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Recent advancements in sequential modeling applied to Electronic Health Records (EHR) have greatly influenced prescription recommender systems. While the recent literature on drug recommendation has shown promising performance, the study of discovering a diversity of coexisting temporal relationships at the level of medical codes over consecutive visits remains less explored. The goal of this study can be motivated from two perspectives. First, there is a need to develop a sophisticated sequential model capable of disentangling the complex relationships across sequential visits. Second, it is crucial to establish multiple and diverse health profiles for the same patient to ensure a comprehensive consideration of different medical intents in drug recommendation. To achieve this goal, we introduce Attentive Recommendation with Contrasted Intents (ARCI), a multi-level transformer-based method designed to capture the different but coexisting temporal paths across a shared sequence of visits. Specifically, we propose a novel intent-aware method with contrastive learning, that links specialized medical intents of the patients to the transformer heads for extracting distinct temporal paths associated with different health profiles. We conducted experiments on two real-world datasets for the prescription recommendation task using both ranking and classification metrics. Our results demonstrate that ARCI has outperformed the state-of-the-art prescription recommendation methods and is capable of providing interpretable insights for healthcare practitioners., Comment: Accepted to the 33rd ACM International Conference on Information and Knowledge Management (CIKM 2024)

Colonoscopy videos provide richer information in polyp segmentation for rectal cancer diagnosis. However, the endoscope's fast moving and close-up observing make the current methods suffer from large spatial incoherence and continuous low-quality frames, and thus yield limited segmentation accuracy. In this context, we focus on robust video polyp segmentation by enhancing the adjacent feature consistency and rebuilding the reliable polyp representation. To achieve this goal, we in this paper propose SALI network, a hybrid of Short-term Alignment Module (SAM) and Long-term Interaction Module (LIM). The SAM learns spatial-aligned features of adjacent frames via deformable convolution and further harmonizes them to capture more stable short-term polyp representation. In case of low-quality frames, the LIM stores the historical polyp representations as a long-term memory bank, and explores the retrospective relations to interactively rebuild more reliable polyp features for the current segmentation. Combing SAM and LIM, the SALI network of video segmentation shows a great robustness to the spatial variations and low-visual cues. Benchmark on the large-scale SUNSEG verifies the superiority of SALI over the current state-of-the-arts by improving Dice by 2.1%, 2.5%, 4.1% and 1.9%, for the four test sub-sets, respectively. Codes are at https://github.com/Scatteredrain/SALI., Comment: Accepted to MICCAI 2024. Code and models: https://github.com/Scatteredrain/SALI

Photometric constraint is indispensable for self-supervised monocular depth estimation. It involves warping a source image onto a target view using estimated depth&pose, and then minimizing the difference between the warped and target images. However, the endoscopic built-in light causes significant brightness fluctuations, and thus makes the photometric constraint unreliable. Previous efforts only mitigate this relying on extra models to calibrate image brightness. In this paper, we propose MonoPCC to address the brightness inconsistency radically by reshaping the photometric constraint into a cycle form. Instead of only warping the source image, MonoPCC constructs a closed loop consisting of two opposite forward-backward warping paths: from target to source and then back to target. Thus, the target image finally receives an image cycle-warped from itself, which naturally makes the constraint invariant to brightness changes. Moreover, MonoPCC transplants the source image's phase-frequency into the intermediate warped image to avoid structure lost, and also stabilizes the training via an exponential moving average (EMA) strategy to avoid frequent changes in the forward warping. The comprehensive and extensive experimental results on four endoscopic datasets demonstrate that our proposed MonoPCC shows a great robustness to the brightness inconsistency, and exceeds other state-of-the-arts by reducing the absolute relative error by at least 7.27%, 9.38%, 9.90% and 3.17%, respectively., Comment: 11 pages, 10 figures

We propose MonoBox, an innovative box-supervised segmentation method constrained by monotonicity to liberate its training from the user-unfriendly box-tightness assumption. In contrast to conventional box-supervised segmentation, where the box edges must precisely touch the target boundaries, MonoBox leverages imprecisely-annotated boxes to achieve robust pixel-wise segmentation. The 'linchpin' is that, within the noisy zones around box edges, MonoBox discards the traditional misguiding multiple-instance learning loss, and instead optimizes a carefully-designed objective, termed monotonicity constraint. Along directions transitioning from the foreground to background, this new constraint steers responses to adhere to a trend of monotonically decreasing values. Consequently, the originally unreliable learning within the noisy zones is transformed into a correct and effective monotonicity optimization. Moreover, an adaptive label correction is introduced, enabling MonoBox to enhance the tightness of box annotations using predicted masks from the previous epoch and dynamically shrink the noisy zones as training progresses. We verify MonoBox in the box-supervised segmentation task of polyps, where satisfying box-tightness is challenging due to the vague boundaries between the polyp and normal tissues. Experiments on both public synthetic and in-house real noisy datasets demonstrate that MonoBox exceeds other anti-noise state-of-the-arts by improving Dice by at least 5.5% and 3.3%, respectively. Codes are at https://github.com/Huster-Hq/MonoBox.

As IoT networks become more complex and generate massive amounts of dynamic data, it is difficult to monitor and detect anomalies using traditional statistical methods and machine learning methods. Deep learning algorithms can process and learn from large amounts of data and can also be trained using unsupervised learning techniques, meaning they don't require labelled data to detect anomalies. This makes it possible to detect new and unknown anomalies that may not have been detected before. Also, deep learning algorithms can be automated and highly scalable; thereby, they can run continuously in the backend and make it achievable to monitor large IoT networks instantly. In this work, we conduct a literature review on the most recent works using deep learning techniques and implement a model using ensemble techniques on the KDD Cup 99 dataset. The experimental results showcase the impressive performance of our deep anomaly detection model, achieving an accuracy of over 98\%., Comment: PerCom 2024 Workshop

Box-supervised polyp segmentation attracts increasing attention for its cost-effective potential. Existing solutions often rely on learning-free methods or pretrained models to laboriously generate pseudo masks, triggering Dice constraint subsequently. In this paper, we found that a model guided by the simplest box-filled masks can accurately predict polyp locations/sizes, but suffers from shape collapsing. In response, we propose two innovative learning fashions, Improved Box-dice (IBox) and Contrastive Latent-Anchors (CLA), and combine them to train a robust box-supervised model IBoxCLA. The core idea behind IBoxCLA is to decouple the learning of location/size and shape, allowing for focused constraints on each of them. Specifically, IBox transforms the segmentation map into a proxy map using shape decoupling and confusion-region swapping sequentially. Within the proxy map, shapes are disentangled, while locations/sizes are encoded as box-like responses. By constraining the proxy map instead of the raw prediction, the box-filled mask can well supervise IBoxCLA without misleading its shape learning. Furthermore, CLA contributes to shape learning by generating two types of latent anchors, which are learned and updated using momentum and segmented polyps to steadily represent polyp and background features. The latent anchors facilitate IBoxCLA to capture discriminative features within and outside boxes in a contrastive manner, yielding clearer boundaries. We benchmark IBoxCLA on five public polyp datasets. The experimental results demonstrate the competitive performance of IBoxCLA compared to recent fully-supervised polyp segmentation methods, and its superiority over other box-supervised state-of-the-arts with a relative increase of overall mDice and mIoU by at least 6.5% and 7.5%, respectively.

Survival analysis plays a crucial role in many healthcare decisions, where the risk prediction for the events of interest can support an informative outlook for a patient's medical journey. Given the existence of data censoring, an effective way of survival analysis is to enforce the pairwise temporal concordance between censored and observed data, aiming to utilize the time interval before censoring as partially observed time-to-event labels for supervised learning. Although existing studies mostly employed ranking methods to pursue an ordering objective, contrastive methods which learn a discriminative embedding by having data contrast against each other, have not been explored thoroughly for survival analysis. Therefore, in this paper, we propose a novel Ontology-aware Temporality-based Contrastive Survival (OTCSurv) analysis framework that utilizes survival durations from both censored and observed data to define temporal distinctiveness and construct negative sample pairs with adjustable hardness for contrastive learning. Specifically, we first use an ontological encoder and a sequential self-attention encoder to represent the longitudinal EHR data with rich contexts. Second, we design a temporal contrastive loss to capture varying survival durations in a supervised setting through a hardness-aware negative sampling mechanism. Last, we incorporate the contrastive task into the time-to-event predictive task with multiple loss components. We conduct extensive experiments using a large EHR dataset to forecast the risk of hospitalized patients who are in danger of developing acute kidney injury (AKI), a critical and urgent medical condition. The effectiveness and explainability of the proposed model are validated through comprehensive quantitative and qualitative studies., Comment: This paper has been accepted for publication at the CIKM 2023 conference

While we pay attention to the latest advances in clinical natural language processing (NLP), we can notice some resistance in the clinical and translational research community to adopt NLP models due to limited transparency, interpretability, and usability. In this study, we proposed an open natural language processing development framework. We evaluated it through the implementation of NLP algorithms for the National COVID Cohort Collaborative (N3C). Based on the interests in information extraction from COVID-19 related clinical notes, our work includes 1) an open data annotation process using COVID-19 signs and symptoms as the use case, 2) a community-driven ruleset composing platform, and 3) a synthetic text data generation workflow to generate texts for information extraction tasks without involving human subjects. The corpora were derived from texts from three different institutions (Mayo Clinic, University of Kentucky, University of Minnesota). The gold standard annotations were tested with a single institution's (Mayo) ruleset. This resulted in performances of 0.876, 0.706, and 0.694 in F-scores for Mayo, Minnesota, and Kentucky test datasets, respectively. The study as a consortium effort of the N3C NLP subgroup demonstrates the feasibility of creating a federated NLP algorithm development and benchmarking platform to enhance multi-institution clinical NLP study and adoption. Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP., Comment: update on contents

Deep neural networks often suffer from poor performance or even training failure due to the ill-conditioned problem, the vanishing/exploding gradient problem, and the saddle point problem. In this paper, a novel method by acting the gradient activation function (GAF) on the gradient is proposed to handle these challenges. Intuitively, the GAF enlarges the tiny gradients and restricts the large gradient. Theoretically, this paper gives conditions that the GAF needs to meet, and on this basis, proves that the GAF alleviates the problems mentioned above. In addition, this paper proves that the convergence rate of SGD with the GAF is faster than that without the GAF under some assumptions. Furthermore, experiments on CIFAR, ImageNet, and PASCAL visual object classes confirm the GAF's effectiveness. The experimental results also demonstrate that the proposed method is able to be adopted in various deep neural networks to improve their performance. The source code is publicly available at https://github.com/LongJin-lab/Activated-Gradients-for-Deep-Neural-Networks.

In deep learning, it is usually assumed that the optimization process is conducted on a shape-fixed loss surface. Differently, we first propose a novel concept of deformation mapping in this paper to affect the behaviour of the optimizer. Vertical deformation mapping (VDM), as a type of deformation mapping, can make the optimizer enter a flat region, which often implies better generalization performance. Moreover, we design various VDMs, and further provide their contributions to the loss surface. After defining the local M region, theoretical analyses show that deforming the loss surface can enhance the gradient descent optimizer's ability to filter out sharp minima. With visualizations of loss landscapes, we evaluate the flatnesses of minima obtained by both the original optimizer and optimizers enhanced by VDMs on CIFAR-100. The experimental results show that VDMs do find flatter regions. Moreover, we compare popular convolutional neural networks enhanced by VDMs with the corresponding original ones on ImageNet, CIFAR-10, and CIFAR-100. The results are surprising: there are significant improvements on all of the involved models equipped with VDMs. For example, the top-1 test accuracy of ResNet-20 on CIFAR-100 increases by 1.46%, with insignificant additional computational overhead., Comment: arXiv admin note: substantial text overlap with arXiv:2007.12515

In deep learning, it is usually assumed that the shape of the loss surface is fixed. Differently, a novel concept of deformation operator is first proposed in this paper to deform the loss surface, thereby improving the optimization. Deformation function, as a type of deformation operator, can improve the generalization performance. Moreover, various deformation functions are designed, and their contributions to the loss surface are further provided. Then, the original stochastic gradient descent optimizer is theoretically proved to be a flat minima filter that owns the talent to filter out the sharp minima. Furthermore, the flatter minima could be obtained by exploiting the proposed deformation functions, which is verified on CIFAR-100, with visualizations of loss landscapes near the critical points obtained by both the original optimizer and optimizer enhanced by deformation functions. The experimental results show that deformation functions do find flatter regions. Moreover, on ImageNet, CIFAR-10, and CIFAR-100, popular convolutional neural networks enhanced by deformation functions are compared with the corresponding original models, where significant improvements are observed on all of the involved models equipped with deformation functions. For example, the top-1 test accuracy of ResNet-20 on CIFAR-100 increases by 1.46%, with insignificant additional computational overhead., Comment: This paper is not perfect yet

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19., Comment: Journal of the American Medical Informatics Association, 2021

This paper studies a partial-fraction expansion for lossless negative imaginary systems and presents a generalized lossless negative imaginary lemma by allowing poles at zero. First, a necessary and sufficient condition for a system to be non-proper lossless negative imaginary is developed, and a minor partial-fraction expansion of lossless negative imaginary property is studied. Second, according to the minor decomposition properties, two different and new relationships between lossless positive real and lossless negative imaginary systems are established. Third, according to one of the relationships, a generalized lossless negative imaginary lemma in terms of a minimal state-space realization is derived by allowing poles at zero. Some important properties of lossless negative imaginary systems are also studied in this paper, and three numerical examples are provided to illustrate the developed theory

Exciton-polaritons in semiconductor microcavities generate fascinating effects such as long-range spatial coherence and Bose-Einstein Condensation (BEC), which are attractive for their potential use in low threshold lasers, vortices and slowing light, etc. However, currently most of exciton-polariton effects either occur at cryogenic temperature or rely on expensive cavity fabrication procedures. Further exploring new semiconductor microcavities with stronger exciton photon interaction strength is extensively needed. Herein, we demonstrate room temperature photon exciton strong coupling in hybrid inorganic-organic CH3NH3PbBr3 Fabry-P\'erot microcavities for the first time. The vacuum Rabi splitting energy is up to ~390 meV, which is ascribed to large oscillator strength and photon confinement in reduced dimension of optical microcavities. With increasing pumping energy, exciton-photon coupling strength is weakened due to carrier screening effect, leading to occurrence of photonic lasing instead of polartion lasing. The demonstrated strong coupling between photons and excitons in perovskite microcavities would be helpful for development of high performance polariton-based incoherent and coherent light sources, nonlinear optics, and slow light applications., Comment: 25 pages,5 figures

A beam line is built after the IHEP RFQ for halo study. To determine transverse emittance and ellipse parameters of the RFQ output beam, beam size data obtained from the first two of 14 wire scanners are employed. By using the transfer matrix method and the least square method, a set of linear equations were set up and solved. The solutions were then applied as initial beam parameters in multi-particle simulations to check the method of calculation. It is shown that difference between the simulated RMS beam size and the measured one at the measurement location is less than 7%, which is acceptable in our experiments., Comment: 6pages,4figures

To solve the discharge of the standard Bulk Micromegas and GEM detector, the GEM-Micromegas detector was developed in Institute of High Energy Physics. Taking into account the advantages of the two detectors, one GEM foil was set as a preamplifier on the mesh of Micromegas in the structure and the GEM preamplification decreased the working voltage of Micromegas to reduce the effect of the discharge significantly. In the paper, the performance of detector in X-ray beam was studied at 1W2B laboratory of Beijing Synchrotron Radiation Facility. Finally, the result of the energy resolution under various X-ray energies was given in different working gases. It indicated that the GEM-Micromegas detector had the energy response capability in all the energy range and it could work better than the standard Bulk-Micromegas., Comment: 5 pages, 6 figures

For an s-wave superconductor/semiconductor/ferromagnetic-insulator structure, the proximity effect can induce the energy gap in the semiconductor rather than the superconducting pair potential of its microscope Hamiltonian. As a result, it is questionable to realize topological superconducting states in that structure.

This study was designed to address questions of differential prediction of law school grades for various racial/ethnic minority subgroups. Differential prediction was evaluated by comparing the predicted and actual law school first-year grade point averages (FYAs) for various racial/ethnic subgroups within individual law schools based on regression equations commonly used in the admission process. The sample was drawn from the 1996, 1997, and 1998 entering law school classes, using data from the Law School Admission Council sponsored Correlation Studies. Data from 167 law schools, each of which enrolled 10 or more first-year students who identified themselves as Asian American, Black, or Latino were analyzed and reported. Statistical regression analyses were carried out to predict FYA using Law School Admission Test (LSAT) alone, undergraduate grade point average (UGPA) alone, and the best predictive linear combination of these two variables. Analyses were carried out separately for each school, resulting in three regression lines for each law school. Analyses were also carried out for the combined group of students in the study. Results indicate that the equation combining LSAT score and UGPA to predict FYA results in more accurate prediction than an equation using either LSAT score or UGPA in isolation. FYA tended to be overpredicted on average very slightly by this equation for all three of the minority groups, with the most overprediction for Black students and the least for Asian American students. The use of UGPA alone to predict FYA consistently resulted I the greatest average overprediction of FYA. These results do not support the concern that LSAT score or the traditional combination of LSAT score and UGPA may result in unfair admission decisions for the minority subgroups studied here. (Contains 4 tables, 6 figures, and 13 references.) (Author/SLD)