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Question Answering (QA) systems on patient-related data can assist both clinicians and patients. They can, for example, assist clinicians in decision-making and enable patients to have a better understanding of their medical history. Significant amounts of patient data are stored in Electronic Health Records (EHRs), making EHR QA an important research area. In EHR QA, the answer is obtained from the medical record of the patient. Because of the differences in data format and modality, this differs greatly from other medical QA tasks that employ medical websites or scientific papers to retrieve answers, making it critical to research EHR question answering. This study aimed to provide a methodological review of existing works on QA over EHRs. We searched for articles from January 1st, 2005 to September 30th, 2023 in four digital sources including Google Scholar, ACL Anthology, ACM Digital Library, and PubMed to collect relevant publications on EHR QA. 4111 papers were identified for our study, and after screening based on our inclusion criteria, we obtained a total of 47 papers for further study. Out of the 47 papers, 25 papers were about EHR QA datasets, and 37 papers were about EHR QA models. It was observed that QA on EHRs is relatively new and unexplored. Most of the works are fairly recent. Also, it was observed that emrQA is by far the most popular EHR QA dataset, both in terms of citations and usage in other papers. Furthermore, we identified the different models used in EHR QA along with the evaluation metrics used for these models.

相關內容

自(zi)(zi)動問(wen)(wen)答(da)(Question Answering, QA)是(shi)指(zhi)利用(yong)計算機自(zi)(zi)動回答(da)用(yong)戶所提出的(de)(de)問(wen)(wen)題以滿足用(yong)戶知識需求的(de)(de)任務(wu)。不同(tong)于(yu)(yu)現有(you)搜(sou)索引擎(qing),問(wen)(wen)答(da)系統是(shi)信息服(fu)務(wu)的(de)(de)一種高級形式,系統返(fan)回用(yong)戶的(de)(de)不再是(shi)基于(yu)(yu)關(guan)(guan)鍵詞(ci)匹(pi)配排序的(de)(de)文檔(dang)列表(biao),而(er)是(shi)精準的(de)(de)自(zi)(zi)然(ran)語言答(da)案。近年(nian)來,隨著人工智能(neng)的(de)(de)飛速發(fa)展,自(zi)(zi)動問(wen)(wen)答(da)已經(jing)成(cheng)為倍受關(guan)(guan)注且發(fa)展前景廣泛的(de)(de)研究方向。

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We study the problem of screening in decision-making processes under uncertainty, focusing on the impact of adding an additional screening stage, commonly known as a 'gatekeeper.' While our primary analysis is rooted in the context of job market hiring, the principles and findings are broadly applicable to areas such as educational admissions, healthcare patient selection, and financial loan approvals. The gatekeeper's role is to assess applicants' suitability before significant investments are made. Our study reveals that while gatekeepers are designed to streamline the selection process by filtering out less likely candidates, they can sometimes inadvertently affect the candidates' own decision-making process. We explore the conditions under which the introduction of a gatekeeper can enhance or impede the efficiency of these processes. Additionally, we consider how adjusting gatekeeping strategies might impact the accuracy of selection decisions. Our research also extends to scenarios where gatekeeping is influenced by historical biases, particularly in competitive settings like hiring. We discover that candidates confronted with a statistically biased gatekeeping process are more likely to withdraw from applying, thereby perpetuating the previously mentioned historical biases. The study suggests that measures such as affirmative action can be effective in addressing these biases. While centered on hiring, the insights and methodologies from our study have significant implications for a wide range of fields where screening and gatekeeping are integral.

Recently, Visual Transformer (ViT) has been extensively used in medical image segmentation (MIS) due to applying self-attention mechanism in the spatial domain to modeling global knowledge. However, many studies have focused on improving models in the spatial domain while neglecting the importance of frequency domain information. Therefore, we propose Multi-axis External Weights UNet (MEW-UNet) based on the U-shape architecture by replacing self-attention in ViT with our Multi-axis External Weights block. Specifically, our block performs a Fourier transform on the three axes of the input features and assigns the external weight in the frequency domain, which is generated by our External Weights Generator. Then, an inverse Fourier transform is performed to change the features back to the spatial domain. We evaluate our model on four datasets, including Synapse, ACDC, ISIC17 and ISIC18 datasets, and our approach demonstrates competitive performance, owing to its effective utilization of frequency domain information.

Adversarial examples are well-known tools to evaluate the vulnerability of deep neural networks (DNNs). Although lots of adversarial attack algorithms have been developed, it is still challenging in the practical scenario that the model's parameters and architectures are inaccessible to the attacker/evaluator, i.e., black-box adversarial attacks. Due to the practical importance, there has been rapid progress from recent algorithms, reflected by the quick increase in attack success rate and the quick decrease in query numbers to the target model. However, there is a lack of thorough evaluations and comparisons among these algorithms, causing difficulties of tracking the real progress, analyzing advantages and disadvantages of different technical routes, as well as designing future development roadmap of this field. Thus, in this work, we aim at building a comprehensive benchmark of black-box adversarial attacks, called BlackboxBench. It mainly provides: 1) a unified, extensible and modular-based codebase, implementing 25 query-based attack algorithms and 30 transfer-based attack algorithms; 2) comprehensive evaluations: we evaluate the implemented algorithms against several mainstreaming model architectures on 2 widely used datasets (CIFAR-10 and a subset of ImageNet), leading to 14,106 evaluations in total; 3) thorough analysis and new insights, as well analytical tools. The website and source codes of BlackboxBench are available at //blackboxbench.github.io/ and //github.com/SCLBD/BlackboxBench/, respectively.

In light of the growing interest in type inference research for Python, both researchers and practitioners require a standardized process to assess the performance of various type inference techniques. This paper introduces TypeEvalPy, a comprehensive micro-benchmarking framework for evaluating type inference tools. TypeEvalPy contains 154 code snippets with 845 type annotations across 18 categories that target various Python features. The framework manages the execution of containerized tools, transforms inferred types into a standardized format, and produces meaningful metrics for assessment. Through our analysis, we compare the performance of six type inference tools, highlighting their strengths and limitations. Our findings provide a foundation for further research and optimization in the domain of Python type inference.

Background: Rim+ lesions in multiple sclerosis (MS), detectable via Quantitative Susceptibility Mapping (QSM), correlate with increased disability. Existing literature lacks quantitative analysis of these lesions. We introduce RimSet for quantitative identification and characterization of rim+ lesions on QSM. Methods: RimSet combines RimSeg, an unsupervised segmentation method using level-set methodology, and radiomic measurements with Local Binary Pattern texture descriptors. We validated RimSet using simulated QSM images and an in vivo dataset of 172 MS subjects with 177 rim+ and 3986 rim-lesions. Results: RimSeg achieved a 78.7% Dice score against the ground truth, with challenges in partial rim lesions. RimSet detected rim+ lesions with a partial ROC AUC of 0.808 and PR AUC of 0.737, surpassing existing methods. QSMRim-Net showed the lowest mean square error (0.85) and high correlation (0.91; 95% CI: 0.88, 0.93) with expert annotations at the subject level.

The effective utilization of structural information in data while ensuring statistical validity poses a significant challenge in false discovery rate (FDR) analyses. Conformal inference provides rigorous theory for grounding complex machine learning methods without relying on strong assumptions or highly idealized models. However, existing conformal methods have limitations in handling structured multiple testing. This is because their validity requires the deployment of symmetric rules, which assume the exchangeability of data points and permutation-invariance of fitting algorithms. To overcome these limitations, we introduce the pseudo local index of significance (PLIS) procedure, which is capable of accommodating asymmetric rules and requires only pairwise exchangeability between the null conformity scores. We demonstrate that PLIS offers finite-sample guarantees in FDR control and the ability to assign higher weights to relevant data points. Numerical results confirm the effectiveness and robustness of PLIS and show improvements in power compared to existing model-free methods in various scenarios.

Multi-modal language models (LM) have recently shown promising performance in high-level reasoning tasks on videos. However, existing methods still fall short in tasks like causal or compositional spatiotemporal reasoning over actions, in which model predictions need to be grounded in fine-grained low-level details, such as object motions and object interactions. In this work, we propose training an LM end-to-end on low-level surrogate tasks, including object detection, re-identification, and tracking, to endow the model with the required low-level visual capabilities. We show that a two-stream video encoder with spatiotemporal attention is effective at capturing the required static and motion-based cues in the video. By leveraging the LM's ability to perform the low-level surrogate tasks, we can cast reasoning in videos as the three-step process of Look, Remember, Reason wherein visual information is extracted using low-level visual skills step-by-step and then integrated to arrive at a final answer. We demonstrate the effectiveness of our framework on diverse visual reasoning tasks from the ACRE, CATER, and Something-Else datasets. Our approach is trainable end-to-end and surpasses state-of-the-art task-specific methods across these tasks by a large margin.

ESGReveal is an innovative method proposed for efficiently extracting and analyzing Environmental, Social, and Governance (ESG) data from corporate reports, catering to the critical need for reliable ESG information retrieval. This approach utilizes Large Language Models (LLM) enhanced with Retrieval Augmented Generation (RAG) techniques. The ESGReveal system includes an ESG metadata module for targeted queries, a preprocessing module for assembling databases, and an LLM agent for data extraction. Its efficacy was appraised using ESG reports from 166 companies across various sectors listed on the Hong Kong Stock Exchange in 2022, ensuring comprehensive industry and market capitalization representation. Utilizing ESGReveal unearthed significant insights into ESG reporting with GPT-4, demonstrating an accuracy of 76.9% in data extraction and 83.7% in disclosure analysis, which is an improvement over baseline models. This highlights the framework's capacity to refine ESG data analysis precision. Moreover, it revealed a demand for reinforced ESG disclosures, with environmental and social data disclosures standing at 69.5% and 57.2%, respectively, suggesting a pursuit for more corporate transparency. While current iterations of ESGReveal do not process pictorial information, a functionality intended for future enhancement, the study calls for continued research to further develop and compare the analytical capabilities of various LLMs. In summary, ESGReveal is a stride forward in ESG data processing, offering stakeholders a sophisticated tool to better evaluate and advance corporate sustainability efforts. Its evolution is promising in promoting transparency in corporate reporting and aligning with broader sustainable development aims.

Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.

We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models, BERT is designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial task-specific architecture modifications. BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5% (7.7% point absolute improvement), MultiNLI accuracy to 86.7% (4.6% absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement).

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