Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology, has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Our proposed few-shot learning approach uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. Our experiments, which involved seven rare tissues from different cancer types, demonstrated that the LLM-based prediction model achieved significant accuracy with very few or zero samples. Our proposed model, the CancerGPT (with $\sim$ 124M parameters), was even comparable to the larger fine-tuned GPT-3 model (with $\sim$ 175B parameters). Our research is the first to tackle drug pair synergy prediction in rare tissues with limited data. We are also the first to utilize an LLM-based prediction model for biological reaction prediction tasks.

The feature determines the vertical position of the point, and the Shapley value determines the horizontal position. The color of the point represents whether the value of the feature is low or high. Our experiment uses red and blue to represent low or high feature values, respectively. For example, for a feature Age, an older man would be drawn as red or a redder point, whereas a younger would be described as blue or a bluer point. Overlapping points are jittered in the y-axis position. The SHAP summary plot indicates a possible relationship between feature value and the impact on model prediction. However, it does not prove any causal relationship.

This paper applies eXplainable Artificial Intelligence (XAI) methods to investigate the socioeconomic disparities in COVID patient mortality. An Extreme Gradient Boosting (XGBoost) prediction model is built based on a de-identified Austin area hospital dataset to predict the mortality of COVID-19 patients. We apply two XAI methods, Shapley Additive exPlanations (SHAP) and Locally Interpretable Model Agnostic Explanations (LIME), to compare the global and local interpretation of feature importance. This paper demonstrates the advantages of using XAI which shows the feature importance and decisive capability. Furthermore, we use the XAI methods to cross-validate their interpretations for individual patients. The XAI models reveal that Medicare financial class, older age, and gender have high impact on the mortality prediction. We find that LIME local interpretation does not show significant differences in feature importance comparing to SHAP, which suggests pattern confirmation. This paper demonstrates the importance of XAI methods in cross-validation of feature attributions.

AI-powered Medical Imaging has recently achieved enormous attention due to its ability to provide fast-paced healthcare diagnoses. However, it usually suffers from a lack of high-quality datasets due to high annotation cost, inter-observer variability, human annotator error, and errors in computer-generated labels. Deep learning models trained on noisy labelled datasets are sensitive to the noise type and lead to less generalization on the unseen samples. To address this challenge, we propose a Robust Stochastic Knowledge Distillation (RoS-KD) framework which mimics the notion of learning a topic from multiple sources to ensure deterrence in learning noisy information. More specifically, RoS-KD learns a smooth, well-informed, and robust student manifold by distilling knowledge from multiple teachers trained on overlapping subsets of training data. Our extensive experiments on popular medical imaging classification tasks (cardiopulmonary disease and lesion classification) using real-world datasets, show the performance benefit of RoS-KD, its ability to distill knowledge from many popular large networks (ResNet-50, DenseNet-121, MobileNet-V2) in a comparatively small network, and its robustness to adversarial attacks (PGD, FSGM). More specifically, RoS-KD achieves >2% and >4% improvement on F1-score for lesion classification and cardiopulmonary disease classification tasks, respectively, when the underlying student is ResNet-18 against recent competitive knowledge distillation baseline. Additionally, on cardiopulmonary disease classification task, RoS-KD outperforms most of the SOTA baselines by ~1% gain in AUC score.

This paper elaborates how to identify and evaluate causal factors to improve scientific impact. Currently, analyzing scientific impact can be beneficial to various academic activities including funding application, mentor recommendation, and discovering potential cooperators etc. It is universally acknowledged that high-impact scholars often have more opportunities to receive awards as an encouragement for their hard working. Therefore, scholars spend great efforts in making scientific achievements and improving scientific impact during their academic life. However, what are the determinate factors that control scholars' academic success? The answer to this question can help scholars conduct their research more efficiently. Under this consideration, our paper presents and analyzes the causal factors that are crucial for scholars' academic success. We first propose five major factors including article-centered factors, author-centered factors, venue-centered factors, institution-centered factors, and temporal factors. Then, we apply recent advanced machine learning algorithms and jackknife method to assess the importance of each causal factor. Our empirical results show that author-centered and article-centered factors have the highest relevancy to scholars' future success in the computer science area. Additionally, we discover an interesting phenomenon that the h-index of scholars within the same institution or university are actually very close to each other.

Teamwork is cooperative, participative and power sharing. In science of science, few studies have looked at the impact of team collaboration from the perspective of team power and hierarchy. This research examines in depth the relationships between team power and team success in the field of Computer Science (CS) using the DBLP dataset. Team power and hierarchy are measured using academic age and team success is quantified by citation. By analyzing 4,106,995 CS teams, we find that high power teams with flat structure have the best performance. On the contrary, low-power teams with hierarchical structure is a facilitator of team performance. These results are consistent across different time periods and team sizes.

Electronic Health Record (EHR) data has been of tremendous utility in Artificial Intelligence (AI) for healthcare such as predicting future clinical events. These tasks, however, often come with many challenges when using classical machine learning models due to a myriad of factors including class imbalance and data heterogeneity (i.e., the complex intra-class variances). To address some of these research gaps, this paper leverages the exciting contrastive learning framework and proposes a novel contrastive regularized clinical classification model. The contrastive loss is found to substantially augment EHR-based prediction: it effectively characterizes the similar/dissimilar patterns (by its "push-and-pull" form), meanwhile mitigating the highly skewed class distribution by learning more balanced feature spaces (as also echoed by recent findings). In particular, when naively exporting the contrastive learning to the EHR data, one hurdle is in generating positive samples, since EHR data is not as amendable to data augmentation as image data. To this end, we have introduced two unique positive sampling strategies specifically tailored for EHR data: a feature-based positive sampling that exploits the feature space neighborhood structure to reinforce the feature learning; and an attribute-based positive sampling that incorporates pre-generated patient similarity metrics to define the sample proximity. Both sampling approaches are designed with an awareness of unique high intra-class variance in EHR data. Our overall framework yields highly competitive experimental results in predicting the mortality risk on real-world COVID-19 EHR data with a total of 5,712 patients admitted to a large, urban health system. Specifically, our method reaches a high AUROC prediction score of 0.959, which outperforms other baselines and alternatives: cross-entropy(0.873) and focal loss(0.931).

We obtained 1,584,175 AI related publications during 1950-2019 from the Microsoft Academic Graph. Three latitude-and-longitude-based indicators were employed to quantify the geographic distance of collaborations in AI over time at domestic and international levels. The results show team collaborations in AI has been more popular in the field over time with around 42,000 (38.4%) multiple-affiliation AI publications in 2019. The changes in geographic distances of team collaborations indicate the increase of breadth and density for both domestic and international collaborations in AI over time. In addition, the United States produced the largest number of single-country and internationally collaborated AI publications, and China has played an important role in international collaborations in AI after 2010.

Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug discovery rely on incorporating information from different biomedical databases. These databases contain various biological entities and relations such as proteins (PDB), genes (Gene Ontology), drugs (DrugBank), diseases (DDB), and protein-protein interactions (BioGRID). The process of semantically integrating heterogeneous biomedical databases is often riddled with imperfections. The quality of data-driven drug discovery relies on the accuracy of the mining methods used and the data's quality as well. Thus, having complete and refined biomedical knowledge graphs is central to achieving more accurate drug discovery outcomes. Here we propose using the latest graph representation learning and embedding models to refine and complete biomedical knowledge graphs. This preliminary work demonstrates learning discrete representations of the integrated biomedical knowledge graph Chem2Bio2RD [3]. We perform a knowledge graph completion and refinement task using a simple top-K cosine similarity measure between the learned embedding vectors to predict missing links between drugs and targets present in the data. We show that this simple procedure can be used alternatively to binary classifiers in link prediction.

The emergence of the novel COVID-19 pandemic has had a significant impact on global healthcare and the economy over the past few months. The virus's rapid widespread has led to a proliferation in biomedical research addressing the pandemic and its related topics. One of the essential Knowledge Discovery tools that could help the biomedical research community understand and eventually find a cure for COVID-19 are Knowledge Graphs. The CORD-19 dataset is a collection of publicly available full-text research articles that have been recently published on COVID-19 and coronavirus topics. Here, we use several Machine Learning, Deep Learning, and Knowledge Graph construction and mining techniques to formalize and extract insights from the PubMed dataset and the CORD-19 dataset to identify COVID-19 related experts and bio-entities. Besides, we suggest possible techniques to predict related diseases, drug candidates, gene, gene mutations, and related compounds as part of a systematic effort to apply Knowledge Discovery methods to help biomedical researchers tackle the pandemic.