A Scalable Workflow to Build Machine Learning Classifiers with Clinician-in-the-Loop to Identify Patients in Specific Diseases

Clinicians may rely on medical coding systems such as International Classification of Diseases (ICD) to identify patients with diseases from Electronic Health Records (EHRs). However, due to the lack of detail and specificity as well as a probability of miscoding, recent studies suggest the ICD codes often cannot characterise patients accurately for specific diseases in real clinical practice, and as a result, using them to find patients for studies or trials can result in high failure rates and missing out on uncoded patients. Manual inspection of all patients at scale is not feasible as it is highly costly and slow. This paper proposes a scalable workflow which leverages both structured data and unstructured textual notes from EHRs with techniques including NLP, AutoML and Clinician-in-the-Loop mechanism to build machine learning classifiers to identify patients at scale with given diseases, especially those who might currently be miscoded or missed by ICD codes. Case studies in the MIMIC-III dataset were conducted where the proposed workflow demonstrates a higher classification performance in terms of F1 scores compared to simply using ICD codes on gold testing subset to identify patients with Ovarian Cancer (0.901 vs 0.814), Lung Cancer (0.859 vs 0.828), Cancer Cachexia (0.862 vs 0.650), and Lupus Nephritis (0.959 vs 0.855). Also, the proposed workflow that leverages unstructured notes consistently outperforms the baseline that uses structured data only with an increase of F1 (Ovarian Cancer 0.901 vs 0.719, Lung Cancer 0.859 vs 0.787, Cancer Cachexia 0.862 vs 0.838 and Lupus Nephritis 0.959 vs 0.785). Experiments on the large testing set also demonstrate the proposed workflow can find more patients who are miscoded or missed by ICD codes. Moreover, interpretability studies are also conducted to clinically validate the top impact features of the classifiers.

Algorithms for Adaptive Experiments that Trade-off Statistical Analysis with Reward: Combining Uniform Random Assignment and Reward Maximization

Multi-armed bandit algorithms like Thompson Sampling can be used to conduct adaptive experiments, in which maximizing reward means that data is used to progressively assign more participants to more effective arms. Such assignment strategies increase the risk of statistical hypothesis tests identifying a difference between arms when there is not one, and failing to conclude there is a difference in arms when there truly is one. We present simulations for 2-arm experiments that explore two algorithms that combine the benefits of uniform randomization for statistical analysis, with the benefits of reward maximization achieved by Thompson Sampling (TS). First, Top-Two Thompson Sampling adds a fixed amount of uniform random allocation (UR) spread evenly over time. Second, a novel heuristic algorithm, called TS PostDiff (Posterior Probability of Difference). TS PostDiff takes a Bayesian approach to mixing TS and UR: the probability a participant is assigned using UR allocation is the posterior probability that the difference between two arms is `small' (below a certain threshold), allowing for more UR exploration when there is little or no reward to be gained. We find that TS PostDiff method performs well across multiple effect sizes, and thus does not require tuning based on a guess for the true effect size.

Self-Supervised Detection of Contextual Synonyms in a Multi-Class Setting: Phenotype Annotation Use Case

Contextualised word embeddings is a powerful tool to detect contextual synonyms. However, most of the current state-of-the-art (SOTA) deep learning concept extraction methods remain supervised and underexploit the potential of the context. In this paper, we propose a self-supervised pre-training approach which is able to detect contextual synonyms of concepts being training on the data created by shallow matching. We apply our methodology in the sparse multi-class setting (over 15,000 concepts) to extract phenotype information from electronic health records. We further investigate data augmentation techniques to address the problem of the class sparsity. Our approach achieves a new SOTA for the unsupervised phenotype concept annotation on clinical text on F1 and Recall outperforming the previous SOTA with a gain of up to 4.5 and 4.0 absolute points, respectively. After fine-tuning with as little as 20\% of the labelled data, we also outperform BioBERT and ClinicalBERT. The extrinsic evaluation on three ICU benchmarks also shows the benefit of using the phenotypes annotated by our model as features.

Self-Adaptive Transfer Learning for Multicenter Glaucoma Classification in Fundus Retina Images

The early diagnosis and screening of glaucoma are important for patients to receive treatment in time and maintain eyesight. Nowadays, deep learning (DL) based models have been successfully used for computer-aided diagnosis (CAD) of glaucoma from retina fundus images. However, a DL model pre-trained using a dataset from one hospital center may have poor performance on a dataset from another new hospital center and therefore its applications in the real scene are limited. In this paper, we propose a self-adaptive transfer learning (SATL) strategy to fill the domain gap between multicenter datasets. Specifically, the encoder of a DL model that is pre-trained on the source domain is used to initialize the encoder of a reconstruction model. Then, the reconstruction model is trained using only unlabeled image data from the target domain, which makes the encoder in the model adapt itself to extract useful high-level features both for target domain images encoding and glaucoma classification, simultaneously. Experimental results demonstrate that the proposed SATL strategy is effective in the domain adaptation task between a private and two public glaucoma diagnosis datasets, i.e. pri-RFG, REFUGE, and LAG. Moreover, the proposed strategy is completely independent of the source domain data, which meets the real scene application and the privacy protection policy.

C-Learning: Horizon-Aware Cumulative Accessibility Estimation

Multi-goal reaching is an important problem in reinforcement learning needed to achieve algorithmic generalization. Despite recent advances in this field, current algorithms suffer from three major challenges: high sample complexity, learning only a single way of reaching the goals, and difficulties in solving complex motion planning tasks. In order to address these limitations, we introduce the concept of cumulative accessibility functions, which measure the reachability of a goal from a given state within a specified horizon. We show that these functions obey a recurrence relation, which enables learning from offline interactions. We also prove that optimal cumulative accessibility functions are monotonic in the planning horizon. Additionally, our method can trade off speed and reliability in goal-reaching by suggesting multiple paths to a single goal depending on the provided horizon. We evaluate our approach on a set of multi-goal discrete and continuous control tasks. We show that our method outperforms state-of-the-art goal-reaching algorithms in success rate, sample complexity, and path optimality. Additional visualizations can be found at https://sites.google.com/view/learning-cae/.

Document-aligned Japanese-English Conversation Parallel Corpus

Sentence-level (SL) machine translation (MT) has reached acceptable quality for many high-resourced languages, but not document-level (DL) MT, which is difficult to 1) train with little amount of DL data; and 2) evaluate, as the main methods and data sets focus on SL evaluation. To address the first issue, we present a document-aligned Japanese-English conversation corpus, including balanced, high-quality business conversation data for tuning and testing. As for the second issue, we manually identify the main areas where SL MT fails to produce adequate translations in lack of context. We then create an evaluation set where these phenomena are annotated to alleviate automatic evaluation of DL systems. We train MT models using our corpus to demonstrate how using context leads to improvements.

Designing the Business Conversation Corpus

While the progress of machine translation of written text has come far in the past several years thanks to the increasing availability of parallel corpora and corpora-based training technologies, automatic translation of spoken text and dialogues remains challenging even for modern systems. In this paper, we aim to boost the machine translation quality of conversational texts by introducing a newly constructed Japanese-English business conversation parallel corpus. A detailed analysis of the corpus is provided along with challenging examples for automatic translation. We also experiment with adding the corpus in a machine translation training scenario and show how the resulting system benefits from its use.

Relation-aware Meta-learning for Market Segment Demand Prediction with Limited Records

Recently, E-commerce platforms have extensive impacts on our human life. To provide an efficient platform, one of the most fundamental problem is how to balance the demand and supply in market segments. While conventional machine learning models have achieved a great success on data-sufficient segments, it may fail in a large-portion of segments in E-commerce platforms, where there are not sufficient records to learn well-trained models. In this paper, we tackle this problem in the context of market segment demand prediction. The goal is to facilitate the learning process in the target segments even facing a shortage of related training data by leveraging the learned knowledge from data-sufficient source segments. Specifically, we propose a novel algorithm, RMLDP, to incorporate a multi-pattern fusion network (MPFN) with a meta-learning paradigm. The multi-pattern fusion network considers both local and global temporal patterns for segment demand prediction. In the meta-learning paradigm, the transferable knowledge is regarded as the model parameter initializations of MPFN, which are learned from diverse source segments. Furthermore, we capture the segment relations by combining data-driven segment representation and segment knowledge graph representation and tailor the segment-specific relations to customize transferable model parameter initializations. Thus, even with limited data, the target segment can quickly find the most relevant transferred knowledge and adapt to the optimal parameters. Extensive experiments are conducted on two large-scale industrial datasets. The results show that our RMLDP outperforms a set of state-of-the-art baselines. In addition, RMLDP has also been deployed in Taobao, a real-world E-commerce platform. The online A/B testing results further demonstrate the practicality of RMLDP.

Urban Anomaly Analytics: Description, Detection, and Prediction

Urban anomalies may result in loss of life or property if not handled properly. Automatically alerting anomalies in their early stage or even predicting anomalies before happening are of great value for populations. Recently, data-driven urban anomaly analysis frameworks have been forming, which utilize urban big data and machine learning algorithms to detect and predict urban anomalies automatically. In this survey, we make a comprehensive review of the state-of-the-art research on urban anomaly analytics. We first give an overview of four main types of urban anomalies, traffic anomaly, unexpected crowds, environment anomaly, and individual anomaly. Next, we summarize various types of urban datasets obtained from diverse devices, i.e., trajectory, trip records, CDRs, urban sensors, event records, environment data, social media and surveillance cameras. Subsequently, a comprehensive survey of issues on detecting and predicting techniques for urban anomalies is presented. Finally, research challenges and open problems as discussed.