Joint nnU-Net and Radiomics Approaches for Segmentation and Prognosis of Head and Neck Cancers with PET/CT images

Automatic segmentation of head and neck cancer (HNC) tumors and lymph nodes plays a crucial role in the optimization treatment strategy and prognosis analysis. This study aims to employ nnU-Net for automatic segmentation and radiomics for recurrence-free survival (RFS) prediction using pretreatment PET/CT images in multi-center HNC cohort. A multi-center HNC dataset with 883 patients (524 patients for training, 359 for testing) was provided in HECKTOR 2022. A bounding box of the extended oropharyngeal region was retrieved for each patient with fixed size of 224 x 224 x 224 $mm^{3}$. Then 3D nnU-Net architecture was adopted to automatic segmentation of primary tumor and lymph nodes synchronously.Based on predicted segmentation, ten conventional features and 346 standardized radiomics features were extracted for each patient. Three prognostic models were constructed containing conventional and radiomics features alone, and their combinations by multivariate CoxPH modelling. The statistical harmonization method, ComBat, was explored towards reducing multicenter variations. Dice score and C-index were used as evaluation metrics for segmentation and prognosis task, respectively. For segmentation task, we achieved mean dice score around 0.701 for primary tumor and lymph nodes by 3D nnU-Net. For prognostic task, conventional and radiomics models obtained the C-index of 0.658 and 0.645 in the test set, respectively, while the combined model did not improve the prognostic performance with the C-index of 0.648.

KnowledgeShovel: An AI-in-the-Loop Document Annotation System for Scientific Knowledge Base Construction

Constructing a comprehensive, accurate, and useful scientific knowledge base is crucial for human researchers synthesizing scientific knowledge and for enabling Al-driven scientific discovery. However, the current process is difficult, error-prone, and laborious due to (1) the enormous amount of scientific literature available; (2) the highly-specialized scientific domains; (3) the diverse modalities of information (text, figure, table); and, (4) the silos of scientific knowledge in different publications with inconsistent formats and structures. Informed by a formative study and iterated with participatory design workshops, we designed and developed KnowledgeShovel, an Al-in-the-Loop document annotation system for researchers to construct scientific knowledge bases. The design of KnowledgeShovel introduces a multi-step multi-modal human-AI collaboration pipeline that aligns with users' existing workflows to improve data accuracy while reducing the human burden. A follow-up user evaluation with 7 geoscience researchers shows that KnowledgeShovel can enable efficient construction of scientific knowledge bases with satisfactory accuracy.

Iterative Adaptively Regularized LASSO-ADMM Algorithm for CFAR Estimation of Sparse Signals: IAR-LASSO-ADMM-CFAR Algorithm

The least-absolute shrinkage and selection operator (LASSO) is a regularization technique for estimating sparse signals of interest emerging in various applications and can be efficiently solved via the alternating direction method of multipliers (ADMM), which will be termed as LASSO-ADMM algorithm. The choice of the regularization parameter has significant impact on the performance of LASSO-ADMM algorithm. However, the optimization for the regularization parameter in the existing LASSO-ADMM algorithms has not been solved yet. In order to optimize this regularization parameter, we propose an efficient iterative adaptively regularized LASSO-ADMM (IAR-LASSO-ADMM) algorithm by iteratively updating the regularization parameter in the LASSO-ADMM algorithm. Moreover, a method is designed to iteratively update the regularization parameter by adding an outer iteration to the LASSO-ADMM algorithm. Specifically, at each outer iteration the zero support of the estimate obtained by the inner LASSO-ADMM algorithm is utilized to estimate the noise variance, and the noise variance is utilized to update the threshold according to a pre-defined const false alarm rate (CFAR). Then, the resulting threshold is utilized to update both the non-zero support of the estimate and the regularization parameter, and proceed to the next inner iteration. In addition, a suitable stopping criterion is designed to terminate the outer iteration process to obtain the final non-zero support of the estimate of the sparse measurement signals. The resulting algorithm is termed as IAR-LASSO-ADMM-CFAR algorithm. Finally, simulation results have been presented to show that the proposed IAR-LASSO-ADMM-CFAR algorithm outperforms the conventional LASSO-ADMM algorithm and other existing algorithms in terms of reconstruction accuracy, and its sparsity order estimate is more accurate than the existing algorithms.

CATNet: Cross-event Attention-based Time-aware Network for Medical Event Prediction

Medical event prediction (MEP) is a fundamental task in the medical domain, which needs to predict medical events, including medications, diagnosis codes, laboratory tests, procedures, outcomes, and so on, according to historical medical records. The task is challenging as medical data is a type of complex time series data with heterogeneous and temporal irregular characteristics. Many machine learning methods that consider the two characteristics have been proposed for medical event prediction. However, most of them consider the two characteristics separately and ignore the correlations among different types of medical events, especially relations between historical medical events and target medical events. In this paper, we propose a novel neural network based on attention mechanism, called cross-event attention-based time-aware network (CATNet), for medical event prediction. It is a time-aware, event-aware and task-adaptive method with the following advantages: 1) modeling heterogeneous information and temporal information in a unified way and considering temporal irregular characteristics locally and globally respectively, 2) taking full advantage of correlations among different types of events via cross-event attention. Experiments on two public datasets (MIMIC-III and eICU) show CATNet can be adaptive with different MEP tasks and outperforms other state-of-the-art methods on various MEP tasks. The source code of CATNet will be released after this manuscript is accepted.

Diverse Preference Augmentation with Multiple Domains for Cold-start Recommendations

Cold-start issues have been more and more challenging for providing accurate recommendations with the fast increase of users and items. Most existing approaches attempt to solve the intractable problems via content-aware recommendations based on auxiliary information and/or cross-domain recommendations with transfer learning. Their performances are often constrained by the extremely sparse user-item interactions, unavailable side information, or very limited domain-shared users. Recently, meta-learners with meta-augmentation by adding noises to labels have been proven to be effective to avoid overfitting and shown good performance on new tasks. Motivated by the idea of meta-augmentation, in this paper, by treating a user's preference over items as a task, we propose a so-called Diverse Preference Augmentation framework with multiple source domains based on meta-learning (referred to as MetaDPA) to i) generate diverse ratings in a new domain of interest (known as target domain) to handle overfitting on the case of sparse interactions, and to ii) learn a preference model in the target domain via a meta-learning scheme to alleviate cold-start issues. Specifically, we first conduct multi-source domain adaptation by dual conditional variational autoencoders and impose a Multi-domain InfoMax (MDI) constraint on the latent representations to learn domain-shared and domain-specific preference properties. To avoid overfitting, we add a Mutually-Exclusive (ME) constraint on the output of decoders to generate diverse ratings given content data. Finally, these generated diverse ratings and the original ratings are introduced into the meta-training procedure to learn a preference meta-learner, which produces good generalization ability on cold-start recommendation tasks. Experiments on real-world datasets show our proposed MetaDPA clearly outperforms the current state-of-the-art baselines.

A Large-scale Comprehensive Dataset and Copy-overlap Aware Evaluation Protocol for Segment-level Video Copy Detection

In this paper, we introduce VCSL (Video Copy Segment Localization), a new comprehensive segment-level annotated video copy dataset. Compared with existing copy detection datasets restricted by either video-level annotation or small-scale, VCSL not only has two orders of magnitude more segment-level labelled data, with 160k realistic video copy pairs containing more than 280k localized copied segment pairs, but also covers a variety of video categories and a wide range of video duration. All the copied segments inside each collected video pair are manually extracted and accompanied by precisely annotated starting and ending timestamps. Alongside the dataset, we also propose a novel evaluation protocol that better measures the prediction accuracy of copy overlapping segments between a video pair and shows improved adaptability in different scenarios. By benchmarking several baseline and state-of-the-art segment-level video copy detection methods with the proposed dataset and evaluation metric, we provide a comprehensive analysis that uncovers the strengths and weaknesses of current approaches, hoping to open up promising directions for future works. The VCSL dataset, metric and benchmark codes are all publicly available at https://github.com/alipay/VCSL.

DeepShovel: An Online Collaborative Platform for Data Extraction in Geoscience Literature with AI Assistance

Geoscientists, as well as researchers in many fields, need to read a huge amount of literature to locate, extract, and aggregate relevant results and data to enable future research or to build a scientific database, but there is no existing system to support this use case well. In this paper, based on the findings of a formative study about how geoscientists collaboratively annotate literature and extract and aggregate data, we proposed DeepShovel, a publicly-available AI-assisted data extraction system to support their needs. DeepShovel leverages the state-of-the-art neural network models to support researcher(s) easily and accurately annotate papers (in the PDF format) and extract data from tables, figures, maps, etc. in a human-AI collaboration manner. A follow-up user evaluation with 14 researchers suggested DeepShovel improved users' efficiency of data extraction for building scientific databases, and encouraged teams to form a larger scale but more tightly-coupled collaboration.

Two heads are better than one: Enhancing medical representations by pre-training over structured and unstructured electronic health records

The massive context of electronic health records (EHRs) has created enormous potentials for improving healthcare, among which structured (coded) data and unstructured (text) data are two important textual modalities. They do not exist in isolation and can complement each other in most real-life clinical scenarios. Most existing researches in medical informatics, however, either only focus on a particular modality or straightforwardly concatenate the information from different modalities, which ignore the interaction and information sharing between them. To address these issues, we proposed a unified deep learning-based medical pre-trained language model, named UMM-PLM, to automatically learn representative features from multimodal EHRs that consist of both structured data and unstructured data. Specifically, we first developed parallel unimodal information representation modules to capture the unimodal-specific characteristic, where unimodal representations were learned from each data source separately. A cross-modal module was further introduced to model the interactions between different modalities. We pre-trained the model on a large EHRs dataset containing both structured data and unstructured data and verified the effectiveness of the model on three downstream clinical tasks, i.e., medication recommendation, 30-day readmission and ICD coding through extensive experiments. The results demonstrate the power of UMM-PLM compared with benchmark methods and state-of-the-art baselines. Analyses show that UMM-PLM can effectively concern with multimodal textual information and has the potential to provide more comprehensive interpretations for clinical decision making.

DROID: Minimizing the Reality Gap using Single-Shot Human Demonstration

Reinforcement learning (RL) has demonstrated great success in the past several years. However, most of the scenarios focus on simulated environments. One of the main challenges of transferring the policy learned in a simulated environment to real world, is the discrepancy between the dynamics of the two environments. In prior works, Domain Randomization (DR) has been used to address the reality gap for both robotic locomotion and manipulation tasks. In this paper, we propose Domain Randomization Optimization IDentification (DROID), a novel framework to exploit single-shot human demonstration for identifying the simulator's distribution of dynamics parameters, and apply it to training a policy on a door opening task. Our results show that the proposed framework can identify the difference in dynamics between the simulated and the real worlds, and thus improve policy transfer by optimizing the simulator's randomization ranges. We further illustrate that based on these same identified parameters, our method can generalize the learned policy to different but related tasks.