media data into actionable medical insights across diverse linguistic and regional landscapes.
Studies often report estimates of the average treatment effect. While the ATE summarizes the effect of a treatment on average, it does not provide any information about the effect of treatment within any individual. A treatment strategy that uses an individual's information to tailor treatment to maximize benefit is known as an optimal dynamic treatment rule. Treatment, however, is typically not limited to a single point in time; consequently, learning an optimal rule for a time-varying treatment may involve not just learning the extent to which the comparative treatments' benefits vary across the characteristics of individuals, but also learning the extent to which the comparative treatments' benefits vary as relevant circumstances evolve within an individual. The goal of this paper is to provide a tutorial for estimating ODTR from longitudinal observational and clinical trial data for applied researchers. We describe an approach that uses a doubly-robust unbiased transformation of the conditional average treatment effect. We then learn a time-varying ODTR for when to increase buprenorphine-naloxone dose to minimize return-to-regular-opioid-use among patients with opioid use disorder. Our analysis highlights the utility of ODTRs in the context of sequential decision making: the learned ODTR outperforms a clinically defined strategy.
The increasing complexity of medical imaging data underscores the need for advanced anomaly detection methods to automatically identify diverse pathologies. Current methods face challenges in capturing the broad spectrum of anomalies, often limiting their use to specific lesion types in brain scans. To address this challenge, we introduce a novel unsupervised approach, termed \textit{Reversed Auto-Encoders (RA)}, designed to create realistic pseudo-healthy reconstructions that enable the detection of a wider range of pathologies. We evaluate the proposed method across various imaging modalities, including magnetic resonance imaging (MRI) of the brain, pediatric wrist X-ray, and chest X-ray, and demonstrate superior performance in detecting anomalies compared to existing state-of-the-art methods. Our unsupervised anomaly detection approach may enhance diagnostic accuracy in medical imaging by identifying a broader range of unknown pathologies. Our code is publicly available at: \url{//github.com/ci-ber/RA}.
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.
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