In the expansive realm of drug discovery, with approximately 15,000 known drugs and only around 4,200 approved, the combinatorial nature of the chemical space presents a formidable challenge. While Artificial Intelligence (AI) has emerged as a powerful ally, traditional AI frameworks face significant hurdles. This manuscript introduces CardiGraphormer, a groundbreaking approach that synergizes self-supervised learning (SSL), Graph Neural Networks (GNNs), and Cardinality Preserving Attention to revolutionize drug discovery. CardiGraphormer, a novel combination of Graphormer and Cardinality Preserving Attention, leverages SSL to learn potent molecular representations and employs GNNs to extract molecular fingerprints, enhancing predictive performance and interpretability while reducing computation time. It excels in handling complex data like molecular structures and performs tasks associated with nodes, pairs of nodes, subgraphs, or entire graph structures. CardiGraphormer's potential applications in drug discovery and drug interactions are vast, from identifying new drug targets to predicting drug-to-drug interactions and enabling novel drug discovery. This innovative approach provides an AI-enhanced methodology in drug development, utilizing SSL combined with GNNs to overcome existing limitations and pave the way for a richer exploration of the vast combinatorial chemical space in drug discovery.
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Recent advancements in large language models (LLMs) have revealed their potential for achieving autonomous agents possessing human-level intelligence. However, existing benchmarks for evaluating LLM Agents either use static datasets, potentially leading to data leakage or focus only on single-agent scenarios, overlooking the complexities of multi-agent interactions. There is a lack of a benchmark that evaluates the diverse capabilities of LLM agents in multi-agent, dynamic environments. To this end, we introduce LLMArena, a novel and easily extensible framework for evaluating the diverse capabilities of LLM in multi-agent dynamic environments. LLMArena encompasses seven distinct gaming environments, employing Trueskill scoring to assess crucial abilities in LLM agents, including spatial reasoning, strategic planning, numerical reasoning, risk assessment, communication, opponent modeling, and team collaboration. We conduct an extensive experiment and human evaluation among different sizes and types of LLMs, showing that LLMs still have a significant journey ahead in their development towards becoming fully autonomous agents, especially in opponent modeling and team collaboration. We hope LLMArena could guide future research towards enhancing these capabilities in LLMs, ultimately leading to more sophisticated and practical applications in dynamic, multi-agent settings. The code and data will be available.
Recent studies have uncovered intriguing phenomena in deep learning, such as grokking, double descent, and emergent abilities in large language models, which challenge human intuition and are crucial for a deeper understanding of neural models. In this paper, we present a comprehensive framework that provides a unified view of these three phenomena, focusing on the competition between memorization and generalization circuits. This approach, initially employed to explain grokking, is extended in our work to encompass a wider range of model sizes and training data volumes. Our framework delineates four distinct training dynamics, each depending on varying combinations of model size and training data quantity. Utilizing this framework, we provide a detailed analysis of the double descent phenomenon and propose two verifiable predictions regarding its occurrence, both substantiated by our experimental results. Moreover, we expand our framework to the multi-task learning paradigm, demonstrating how algorithm tasks can be turned into emergent abilities. This offers a novel perspective to understand emergent abilities in Large Language Models.
Medical imaging is a very useful tool in healthcare, various technologies being employed to non-invasively peek inside the human body. Deep learning with neural networks in radiology was welcome - albeit cautiously - by the radiologist community. Most of the currently deployed or researched deep learning solutions are applied on already generated images of medical scans, use the neural networks to aid in the generation of such images, or use them for identifying specific substance markers in spectrographs. This paper's author posits that if the neural networks were trained directly on the raw signals from the scanning machines, they would gain access to more nuanced information than from the already processed images, hence the training - and later, the inferences - would become more accurate. The paper presents the main current applications of deep learning in radiography, ultrasonography, and electrophysiology, and discusses whether the proposed neural network training directly on raw signals is feasible.
Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.
With the rapid proliferation of scientific literature, versatile academic knowledge services increasingly rely on comprehensive academic graph mining. Despite the availability of public academic graphs, benchmarks, and datasets, these resources often fall short in multi-aspect and fine-grained annotations, are constrained to specific task types and domains, or lack underlying real academic graphs. In this paper, we present OAG-Bench, a comprehensive, multi-aspect, and fine-grained human-curated benchmark based on the Open Academic Graph (OAG). OAG-Bench covers 10 tasks, 20 datasets, 70+ baselines, and 120+ experimental results to date. We propose new data annotation strategies for certain tasks and offer a suite of data pre-processing codes, algorithm implementations, and standardized evaluation protocols to facilitate academic graph mining. Extensive experiments reveal that even advanced algorithms like large language models (LLMs) encounter difficulties in addressing key challenges in certain tasks, such as paper source tracing and scholar profiling. We also introduce the Open Academic Graph Challenge (OAG-Challenge) to encourage community input and sharing. We envisage that OAG-Bench can serve as a common ground for the community to evaluate and compare algorithms in academic graph mining, thereby accelerating algorithm development and advancement in this field. OAG-Bench is accessible at //www.aminer.cn/data/.
The use of machine learning algorithms in healthcare can amplify social injustices and health inequities. While the exacerbation of biases can occur and compound during the problem selection, data collection, and outcome definition, this research pertains to some generalizability impediments that occur during the development and the post-deployment of machine learning classification algorithms. Using the Framingham coronary heart disease data as a case study, we show how to effectively select a probability cutoff to convert a regression model for a dichotomous variable into a classifier. We then compare the sampling distribution of the predictive performance of eight machine learning classification algorithms under four training/testing scenarios to test their generalizability and their potential to perpetuate biases. We show that both the Extreme Gradient Boosting, and Support Vector Machine are flawed when trained on an unbalanced dataset. We introduced and show that the double discriminant scoring of type I is the most generalizable as it consistently outperforms the other classification algorithms regardless of the training/testing scenario. Finally, we introduce a methodology to extract an optimal variable hierarchy for a classification algorithm, and illustrate it on the overall, male and female Framingham coronary heart disease data.
The therapeutic working alliance is a critical factor in predicting the success of psychotherapy treatment. Traditionally, working alliance assessment relies on questionnaires completed by both therapists and patients. In this paper, we present COMPASS, a novel framework to directly infer the therapeutic working alliance from the natural language used in psychotherapy sessions. Our approach utilizes advanced large language models to analyze transcripts of psychotherapy sessions and compare them with distributed representations of statements in the working alliance inventory. Analyzing a dataset of over 950 sessions covering diverse psychiatric conditions, we demonstrate the effectiveness of our method in microscopically mapping patient-therapist alignment trajectories and providing interpretability for clinical psychiatry and in identifying emerging patterns related to the condition being treated. By employing various neural topic modeling techniques in combination with generative language prompting, we analyze the topical characteristics of different psychiatric conditions and incorporate temporal modeling to capture the evolution of topics at a turn-level resolution. This combined framework enhances the understanding of therapeutic interactions, enabling timely feedback for therapists regarding conversation quality and providing interpretable insights to improve the effectiveness of psychotherapy.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.
In order to answer natural language questions over knowledge graphs, most processing pipelines involve entity and relation linking. Traditionally, entity linking and relation linking has been performed either as dependent sequential tasks or independent parallel tasks. In this paper, we propose a framework called "EARL", which performs entity linking and relation linking as a joint single task. EARL uses a graph connection based solution to the problem. We model the linking task as an instance of the Generalised Travelling Salesman Problem (GTSP) and use GTSP approximate algorithm solutions. We later develop EARL which uses a pair-wise graph-distance based solution to the problem.The system determines the best semantic connection between all keywords of the question by referring to a knowledge graph. This is achieved by exploiting the "connection density" between entity candidates and relation candidates. The "connection density" based solution performs at par with the approximate GTSP solution.We have empirically evaluated the framework on a dataset with 5000 questions. Our system surpasses state-of-the-art scores for entity linking task by reporting an accuracy of 0.65 to 0.40 from the next best entity linker.
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