Luyao Chen

Liuchang Xu, Shuo Zhao, Qingming Lin et al.

The emergence of large language models such as ChatGPT, Gemini, and others highlights the importance of evaluating their diverse capabilities, ranging from natural language understanding to code generation. However, their performance on spatial tasks has not been thoroughly assessed. This study addresses this gap by introducing a new multi-task spatial evaluation dataset designed to systematically explore and compare the performance of several advanced models on spatial tasks. The dataset includes twelve distinct task types, such as spatial understanding and simple route planning, each with verified and accurate answers. We evaluated multiple models, including OpenAI's gpt-3.5-turbo, gpt-4-turbo, gpt-4o, ZhipuAI's glm-4, Anthropic's claude-3-sonnet-20240229, and MoonShot's moonshot-v1-8k, using a two-phase testing approach. First, we conducted zero-shot testing. Then, we categorized the dataset by difficulty and performed prompt-tuning tests. Results show that gpt-4o achieved the highest overall accuracy in the first phase, with an average of 71.3%. Although moonshot-v1-8k slightly underperformed overall, it outperformed gpt-4o in place name recognition tasks. The study also highlights the impact of prompt strategies on model performance in specific tasks. For instance, the Chain-of-Thought (CoT) strategy increased gpt-4o's accuracy in simple route planning from 12.4% to 87.5%, while a one-shot strategy improved moonshot-v1-8k's accuracy in mapping tasks from 10.1% to 76.3%.

Tanjida Kabir, Chun-Teh Lee, Jiman Nelson et al.

Periodontitis is a biofilm-related chronic inflammatory disease characterized by gingivitis and bone loss in the teeth area. Approximately 61 million adults over 30 suffer from periodontitis (42.2%), with 7.8% having severe periodontitis in the United States. The measurement of radiographic bone loss (RBL) is necessary to make a correct periodontal diagnosis, especially if the comprehensive and longitudinal periodontal mapping is unavailable. However, doctors can interpret X-rays differently depending on their experience and knowledge. Computerized diagnosis support for doctors sheds light on making the diagnosis with high accuracy and consistency and drawing up an appropriate treatment plan for preventing or controlling periodontitis. We developed an end-to-end deep learning network HYNETS (Hybrid NETwork for pEriodoNTiTiS STagES from radiograpH) by integrating segmentation and classification tasks for grading periodontitis from periapical radiographic images. HYNETS leverages a multi-task learning strategy by combining a set of segmentation networks and a classification network to provide an end-to-end interpretable solution and highly accurate and consistent results. HYNETS achieved the average dice coefficient of 0.96 and 0.94 for the bone area and tooth segmentation and the average AUC of 0.97 for periodontitis stage assignment. Additionally, conventional image processing techniques provide RBL measurements and build transparency and trust in the model's prediction. HYNETS will potentially transform clinical diagnosis from a manual time-consuming, and error-prone task to an efficient and automated periodontitis stage assignment based on periapical radiographic images.

Yaobin Ling, Pulakesh Upadhyaya, Luyao Chen et al.

Developing new drugs for target diseases is a time-consuming and expensive task, drug repurposing has become a popular topic in the drug development field. As much health claim data become available, many studies have been conducted on the data. The real-world data is noisy, sparse, and has many confounding factors. In addition, many studies have shown that drugs effects are heterogeneous among the population. Lots of advanced machine learning models about estimating heterogeneous treatment effects (HTE) have emerged in recent years, and have been applied to in econometrics and machine learning communities. These studies acknowledge medicine and drug development as the main application area, but there has been limited translational research from the HTE methodology to drug development. We aim to introduce the HTE methodology to the healthcare area and provide feasibility consideration when translating the methodology with benchmark experiments on healthcare administrative claim data. Also, we want to use benchmark experiments to show how to interpret and evaluate the model when it is applied to healthcare research. By introducing the recent HTE techniques to a broad readership in biomedical informatics communities, we expect to promote the wide adoption of causal inference using machine learning. We also expect to provide the feasibility of HTE for personalized drug effectiveness.

Kanglin Hsieh, Yinyin Wang, Luyao Chen et al.

Amid the pandemic of 2019 novel coronavirus disease (COVID-19) infected by SARS-CoV-2, a vast amount of drug research for prevention and treatment has been quickly conducted, but these efforts have been unsuccessful thus far. Our objective is to prioritize repurposable drugs using a drug repurposing pipeline that systematically integrates multiple SARS-CoV-2 and drug interactions, deep graph neural networks, and in-vitro/population-based validations. We first collected all the available drugs (n= 3,635) involved in COVID-19 patient treatment through CTDbase. We built a SARS-CoV-2 knowledge graph based on the interactions among virus baits, host genes, pathways, drugs, and phenotypes. A deep graph neural network approach was used to derive the candidate representation based on the biological interactions. We prioritized the candidate drugs using clinical trial history, and then validated them with their genetic profiles, in vitro experimental efficacy, and electronic health records. We highlight the top 22 drugs including Azithromycin, Atorvastatin, Aspirin, Acetaminophen, and Albuterol. We further pinpointed drug combinations that may synergistically target COVID-19. In summary, we demonstrated that the integration of extensive interactions, deep neural networks, and rigorous validation can facilitate the rapid identification of candidate drugs for COVID-19 treatment. This is a post-peer-review, pre-copyedit version of an article published in Scientific Reports The final authenticated version is available online at: https://www.nature.com/articles/s41598-021-02353-5

Tao Yu, Rui Zhang, He Yang Er et al.

We present CoSQL, a corpus for building cross-domain, general-purpose database (DB) querying dialogue systems. It consists of 30k+ turns plus 10k+ annotated SQL queries, obtained from a Wizard-of-Oz (WOZ) collection of 3k dialogues querying 200 complex DBs spanning 138 domains. Each dialogue simulates a real-world DB query scenario with a crowd worker as a user exploring the DB and a SQL expert retrieving answers with SQL, clarifying ambiguous questions, or otherwise informing of unanswerable questions. When user questions are answerable by SQL, the expert describes the SQL and execution results to the user, hence maintaining a natural interaction flow. CoSQL introduces new challenges compared to existing task-oriented dialogue datasets:(1) the dialogue states are grounded in SQL, a domain-independent executable representation, instead of domain-specific slot-value pairs, and (2) because testing is done on unseen databases, success requires generalizing to new domains. CoSQL includes three tasks: SQL-grounded dialogue state tracking, response generation from query results, and user dialogue act prediction. We evaluate a set of strong baselines for each task and show that CoSQL presents significant challenges for future research. The dataset, baselines, and leaderboard will be released at https://yale-lily.github.io/cosql.

Xiaoqian Jiang, Samden Lhatoo, Guo-Qiang Zhang et al.

Existing studies consider Alzheimer's disease (AD) a comorbidity of epilepsy, but also recognize epilepsy to occur more frequently in patients with AD than those without. The goal of this paper is to understand the relationship between epilepsy and AD by studying causal relations among subgroups of epilepsy patients. We develop an approach combining representation learning with tensor factorization to provide an in-depth analysis of the risk factors among epilepsy patients for AD. An epilepsy-AD cohort of ~600,000 patients were extracted from Cerner Health Facts data (50M patients). Our experimental results not only suggested a causal relationship between epilepsy and later onset of AD ( p = 1.92e-51), but also identified five epilepsy subgroups with distinct phenotypic patterns leading to AD. While such findings are preliminary, the proposed method combining representation learning with tensor factorization seems to be an effective approach for risk factor analysis.

Yejin Kim, Xiaoqian Jiang, Luyao Chen et al.

Sleep change is commonly reported in Alzheimer's disease (AD) patients and their brain wave studies show decrease in dreaming and non-dreaming stages. Although sleep disturbance is generally considered as a consequence of AD, it might also be a risk factor of AD as new biological evidence shows. Leveraging National Sleep Research Resource (NSRR), we built a unique cohort of 83 cases and 331 controls with clinical variables and EEG signals. Supervised tensor factorization method was applied for this temporal dataset to extract discriminative sleep patterns. Among the 30 patterns extracted, we identified 5 significant patterns (4 patterns for AD likely and 1 pattern for normal ones) and their visual patterns provide interesting linkage to sleep with repeated wakefulness, insomnia, epileptic seizure, and etc. This study is preliminary but findings are interesting, which is a first step to provide quantifiable evidences to measure sleep as a risk factor of AD.