A Language Model based Framework for New Concept Placement in Ontologies

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

Can GPT-3.5 Generate and Code Discharge Summaries?

Objective: To investigate GPT-3.5 in generating and coding medical documents with ICD-10 codes for data augmentation on low-resources labels. Materials and Methods: Employing GPT-3.5 we generated and coded 9,606 discharge summaries based on lists of ICD-10 code descriptions of patients with infrequent (generation) codes within the MIMIC-IV dataset. Combined with the baseline training set, this formed an augmented training set. Neural coding models were trained on baseline and augmented data and evaluated on a MIMIC-IV test set. We report micro- and macro-F1 scores on the full codeset, generation codes, and their families. Weak Hierarchical Confusion Matrices were employed to determine within-family and outside-of-family coding errors in the latter codesets. The coding performance of GPT-3.5 was evaluated both on prompt-guided self-generated data and real MIMIC-IV data. Clinical professionals evaluated the clinical acceptability of the generated documents. Results: Augmentation slightly hinders the overall performance of the models but improves performance for the generation candidate codes and their families, including one unseen in the baseline training data. Augmented models display lower out-of-family error rates. GPT-3.5 can identify ICD-10 codes by the prompted descriptions, but performs poorly on real data. Evaluators note the correctness of generated concepts while suffering in variety, supporting information, and narrative. Discussion and Conclusion: GPT-3.5 alone is unsuitable for ICD-10 coding. Augmentation positively affects generation code families but mainly benefits codes with existing examples. Augmentation reduces out-of-family errors. Discharge summaries generated by GPT-3.5 state prompted concepts correctly but lack variety, and authenticity in narratives. They are unsuitable for clinical practice.

COIN: Chance-Constrained Imitation Learning for Uncertainty-aware Adaptive Resource Oversubscription Policy

We address the challenge of learning safe and robust decision policies in presence of uncertainty in context of the real scientific problem of adaptive resource oversubscription to enhance resource efficiency while ensuring safety against resource congestion risk. Traditional supervised prediction or forecasting models are ineffective in learning adaptive policies whereas standard online optimization or reinforcement learning is difficult to deploy on real systems. Offline methods such as imitation learning (IL) are ideal since we can directly leverage historical resource usage telemetry. But, the underlying aleatoric uncertainty in such telemetry is a critical bottleneck. We solve this with our proposed novel chance-constrained imitation learning framework, which ensures implicit safety against uncertainty in a principled manner via a combination of stochastic (chance) constraints on resource congestion risk and ensemble value functions. This leads to substantial ($\approx 3-4\times$) improvement in resource efficiency and safety in many oversubscription scenarios, including resource management in cloud services.

TaskWeaver: A Code-First Agent Framework

Large Language Models (LLMs) have shown impressive abilities in natural language understanding and generation, leading to their use in applications such as chatbots and virtual assistants. However, existing LLM frameworks face limitations in handling domain-specific data analytics tasks with rich data structures. Moreover, they struggle with flexibility to meet diverse user requirements. To address these issues, TaskWeaver is proposed as a code-first framework for building LLM-powered autonomous agents. It converts user requests into executable code and treats user-defined plugins as callable functions. TaskWeaver provides support for rich data structures, flexible plugin usage, and dynamic plugin selection, and leverages LLM coding capabilities for complex logic. It also incorporates domain-specific knowledge through examples and ensures the secure execution of generated code. TaskWeaver offers a powerful and flexible framework for creating intelligent conversational agents that can handle complex tasks and adapt to domain-specific scenarios. The code is open-sourced at https://github.com/microsoft/TaskWeaver/.

Counter-Empirical Attacking based on Adversarial Reinforcement Learning for Time-Relevant Scoring System

Scoring systems are commonly seen for platforms in the era of big data. From credit scoring systems in financial services to membership scores in E-commerce shopping platforms, platform managers use such systems to guide users towards the encouraged activity pattern, and manage resources more effectively and more efficiently thereby. To establish such scoring systems, several "empirical criteria" are firstly determined, followed by dedicated top-down design for each factor of the score, which usually requires enormous effort to adjust and tune the scoring function in the new application scenario. What's worse, many fresh projects usually have no ground-truth or any experience to evaluate a reasonable scoring system, making the designing even harder. To reduce the effort of manual adjustment of the scoring function in every new scoring system, we innovatively study the scoring system from the preset empirical criteria without any ground truth, and propose a novel framework to improve the system from scratch. In this paper, we propose a "counter-empirical attacking" mechanism that can generate "attacking" behavior traces and try to break the empirical rules of the scoring system. Then an adversarial "enhancer" is applied to evaluate the scoring system and find the improvement strategy. By training the adversarial learning problem, a proper scoring function can be learned to be robust to the attacking activity traces that are trying to violate the empirical criteria. Extensive experiments have been conducted on two scoring systems including a shared computing resource platform and a financial credit system. The experimental results have validated the effectiveness of our proposed framework.

Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Exploring Large Language Models for Ontology Alignment

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.