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At least 181 records · Page 10

Harnessing large language models’ zero-shot and few-shot learning capabilities for regulatory research

Abstract Large language models (LLMs) are sophisticated AI-driven models trained on vast sources of natural language data. They are adept at generating responses that closely mimic human conversational patterns. One of the most notable examples is OpenAI's ChatGPT, which has been extensively used across diverse sectors. Despite their flexibility, a significant challenge arises as most users must transmit their data to the servers of companies operating these models. Utilizing ChatGPT or similar models online may inadvertently expose sensitive information to the risk of data breaches. Therefore, implementing LLMs that are open source and smaller in scale within a secure local network becomes a crucial step for organizations where ensuring data privacy and protection has the highest priority, such as regulatory agencies. As a feasibility evaluation, we implemented a series of open-source LLMs within a regulatory agency’s local network and assessed their performance on specific tasks involving extracting relevant clinical pharmacology information from regulatory drug labels. Our research shows that some models work well in the context of few- or zero-shot learning, achieving performance comparable, or even better than, neural network models that needed thousands of training samples. One of the models was selected to address a real-world issue of finding intrinsic factors that affect drugs' clinical exposure without any training or fine-tuning. In a dataset of over 700 000 sentences, the model showed a 78.5% accuracy rate. Our work pointed to the possibility of implementing open-source LLMs within a secure local network and using these models to perform various natural language processing tasks when large numbers of training examples are unavailable.

Biochemistry & Molecular Biology↗

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

Radio galaxy zoo EMU: towards a semantic radio galaxy morphology taxonomy

We present a novel natural language processing (NLP) approach to deriving plain English descriptors for science cases otherwise restricted by obfuscating technical terminology. We address the limitations of common radio galaxy morphology classifications by applying this approach. We experimentally derive a set of semantic tags for the Radio Galaxy Zoo EMU (Evolutionary Map of the Universe) project and the wider astronomical community. We collect 8486 plain English annotations of radio galaxy morphology, from which we derive a taxonomy of tags. The tags are plain English. The result is an extensible framework, which is more flexible, more easily communicated, and more sensitive to rare feature combinations, which are indescribable using the current framework of radio astronomy classifications.

79 ASTRONOMY AND ASTROPHYSICS↗

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

Abstract Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of >530 PKs have been targeted by FDA-approved medications, and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to investigate the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on word and concept neighborhoods in PubMed abstracts. We use information about phase I-IV trials in ClinicalTrials.gov to construct a training set for random forest classification. Our results with historical data show that associations between PKs and specific cancers can be predicted years in advance with good accuracy. Our tool can be used to predict the relevance of inhibiting PKs for specific cancers and to support the design of well-focused clinical trials to discover novel PKIs for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Probabilistic simulation of quantum circuits using a deep-learning architecture

The fundamental question of how to best simulate quantum systems using conventional computational resources lies at the forefront of condensed matter and quantum computation. It impacts both our understanding of quantum materials and our ability to emulate quantum circuits. Here we present an exact formulation of quantum dynamics via factorized generalized measurements which maps quantum states to probability distributions with the advantage that local unitary dynamics and quantum channels map to local quasistochastic matrices. This representation provides a general framework for using state-of-the-art probabilistic models in machine learning for the simulation of quantum many-body dynamics. Using this framework, we have developed a practical algorithm to simulate quantum circuits using an attention network based on a powerful neural network ansatz responsible for the most recent breakthroughs in natural language processing. We demonstrate our approach by simulating circuits that build Greenberger-Horne-Zeilinger and linear graph states of up to 60 qubits, as well as a variational quantum eigensolver circuit for preparing the ground state of the transverse field Ising model on several system sizes. Our methodology constitutes a modern machine learning approach to the simulation of quantum physics with applicability both to quantum circuits as well as other quantum many-body systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Domain-specific text embedding model for accelerator physics

Accelerator physics presents unique challenges for natural language processing (NLP) due to its specialized terminology and complex concepts. A key component in overcoming these challenges is the development of robust text embedding models that transform textual data into dense vector representations, facilitating efficient information retrieval and semantic understanding. In this work, we introduce AccPhysBERT, a sentence embedding model fine-tuned specifically for accelerator physics. Our model demonstrates superior performance across a range of downstream NLP tasks, surpassing existing models in capturing the domain-specific nuances of the field. We further showcase its practical applications, including semantic paper-reviewer matching and integration into retrieval-augmented generation systems, highlighting its potential to enhance information retrieval and knowledge discovery in accelerator physics. Published by the American Physical Society 2025

Hellert, Thorsten (ORCID:0000000227970926)↗

Training toward significance with the decorrelated event classifier transformer neural network

Experimental particle physics uses machine learning for many tasks, where one application is to classify signal and background events. This classification can be used to bin an analysis region to enhance the expected significance for a mass resonance search. In natural language processing, one of the leading neural network architectures is the transformer. In this work, an event classifier transformer is proposed to bin an analysis region, in which the network is trained with special techniques. The techniques developed here can enhance the significance and reduce the correlation between the network’s output and the reconstructed mass. It is found that this trained network can perform better than boosted decision trees and feed-forward networks. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Neural Architecture Search Benchmarks: Insights and Survey

Neural Architecture Search (NAS), a promising and fast-moving research field, aims to automate the architectural design of Deep Neural Networks (DNNs) to achieve better performance on the given task and dataset. NAS methods have been very successful in discovering efficient models for various Computer Vision, Natural Language Processing, etc. The major obstacles to the advancement of NAS techniques are the demand for large computation resources and fair evaluation of various search methods. The differences in training pipeline and setting make it challenging to compare the efficiency of two NAS algorithms. A large number of NAS Benchmarks to simulate the architecture evaluation in seconds have been released over the last few years to ease the computation burden of training neural networks and can aid in the unbiased assessment of different search methods. This paper provides an extensive review of several publicly available NAS Benchmarks in the literature. We provide technical details and a deeper understanding of each benchmark and point out future directions.

97 MATHEMATICS AND COMPUTING↗

Filter pruning of Convolutional Neural Networks for text classification: A case study of cancer pathology report comprehension

Convolutional Neural Networks (CNN) have recently demonstrated effective performance in many Natural Language Processing tasks. In this study, we explore a novel approach for pruning a CNN's convolution filters using our new data-driven utility score. We have applied this technique to an information extraction task of classifying a dataset of cancer pathology reports by cancer type, a highly imbalanced dataset. Compared to standard CNN training, our new algorithm resulted in a nearly .07 increase in the micro-averaged F1-score and a strong .22 increase in the macro-averaged F1-score using a model with nearly a third fewer network weights. We show how directly utilizing a network's interpretation of data can result in strong performance gains, particularly with severely imbalanced datasets.

Yoon, Hong-Jun↗

Adversarial Training for Privacy-Preserving Deep Learning Model Distribution

Collaboration among cancer registries is essential to develop accurate, robust, and generalizable deep learning models for automated information extraction from cancer pathology reports. Sharing data presents a serious privacy issue, especially in biomedical research and healthcare delivery domains. Distributing pretrained deep learning (DL) models has been proposed to avoid critical data sharing. However, there is growing recognition that collaboration among clinical institutes through DL model distribution exposes new security and privacy vulnerabilities. These vulnerabilities increase in natural language processing (NLP) applications, in which the dataset vocabulary with word vector representations needs to be associated with the other model parameters. In this paper, we propose a novel privacy-preserving DL model distribution across cancer registries for information extraction from cancer pathology reports with privacy and confidentiality considerations. The proposed approach exploits the adversarial training framework to distinguish private features from shared features among different datasets. It only shares registry-invariant model parameters, without sharing raw data nor registry-specific model parameters among cancer registries. Thus, it protects both the data and the trained model simultaneously. We compare our proposed approach to single-registry models, and a model trained on centrally hosted data from different cancer registries. The results show that the proposed approach significantly outperforms the single-registry models and achieves statistically indistinguishable micro and macro F1-score as compared to the centralized model.

Alawad, Mohammed↗

VWC-BERT: Scaling Vulnerability–Weakness–Exploit Mapping on Modern AI Accelerators

Defending cybersystems needs accurate mapping of software and hardware vulnerabilities to generalized descriptions of weaknesses, and weaknesses to exploits. These mappings enable cyber defenders to build plans for effective defense and assessment of potential risks to a cybersystem. With close to 170k vulnerabilities, manual mapping is not a feasible option. However, automated mapping is challenging due to limited training data, computational intractability, and limitations in computational natural language processing. Tools based on breakthroughs in Transformer-based language models have been demonstrated to classify vulnerabilities with high accuracy. We make three key contributions in this paper: (1) We present a new framework, \VWCBERT, that augments the Transformer-based hierarchical multi-class classification framework of Das et al. (\textsc{V2W-BERT}) with the ability to map weaknesses to exploits. (2) We implement \VWCBERT~ on modern AI accelerator platforms using two data parallel techniques for the pre-training phase and demonstrate nearly linear speedups across NVIDIA and Graphcore accelerator platforms. We observe nearly linear speedups for up to 16 V100 and 8 A100 GPUs, and about 3.4$\times$ speedup for A100 relative to V100 GPUs. We also observe excellent speedups on Graphcore, with $5.7\times$ speedup on 128 IPUs relative to 16 IPUs. Enabled by scaling, we also demonstrate higher accuracy using a larger language model, RoBERTa-Large. We show up to 87\% accuracy for strict and up to 98\% accuracy for relaxed classification. (3) We develop a novel parallel link manager for the link prediction phase and demonstrate up to 21$\times$ speedup with 16 V100 GPUs relative to one V100 GPU, and thus reducing the runtime from 2.5 hours to 10 minutes. We believe that generalizability and scalability of \VWCBERT~ will benefit both the theoretical development and practical deployment of novel cyberdefense solutions and vulnerability classification.

Das, Siddhartha Shankar↗

Forecast of Wildfire Potential Across California USA Using a Transformer

Wildfires are a major issue facing the United States, a matter further exacerbated by an ever-changing climate. In California alone, wildfires are responsible for billions of dollars in damages and take lives each year. Accurately predicting fire danger conditions allows preparation awareness before wildfires start. Transformers are a class of deep learning models designed to identify patterns in sequential datasets. In recent years, transformers have gained popularity through their impressive performance in natural language processing and other applications of signal recognition. This analysis demonstrates the ability of a transformer with a residual connection to forecast fire danger potential over the state of California. Wildland fire potential index (WFPI) maps collected from the US Geological Survey database from January 1st 2020 to December 31st 2023 were used to tune, train and evaluate the transformer. Meteorological inputs (provided by Daymet daily weather and climatological summaries), the normalized difference vegetation index (NDVI) (calculated from the Moderate Resolution Imaging Spectroradiometer (MODIS)), and outputs from the Scott and Burgman fire behavior fuel models (to characterize maps of fuel types), were used as inputs. Our results show that a transformer can effectively emulate the US Forest Service modeled WFPI maps of California USA for four week long forecasts over the month of July, 2023, with correlations ranging from 0.85 – 0.98.

Limber, Russell [ORNL]↗

Efficient Clustering of Software Vulnerabilities using Self Organizing Map (SOM)

The common vulnerabilities and exposures (CVE) database was created with a mission to ``identify, define, and catalog publicly disclosed cybersecurity vulnerabilities''. This rich body of information can be used to enable rapid and efficient response to secure and defend cyber operations and protect critical cyber infrastructure. The main goal of this paper is to develop a visual analytics tool to enable deep analysis of CVEs using unsupervised clustering techniques. We enhance our analysis by first mapping CVEs to hierarchical-classes in Common Weakness Enumeration (CWE) using information in the National Vulnerability Database (NVD). Both the mapping and the numerical representation of CVEs are enabled by V2W-BERT, which uses natural language processing of the extensive information in NVD to generate a large tabular database of 137,226 CVE entries from 1999 to 2020, where each CVE is represented by a vector of 768 numerical features. The vectorized data is processed by Self-Organizing Maps (SOM), which is an unsupervised machine learning technique for dimensionality reduction, visual representation and clustering. Using a Torus map of 6417 units, we achieve ~10-fold data compression of ~140k CVEs using SOM. The trained map is further clustered using standard K-means clustering into 138 clusters of CVEs. We conducted a brief investigation of the rich mapping of CVEs to best-matching-units to K-means clusters, as well as CVEs to CWEs. For example, this novel mapping provided insight into the role of CWE-59 and CWE-264 in several CVEs that is otherwise hard to explore in the original data. We conclude that our this novel approach will not only enable deep analysis of the complex relationships between CVEs and CWEs, but also a mechanism to quickly respond to and design mitigation actions for rapidly evolving vulnerabilities that have not been mapped to existing CWEs.

Panchal, Khyati↗

Towards Automatic Mapping of Vulnerabilities to Attack Patterns using Large Language Models

With the advent of new devices and applications, cyber attack surface is continuously evolving due to the emergence of new attack techniques and vulnerabilities. Hence, security management tool must assess the cyber risk of an enterprise at regular interval basis through comprehensively identifying associations among attack techniques, weakness, and vulnerabilities. However, existing repositories providing such associations are incomplete (i.e., missing associations), inducing the likelihood of undermining the risk of particular set of attack techniques. Moreover, such associations still rely on manual interpretation, which is slow compared to attack speed and ineffective for the increasing list of vulnerabilities and attack actions. Therefore, there is an urge to develop methodologies for automatically associating vulnerabilities to all relevant attack techniques. In this paper, we present a framework, named VWC-MAP, that can automatically identify all relevant attack techniques of a vulnerability via weakness based on their text descriptions, applying natural language process (NLP) techniques. To achieve that, we present a novel two-tiered classification approach, where the first tier classifies vulnerabilities to weakness, and the second tier classifies weakness to attack techniques. This research has improved the scalability of the current state-of-the-art tool to make vulnerability to weakness mapping significantly faster. Moreover, this paper presents two novel approaches for weakness to attack technique mapping applying Text-to-Text and link prediction techniques. Our experiment results cross-validated through cyber-security experts show that VWC-MAP can associate vulnerabilities to weakness types with 87% accuracy and to new attack patterns with 80% accuracy.

Das, Siddhartha Shankar↗

Quapprox: A Framework for Benchmarking the Approximability of Variational Quantum Circuit

Most of the existing quantum neural network models, such as variational quantum circuits (VQCs), are limited in their ability to explore the non-linear relationships in input data. This gradually becomes the main obstacle for it to tackle realistic applications, such as natural language processing, medical image processing, and wireless communications. Recently, there have emerged research efforts that enable VQCs to perform non-linear operations. However, it is still unclear on the approximability of a given VQC (i.e., the order of non-linearity that can be handled by a specified design). In response to this issue, we developed an automated tool designed to benchmark the approximation of a given VQC. The proposed tool will generate a set of synthetic datasets with different orders of non-linearity and train the given VQC on these datasets to estimate their approximability. Our experiments benchmark VQCs with different designs, where we know their theoretic approximability. We then show that the proposed tool can precisely estimate the approximability, which is consistent with the theoretic value, indicating that the proposed tool can be used for benchmarking the approximability of a given quantum circuit for learning tasks.

artificial intelligence↗

Evaluating Text Analytic Frameworks for Mental Health Surveillance

Reducing suicide incidence among US veterans is one of the highest priorities for the US Department of Veterans Affairs (VA). We are implementing a suicide risk detection system, in collaboration with the VA, that would serve as a surveillance system for risk factors appearing in clinical text data. Primary requirements for this system are fast search capability, feature and information extraction, and delivery of data to up-stream natural language processing models. As such, we are evaluating scalable storage solutions on the basis of performance, fault tolerance, and scalability. In this paper we present our current approach to evaluation, preliminary findings, and the work in progress towards a more robust text analysis pipeline.

Mayer, Benjamin W.↗

Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks

We describe MedstractPlus, a resource for mining relations from the Medline bibliographic database that is currently under construction. It was built on the remains of Medstract, a previously created resource that included a biorelation server and an acronym database. MedstractPlus uses simple and scalable natural language processing modules to structure text, is designed with reusability and extendibility in mind, and adheres to the philosophy of the Linguistic Annotation Framework. We show how MedstractPlus has been used to provide seeds for a novel approach to inferring transcriptional regulatory networks from gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Adversarial Attacks on Deep Neural Network-based Power System Event Classification Models

Online event classification is essential to strengthening the reliability of the power transmission system. Recently, deep learning based methods have achieved great success in numerous domains such as computer vision and natural language processing. Researchers began to adopt deep learning based methods to solve the power system event identification problem and achieved effective results. However, these previous works do not consider that deep learning models are vulnerable to adversarial attacks, potentially influencing real-world applications' reliability. In this paper, we adopt several adversarial attack mechanisms by adding tailored noise signal to the input Phasor Measurement Units (PMU) time series and make the deep learning model misclassify the power system event. This numerical study discloses that current state-of-the-art deep learning based power system event classifiers are extremely vulnerable to adversarial attacks, which may jeopardize the reliability of the power transmission system.

24 POWER TRANSMISSION AND DISTRIBUTION↗