arXiv subjects

Linda Petzold

Publications and source records attributed to Linda Petzold.

At least 37 records · Page 2Linked to original sources

arXiv2023

Dynamic Prompting: A Unified Framework for Prompt Tuning

It has been demonstrated that the art of prompt tuning is highly effective in efficiently extracting knowledge from pretrained foundation models, encompassing pretrained language models (PLMs), vision pretrained models, and vision-language (V-L) models. However, the efficacy of employing fixed soft prompts with a predetermined position for concatenation with inputs for all instances, irrespective of their inherent disparities, remains uncertain. Variables such as the position, length, and representations of prompts across diverse instances and tasks can substantially influence the performance of prompt tuning. In this context, we provide a theoretical analysis, which reveals that optimizing the position of the prompt to encompass the input can capture additional semantic information that traditional prefix or postfix prompt tuning methods fail to capture. Building upon our analysis, we present a unified dynamic prompt (DP) tuning strategy that dynamically determines different factors of prompts based on specific tasks and instances. To accomplish this, we employ a lightweight learning network with Gumble-Softmax, allowing us to learn instance-dependent guidance. Experimental results underscore the significant performance improvement achieved by dynamic prompt tuning across a wide range of tasks, including NLP tasks, vision recognition tasks, and vision-language tasks. Furthermore, we establish the universal applicability of our approach under full-data, few-shot, and multitask scenarios. Codes are available at https://github.com/Xianjun-Yang/DPT.

cs.CL↗

arXiv2023

Few-Shot Document-Level Event Argument Extraction

Event argument extraction (EAE) has been well studied at the sentence level but under-explored at the document level. In this paper, we study to capture event arguments that actually spread across sentences in documents. Prior works usually assume full access to rich document supervision, ignoring the fact that the available argument annotation is usually limited. To fill this gap, we present FewDocAE, a Few-Shot Document-Level Event Argument Extraction benchmark, based on the existing document-level event extraction dataset. We first define the new problem and reconstruct the corpus by a novel N -Way-D-Doc sampling instead of the traditional N -Way-K-Shot strategy. Then we adjust the current document-level neural models into the few-shot setting to provide baseline results under in- and cross-domain settings. Since the argument extraction depends on the context from multiple sentences and the learning process is limited to very few examples, we find this novel task to be very challenging with substantively low performance. Considering FewDocAE is closely related to practical use under low-resource regimes, we hope this benchmark encourages more research in this direction. Our data and codes will be available online.

cs.CL↗

arXiv2023

OASum: Large-Scale Open Domain Aspect-based Summarization

Aspect or query-based summarization has recently caught more attention, as it can generate differentiated summaries based on users' interests. However, the current dataset for aspect or query-based summarization either focuses on specific domains, contains relatively small-scale instances, or includes only a few aspect types. Such limitations hinder further explorations in this direction. In this work, we take advantage of crowd-sourcing knowledge on Wikipedia.org and automatically create a high-quality, large-scale open-domain aspect-based summarization dataset named OASum, which contains more than 3.7 million instances with around 1 million different aspects on 2 million Wikipedia pages. We provide benchmark results on OASum and demonstrate its ability for diverse aspect-based summarization generation. To overcome the data scarcity problem on specific domains, we also perform zero-shot, few-shot, and fine-tuning on seven downstream datasets. Specifically, zero/few-shot and fine-tuning results show that the model pre-trained on our corpus demonstrates a strong aspect or query-focused generation ability compared with the backbone model. Our dataset and pre-trained checkpoints are publicly available.

cs.CL↗

arXiv2023

An Empirical Study on the Robustness of the Segment Anything Model (SAM)

The Segment Anything Model (SAM) is a foundation model for general image segmentation. Although it exhibits impressive performance predominantly on natural images, understanding its robustness against various image perturbations and domains is critical for real-world applications where such challenges frequently arise. In this study we conduct a comprehensive robustness investigation of SAM under diverse real-world conditions. Our experiments encompass a wide range of image perturbations. Our experimental results demonstrate that SAM's performance generally declines under perturbed images, with varying degrees of vulnerability across different perturbations. By customizing prompting techniques and leveraging domain knowledge based on the unique characteristics of each dataset, the model's resilience to these perturbations can be enhanced, addressing dataset-specific challenges. This work sheds light on the limitations and strengths of SAM in real-world applications, promoting the development of more robust and versatile image segmentation solutions.

cs.CV↗

arXiv2023

MatKB: Semantic Search for Polycrystalline Materials Synthesis Procedures

In this paper, we present a novel approach to knowledge extraction and retrieval using Natural Language Processing (NLP) techniques for material science. Our goal is to automatically mine structured knowledge from millions of research articles in the field of polycrystalline materials and make it easily accessible to the broader community. The proposed method leverages NLP techniques such as entity recognition and document classification to extract relevant information and build an extensive knowledge base, from a collection of 9.5 Million publications. The resulting knowledge base is integrated into a search engine, which enables users to search for information about specific materials, properties, and experiments with greater precision than traditional search engines like Google. We hope our results can enable material scientists quickly locate desired experimental procedures, compare their differences, and even inspire them to design new experiments. Our website will be available at Github \footnote{https://github.com/Xianjun-Yang/PcMSP.git} soon.

cs.CL↗

arXiv2022

PcMSP: A Dataset for Scientific Action Graphs Extraction from Polycrystalline Materials Synthesis Procedure Text

Scientific action graphs extraction from materials synthesis procedures is important for reproducible research, machine automation, and material prediction. But the lack of annotated data has hindered progress in this field. We demonstrate an effort to annotate Polycrystalline Materials Synthesis Procedures (PcMSP) from 305 open access scientific articles for the construction of synthesis action graphs. This is a new dataset for material science information extraction that simultaneously contains the synthesis sentences extracted from the experimental paragraphs, as well as the entity mentions and intra-sentence relations. A two-step human annotation and inter-annotator agreement study guarantee the high quality of the PcMSP corpus. We introduce four natural language processing tasks: sentence classification, named entity recognition, relation classification, and joint extraction of entities and relations. Comprehensive experiments validate the effectiveness of several state-of-the-art models for these challenges while leaving large space for improvement. We also perform the error analysis and point out some unique challenges that require further investigation. We will release our annotation scheme, the corpus, and codes to the research community to alleviate the scarcity of labeled data in this domain.

cs.CL↗

arXiv2022

Interpretable Polynomial Neural Ordinary Differential Equations

Neural networks have the ability to serve as universal function approximators, but they are not interpretable and don't generalize well outside of their training region. Both of these issues are problematic when trying to apply standard neural ordinary differential equations (neural ODEs) to dynamical systems. We introduce the polynomial neural ODE, which is a deep polynomial neural network inside of the neural ODE framework. We demonstrate the capability of polynomial neural ODEs to predict outside of the training region, as well as perform direct symbolic regression without additional tools such as SINDy.

cs.LG↗

arXiv2022

Predicting the Need for Blood Transfusion in Intensive Care Units with Reinforcement Learning

As critically ill patients frequently develop anemia or coagulopathy, transfusion of blood products is a frequent intervention in the Intensive Care Units (ICU). However, inappropriate transfusion decisions made by physicians are often associated with increased risk of complications and higher hospital costs. In this work, we aim to develop a decision support tool that uses available patient information for transfusion decision-making on three common blood products (red blood cells, platelets, and fresh frozen plasma). To this end, we adopt an off-policy batch reinforcement learning (RL) algorithm, namely, discretized Batch Constrained Q-learning, to determine the best action (transfusion or not) given observed patient trajectories. Simultaneously, we consider different state representation approaches and reward design mechanisms to evaluate their impacts on policy learning. Experiments are conducted on two real-world critical care datasets: the MIMIC-III and the UCSF. Results demonstrate that policy recommendations on transfusion achieved comparable matching against true hospital policies via accuracy and weighted importance sampling evaluations on the MIMIC-III dataset. Furthermore, a combination of transfer learning (TL) and RL on the data-scarce UCSF dataset can provide up to $17.02% improvement in terms of accuracy, and up to 18.94% and 21.63% improvement in jump-start and asymptotic performance in terms of weighted importance sampling averaged over three transfusion tasks. Finally, simulations on transfusion decisions suggest that the transferred RL policy could reduce patients' estimated 28-day mortality rate by 2.74% and decreased acuity rate by 1.18% on the UCSF dataset.

cs.LG↗

arXiv2022

Integrating Physiological Time Series and Clinical Notes with Transformer for Early Prediction of Sepsis

Sepsis is a leading cause of death in the Intensive Care Units (ICU). Early detection of sepsis is critical for patient survival. In this paper, we propose a multimodal Transformer model for early sepsis prediction, using the physiological time series data and clinical notes for each patient within $36$ hours of ICU admission. Specifically, we aim to predict sepsis using only the first 12, 18, 24, 30 and 36 hours of laboratory measurements, vital signs, patient demographics, and clinical notes. We evaluate our model on two large critical care datasets: MIMIC-III and eICU-CRD. The proposed method is compared with six baselines. In addition, ablation analysis and case studies are conducted to study the influence of each individual component of the model and the contribution of each data modality for early sepsis prediction. Experimental results demonstrate the effectiveness of our method, which outperforms competitive baselines on all metrics.

cs.LG↗

arXiv2022

Enhancing Transformer Efficiency for Multivariate Time Series Classification

Most current multivariate time series (MTS) classification algorithms focus on improving the predictive accuracy. However, for large-scale (either high-dimensional or long-sequential) time series (TS) datasets, there is an additional consideration: to design an efficient network architecture to reduce computational costs such as training time and memory footprint. In this work we propose a methodology based on module-wise pruning and Pareto analysis to investigate the relationship between model efficiency and accuracy, as well as its complexity. Comprehensive experiments on benchmark MTS datasets illustrate the effectiveness of our method.

cs.LG↗

arXiv2021

Empirical Quantitative Analysis of COVID-19 Forecasting Models

COVID-19 has been a public health emergency of international concern since early 2020. Reliable forecasting is critical to diminish the impact of this disease. To date, a large number of different forecasting models have been proposed, mainly including statistical models, compartmental models, and deep learning models. However, due to various uncertain factors across different regions such as economics and government policy, no forecasting model appears to be the best for all scenarios. In this paper, we perform quantitative analysis of COVID-19 forecasting of confirmed cases and deaths across different regions in the United States with different forecasting horizons, and evaluate the relative impacts of the following three dimensions on the predictive performance (improvement and variation) through different evaluation metrics: model selection, hyperparameter tuning, and the length of time series required for training. We find that if a dimension brings about higher performance gains, if not well-tuned, it may also lead to harsher performance penalties. Furthermore, model selection is the dominant factor in determining the predictive performance. It is responsible for both the largest improvement and the largest variation in performance in all prediction tasks across different regions. While practitioners may perform more complicated time series analysis in practice, they should be able to achieve reasonable results if they have adequate insight into key decisions like model selection.

cs.LG↗

arXiv2021

Multiple Organ Failure Prediction with Classifier-Guided Generative Adversarial Imputation Networks

Multiple organ failure (MOF) is a severe syndrome with a high mortality rate among Intensive Care Unit (ICU) patients. Early and precise detection is critical for clinicians to make timely decisions. An essential challenge in applying machine learning models to electronic health records (EHRs) is the pervasiveness of missing values. Most existing imputation methods are involved in the data preprocessing phase, failing to capture the relationship between data and outcome for downstream predictions. In this paper, we propose classifier-guided generative adversarial imputation networks Classifier-GAIN) for MOF prediction to bridge this gap, by incorporating both observed data and label information. Specifically, the classifier takes imputed values from the generator(imputer) to predict task outcomes and provides additional supervision signals to the generator by joint training. The classifier-guide generator imputes missing values with label-awareness during training, improving the classifier's performance during inference. We conduct extensive experiments showing that our approach consistently outperforms classical and state-of-art neural baselines across a range of missing data scenarios and evaluation metrics.

cs.LG↗

arXiv2021

Robust and integrative Bayesian neural networks for likelihood-free parameter inference

State-of-the-art neural network-based methods for learning summary statistics have delivered promising results for simulation-based likelihood-free parameter inference. Existing approaches require density estimation as a post-processing step building upon deterministic neural networks, and do not take network prediction uncertainty into account. This work proposes a robust integrated approach that learns summary statistics using Bayesian neural networks, and directly estimates the posterior density using categorical distributions. An adaptive sampling scheme selects simulation locations to efficiently and iteratively refine the predictive posterior of the network conditioned on observations. This allows for more efficient and robust convergence on comparatively large prior spaces. We demonstrate our approach on benchmark examples and compare against related methods.

stat.ML↗

arXiv2021

Empirical Analysis of Machine Learning Configurations for Prediction of Multiple Organ Failure in Trauma Patients

Multiple organ failure (MOF) is a life-threatening condition. Due to its urgency and high mortality rate, early detection is critical for clinicians to provide appropriate treatment. In this paper, we perform quantitative analysis on early MOF prediction with comprehensive machine learning (ML) configurations, including data preprocessing (missing value treatment, label balancing, feature scaling), feature selection, classifier choice, and hyperparameter tuning. Results show that classifier choice impacts both the performance improvement and variation most among all the configurations. In general, complex classifiers including ensemble methods can provide better performance than simple classifiers. However, blindly pursuing complex classifiers is unwise as it also brings the risk of greater performance variation.

cs.LG↗

arXiv2021

BERTSurv: BERT-Based Survival Models for Predicting Outcomes of Trauma Patients

Survival analysis is a technique to predict the times of specific outcomes, and is widely used in predicting the outcomes for intensive care unit (ICU) trauma patients. Recently, deep learning models have drawn increasing attention in healthcare. However, there is a lack of deep learning methods that can model the relationship between measurements, clinical notes and mortality outcomes. In this paper we introduce BERTSurv, a deep learning survival framework which applies Bidirectional Encoder Representations from Transformers (BERT) as a language representation model on unstructured clinical notes, for mortality prediction and survival analysis. We also incorporate clinical measurements in BERTSurv. With binary cross-entropy (BCE) loss, BERTSurv can predict mortality as a binary outcome (mortality prediction). With partial log-likelihood (PLL) loss, BERTSurv predicts the probability of mortality as a time-to-event outcome (survival analysis). We apply BERTSurv on Medical Information Mart for Intensive Care III (MIMIC III) trauma patient data. For mortality prediction, BERTSurv obtained an area under the curve of receiver operating characteristic curve (AUC-ROC) of 0.86, which is an improvement of 3.6% over baseline of multilayer perceptron (MLP) without notes. For survival analysis, BERTSurv achieved a concordance index (C-index) of 0.7. In addition, visualizations of BERT's attention heads help to extract patterns in clinical notes and improve model interpretability by showing how the model assigns weights to different inputs.

cs.AI↗

arXiv2020

Model Optimization for Deep Space Exploration via Simulators and Deep Learning

Machine learning, and eventually true artificial intelligence techniques, are extremely important advancements in astrophysics and astronomy. We explore the application of deep learning using neural networks in order to automate the detection of astronomical bodies for future exploration missions, such as missions to search for signatures or suitability of life. The ability to acquire images, analyze them, and send back those that are important, as determined by the deep learning algorithm, is critical in bandwidth-limited applications. Our previous foundational work solidified the concept of using simulator images and deep learning in order to detect planets. Optimization of this process is of vital importance, as even a small loss in accuracy might be the difference between capturing and completely missing a possibly-habitable nearby planet. Through computer vision, deep learning, and simulators, we introduce methods that optimize the detection of exoplanets. We show that maximum achieved accuracy can hit above 98% for multiple model architectures, even with a relatively small training set.

astro-ph.IM↗

arXiv2020

How Much Does It Hurt: A Deep Learning Framework for Chronic Pain Score Assessment

Chronic pain is defined as pain that lasts or recurs for more than 3 to 6 months, often long after the injury or illness that initially caused the pain has healed. The "gold standard" for chronic pain assessment remains self report and clinical assessment via a biopsychosocial interview, since there has been no device that can measure it. A device to measure pain would be useful not only for clinical assessment, but potentially also as a biofeedback device leading to pain reduction. In this paper we propose an end-to-end deep learning framework for chronic pain score assessment. Our deep learning framework splits the long time-course data samples into shorter sequences, and uses Consensus Prediction to classify the results. We evaluate the performance of our framework on two chronic pain score datasets collected from two iterations of prototype Pain Meters that we have developed to help chronic pain subjects better understand their health condition.

eess.SP↗

arXiv2020

Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings

Multi-electrode arrays (MEAs) can record extracellular action potentials (also known as 'spikes') from hundreds or thousands of neurons simultaneously. Inference of a functional network from a spike train is a fundamental and formidable computational task in neuroscience. With the advancement of MEA technology, it has become increasingly crucial to develop statistical tools for analyzing multiple neuronal activity as a network. In this paper, we propose a scalable Bayesian framework for inference of functional networks from MEA data. Our framework makes use of the hierarchical structure of networks of neurons. We split the large scale recordings into smaller local networks for network inference, which not only eases the computational burden from Bayesian sampling but also provides useful insights on regional connections in organoids and brains. We speed up the expensive Bayesian sampling process by using parallel computing. Experiments on both synthetic datasets and large-scale real-world MEA recordings show the effectiveness and efficiency of the scalable Bayesian framework. Inference of networks from controlled experiments exposing neural cultures to cadmium presents distinguishable results and further confirms the utility of our framework.

cs.CE↗