Leveraging Large Language Models to Extract Information on Substance Use Disorder Severity from Clinical Notes: A Zero-shot Learning Approach

Substance use disorder (SUD) poses a major concern due to its detrimental effects on health and society. SUD identification and treatment depend on a variety of factors such as severity, co-determinants (e.g., withdrawal symptoms), and social determinants of health. Existing diagnostic coding systems used by American insurance providers, like the International Classification of Diseases (ICD-10), lack granularity for certain diagnoses, but clinicians will add this granularity (as that found within the Diagnostic and Statistical Manual of Mental Disorders classification or DSM-5) as supplemental unstructured text in clinical notes. Traditional natural language processing (NLP) methods face limitations in accurately parsing such diverse clinical language. Large Language Models (LLMs) offer promise in overcoming these challenges by adapting to diverse language patterns. This study investigates the application of LLMs for extracting severity-related information for various SUD diagnoses from clinical notes. We propose a workflow employing zero-shot learning of LLMs with carefully crafted prompts and post-processing techniques. Through experimentation with Flan-T5, an open-source LLM, we demonstrate its superior recall compared to the rule-based approach. Focusing on 11 categories of SUD diagnoses, we show the effectiveness of LLMs in extracting severity information, contributing to improved risk assessment and treatment planning for SUD patients.

Dynamic Q&A of Clinical Documents with Large Language Models

Electronic health records (EHRs) house crucial patient data in clinical notes. As these notes grow in volume and complexity, manual extraction becomes challenging. This work introduces a natural language interface using large language models (LLMs) for dynamic question-answering on clinical notes. Our chatbot, powered by Langchain and transformer-based LLMs, allows users to query in natural language, receiving relevant answers from clinical notes. Experiments, utilizing various embedding models and advanced LLMs, show Wizard Vicuna's superior accuracy, albeit with high compute demands. Model optimization, including weight quantization, improves latency by approximately 48 times. Promising results indicate potential, yet challenges such as model hallucinations and limited diverse medical case evaluations remain. Addressing these gaps is crucial for unlocking the value in clinical notes and advancing AI-driven clinical decision-making.

Question-Answering System Extracts Information on Injection Drug Use from Clinical Progress Notes

Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients' electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated are unstructured free-text clinical progress notes. Although natural language processing (NLP) can efficiently extract this information from unstructured data, there are no validated tools. To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical progress notes. Unlike other methods discussed in the literature, the QA model is able to extract various types of information without being constrained by predefined entities, relations, or concepts. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. This paper also demonstrates the QA model's ability to extract IDU-related information on temporally out-of-distribution data. The results indicate that the majority (51%) of the extracted information by the QA model exactly matches the gold-standard answer and 73% of them contain the gold-standard answer with some additional surrounding words.

TACOS: Topology-Aware Collective Algorithm Synthesizer for Distributed Training

Collective communications are an indispensable part of distributed training. Running a topology-aware collective algorithm is crucial for optimizing communication performance by minimizing congestion. Today such algorithms only exist for a small set of simple topologies, limiting the topologies employed in training clusters and handling irregular topologies due to network failures. In this paper, we propose TACOS, an automated topology-aware collective synthesizer for arbitrary input network topologies. TACOS synthesized 3.73x faster All-Reduce algorithm over baselines, and synthesized collective algorithms for 512-NPU system in just 6.1 minutes.

ASTRA-sim2.0: Modeling Hierarchical Networks and Disaggregated Systems for Large-model Training at Scale

As deep learning models and input data are scaling at an unprecedented rate, it is inevitable to move towards distributed training platforms to fit the model and increase training throughput. State-of-the-art approaches and techniques, such as wafer-scale nodes, multi-dimensional network topologies, disaggregated memory systems, and parallelization strategies, have been actively adopted by emerging distributed training systems. This results in a complex SW/HW co-design stack of distributed training, necessitating a modeling/simulation infrastructure for design-space exploration. In this paper, we extend the open-source ASTRA-sim infrastructure and endow it with the capabilities to model state-of-the-art and emerging distributed training models and platforms. More specifically, (i) we enable ASTRA-sim to support arbitrary model parallelization strategies via a graph-based training-loop implementation, (ii) we implement a parameterizable multi-dimensional heterogeneous topology generation infrastructure with analytical performance estimates enabling simulating target systems at scale, and (iii) we enhance the memory system modeling to support accurate modeling of in-network collective communication and disaggregated memory systems. With such capabilities, we run comprehensive case studies targeting emerging distributed models and platforms. This infrastructure lets system designers swiftly traverse the complex co-design stack and give meaningful insights when designing and deploying distributed training platforms at scale.

BioADAPT-MRC: Adversarial Learning-based Domain Adaptation Improves Biomedical Machine Reading Comprehension Task

Motivation: Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model's performance. Results: We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets -- BioASQ-7b, BioASQ-8b, and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets. Availability: BioADAPT-MRC is freely available as an open-source project at\\https://github.com/mmahbub/BioADAPT-MRC

Themis: A Network Bandwidth-Aware Collective Scheduling Policy for Distributed Training of DL Models

The continuous growth in both size and training data for modern Deep Neural Networks (DNNs) models has led to training tasks taking days or even months. Distributed training is a solution to reduce training time by splitting the task across multiple NPUs (e.g., GPU/TPU). However, distributed training adds communication overhead between the NPUs in order to synchronize the gradients and/or activation, depending on the parallelization strategy. In today's datacenters, for training at scale, NPUs are connected through multi-dimensional interconnection links with different bandwidth and latency. Hence, keeping all network dimensions busy and maximizing the network BW is a challenging task in such a hybrid network environment, as this work identifies. We propose Themis, a novel collective scheduling scheme that dynamically schedules collectives (divided into chunks) to balance the communication loads across all dimensions, further improving the network BW utilization. Our results show that on average, Themis can improve the network BW utilization of single All-Reduce by 1.88x (2.92x max), and improve the end-to-end training iteration performance of real workloads such as ResNet-50, GNMT, DLRM, and Transformer- 1T by 1.49x (1.96x max), 1.41x (1.81x max), 1.42x (1.80x max), and 1.35x (1.78x max), respectively.

Exploring Multi-dimensional Hierarchical Network Topologies for Efficient Distributed Training of Trillion Parameter DL Models

Deep Neural Networks have gained significant attraction due to their wide applicability in different domains. DNN sizes and training samples are constantly growing, making training of such workloads more challenging. Distributed training is a solution to reduce the training time. High-performance distributed training platforms should leverage multi-dimensional hierarchical networks, which interconnect accelerators through different levels of the network, to dramatically reduce expensive NICs required for the scale-out network. However, it comes at the expense of communication overhead between distributed accelerators to exchange gradients or input/output activation. In order to allow for further scaling of the workloads, communication overhead needs to be minimized. In this paper, we motivate the fact that in training platforms, adding more intermediate network dimensions is beneficial for efficiently mitigating the excessive use of expensive NIC resources. Further, we address different challenges of the DNN training on hierarchical networks. We discuss when designing the interconnect, how to distribute network bandwidth resources across different dimensions in order to (i) maximize BW utilization of all dimensions, and (ii) minimizing the overall training time for the target workload. We then implement a framework that, for a given workload, determines the best network configuration that maximizes performance, or performance-per-cost.

The Sensitivity of Word Embeddings-based Author Detection Models to Semantic-preserving Adversarial Perturbations

Authorship analysis is an important subject in the field of natural language processing. It allows the detection of the most likely writer of articles, news, books, or messages. This technique has multiple uses in tasks related to authorship attribution, detection of plagiarism, style analysis, sources of misinformation, etc. The focus of this paper is to explore the limitations and sensitiveness of established approaches to adversarial manipulations of inputs. To this end, and using those established techniques, we first developed an experimental frame-work for author detection and input perturbations. Next, we experimentally evaluated the performance of the authorship detection model to a collection of semantic-preserving adversarial perturbations of input narratives. Finally, we compare and analyze the effects of different perturbation strategies, input and model configurations, and the effects of these on the author detection model.

Optimizing Deep Learning Recommender Systems' Training On CPU Cluster Architectures

During the last two years, the goal of many researchers has been to squeeze the last bit of performance out of HPC system for AI tasks. Often this discussion is held in the context of how fast ResNet50 can be trained. Unfortunately, ResNet50 is no longer a representative workload in 2020. Thus, we focus on Recommender Systems which account for most of the AI cycles in cloud computing centers. More specifically, we focus on Facebook's DLRM benchmark. By enabling it to run on latest CPU hardware and software tailored for HPC, we are able to achieve more than two-orders of magnitude improvement in performance (110x) on a single socket compared to the reference CPU implementation, and high scaling efficiency up to 64 sockets, while fitting ultra-large datasets. This paper discusses the optimization techniques for the various operators in DLRM and which component of the systems are stressed by these different operators. The presented techniques are applicable to a broader set of DL workloads that pose the same scaling challenges/characteristics as DLRM.