Artificial Intelligence and Robotics Commons^™

Machine Learning And Protein Allostery, Sian Xiao, Gennady M. Verkhivker, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fundamental biological importance and complexity of allosterically regulated proteins stem from their central role in signal transduction and cellular processes. Recently, machine-learning approaches have been developed and actively deployed to facilitate theoretical and experimental studies of protein dynamics and allosteric mechanisms. In this review, we survey recent developments in applications of machine-learning methods for studies of allosteric mechanisms, prediction of allosteric effects and allostery-related physicochemical properties, and allosteric protein engineering. We also review the applications of machine-learning strategies for characterization of allosteric mechanisms and drug design targeting SARS-CoV-2. Continuous development and task-specific adaptation of machine-learning methods for protein allosteric …

Creating Data From Unstructured Text With Context Rule Assisted Machine Learning (Craml), Stephen Meisenbacher, Peter Norlander

School of Business: Faculty Publications and Other Works

Popular approaches to building data from unstructured text come with limitations, such as scalability, interpretability, replicability, and real-world applicability. These can be overcome with Context Rule Assisted Machine Learning (CRAML), a method and no-code suite of software tools that builds structured, labeled datasets which are accurate and reproducible. CRAML enables domain experts to access uncommon constructs within a document corpus in a low-resource, transparent, and flexible manner. CRAML produces document-level datasets for quantitative research and makes qualitative classification schemes scalable over large volumes of text. We demonstrate that the method is useful for bibliographic analysis, transparent analysis of proprietary data, …

A Hybrid Artificial Intelligence Model For Detecting Keratoconus, Zaid Abdi Alkareem Alyasseri, Ali H. Al-Timemy, Ammar Kamal Abasi, Alexandru Lavric, Husam Jasim Mohammed, Hidenori Takahashi, Jose Arthur Milhomens Filho, Mauro Campos, Rossen M. Hazarbassanov, Siamak Yousefi

Machine Learning Faculty Publications

Machine learning models have recently provided great promise in diagnosis of several ophthalmic disorders, including keratoconus (KCN). Keratoconus, a noninflammatory ectatic corneal disorder characterized by progressive cornea thinning, is challenging to detect as signs may be subtle. Several machine learning models have been proposed to detect KCN, however most of the models are supervised and thus require large well-annotated data. This paper proposes a new unsupervised model to detect KCN, based on adapted flower pollination algorithm (FPA) and the k-means algorithm. We will evaluate the proposed models using corneal data collected from 5430 eyes at different stages of KCN severity …

Towards A Machine Learning-Based Digital Twin For Non-Invasive Human Bio-Signal Fusion, Izaldein Al-Zyoud, Fedwa Laamarti, Xiaocong Ma, Diana Tobón, Abdulmotaleb Elsaddik

Computer Vision Faculty Publications

Human bio-signal fusion is considered a critical technological solution that needs to be advanced to enable modern and secure digital health and well-being applications in the metaverse. To support such efforts, we propose a new data-driven digital twin (DT) system to fuse three human physiological bio-signals: heart rate (HR), breathing rate (BR), and blood oxygen saturation level (SpO2). To accomplish this goal, we design a computer vision technology based on the non-invasive photoplethysmography (PPG) technique to extract raw time-series bio-signal data from facial video frames. Then, we implement machine learning (ML) technology to model and measure the bio-signals. We accurately …

The Interaction Of Normalisation And Clustering In Sub-Domain Definition For Multi-Source Transfer Learning Based Time Series Anomaly Detection, Matthew Nicholson, Rahul Agrahari, Clare Conran, Haythem Assem, John D. Kelleher

Articles

This paper examines how data normalisation and clustering interact in the definition of sub-domains within multi-source transfer learning systems for time series anomaly detection. The paper introduces a distinction between (i) clustering as a primary/direct method for anomaly detection, and (ii) clustering as a method for identifying sub-domains within the source or target datasets. Reporting the results of three sets of experiments, we find that normalisation after feature extraction and before clustering results in the best performance for anomaly detection. Interestingly, we find that in the multi-source transfer learning scenario clustering on the target dataset and identifying subdomains in the …

Predicting Publication Of Clinical Trials Using Structured And Unstructured Data: Model Development And Validation Study, Siyang Wang, Simon Šuster, Timothy Baldwin, Karin Verspoor

Natural Language Processing Faculty Publications

Background: Publication of registered clinical trials is a critical step in the timely dissemination of trial findings. However, a significant proportion of completed clinical trials are never published, motivating the need to analyze the factors behind success or failure to publish. This could inform study design, help regulatory decision-making, and improve resource allocation. It could also enhance our understanding of bias in the publication of trials and publication trends based on the research direction or strength of the findings. Although the publication of clinical trials has been addressed in several descriptive studies at an aggregate level, there is a lack …

Towards Reinterpreting Neural Topic Models Via Composite Activations, Jia Peng Lim, Hady Wirawan Lauw

Research Collection School Of Computing and Information Systems

Most Neural Topic Models (NTM) use a variational auto-encoder framework producing K topics limited to the size of the encoder’s output. These topics are interpreted through the selection of the top activated words via the weights or reconstructed vector of the decoder that are directly connected to each neuron. In this paper, we present a model-free two-stage process to reinterpret NTM and derive further insights on the state of the trained model. Firstly, building on the original information from a trained NTM, we generate a pool of potential candidate “composite topics” by exploiting possible co-occurrences within the original set of …

An Empirical Study Of Artifacts And Security Risks In The Pre-Trained Model Supply Chain, Wenxin Jiang, Nicholas Synovic, Rohan Sethi, Aryan Indarapu, Matt Hyattt, Taylor R. Schorlemmer, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Deep neural networks achieve state-of-the-art performance on many tasks, but require increasingly complex architectures and costly training procedures. Engineers can reduce costs by reusing a pre-trained model (PTM) and fine-tuning it for their own tasks. To facilitate software reuse, engineers collaborate around model hubs, collections of PTMs and datasets organized by problem domain. Although model hubs are now comparable in popularity and size to other software ecosystems, the associated PTM supply chain has not yet been examined from a software engineering perspective.

We present an empirical study of artifacts and security features in 8 model hubs. We indicate the potential …

Open-Source Clinical Machine Learning Models: Critical Appraisal Of Feasibility, Advantages, And Challenges, Keerthi B. Harish, W. Nicholson Price Ii, Yindalon Aphinyanaphongs

Articles

Machine learning applications promise to augment clinical capabilities and at least 64 models have already been approved by the US Food and Drug Administration. These tools are developed, shared, and used in an environment in which regulations and market forces remain immature. An important consideration when evaluating this environment is the introduction of open-source solutions in which innovations are freely shared; such solutions have long been a facet of digital culture. We discuss the feasibility and implications of open-source machine learning in a health care infrastructure built upon proprietary information. The decreased cost of development as compared to drugs and …

Shell Theory: A Statistical Model Of Reality, Wen-Yan Lin, Siying Liu, Changhao Ren, Ngai-Man Cheung, Hongdong Li, Yasuyuki Matsushita

Research Collection School Of Computing and Information Systems

Machine learning's grand ambition is the mathematical modeling of reality. The recent years have seen major advances using deep-learned techniques that model reality implicitly; however, corresponding advances in explicit mathematical models have been noticeably lacking. We believe this dichotomy is rooted in the limitations of the current statistical tools, which struggle to make sense of the high dimensional generative processes that natural data seems to originate from. This paper proposes a new, distance based statistical technique which allows us to develop elegant mathematical models of such generative processes. Our model suggests that each semantic concept has an associated distinctive-shell which …

Artificial Intelligence In The Radiomic Analysis Of Glioblastomas: A Review, Taxonomy, And Perspective, Ming Zhu, Sijia Li, Yu Kuang, Virginia B. Hill, Amy B. Heimberger, Lijie Zhai, Shenjie Zhai

Electrical & Computer Engineering Faculty Research

Radiological imaging techniques, including magnetic resonance imaging (MRI) and positron emission tomography (PET), are the standard-of-care non-invasive diagnostic approaches widely applied in neuro-oncology. Unfortunately, accurate interpretation of radiological imaging data is constantly challenged by the indistinguishable radiological image features shared by different pathological changes associated with tumor progression and/or various therapeutic interventions. In recent years, machine learning (ML)-based artificial intelligence (AI) technology has been widely applied in medical image processing and bioinformatics due to its advantages in implicit image feature extraction and integrative data analysis. Despite its recent rapid development, ML technology still faces many hurdles for its broader applications …

Directed Acyclic Graph-Based Neural Networks For Tunable Low-Power Computer Vision, Abhinav Goel, Caleb Tung, Nick Eliopoulos, Xiao Hu, George K. Thiruvathukal, James C. Davis, Yung-Hisang Lu

Computer Science: Faculty Publications and Other Works

Processing visual data on mobile devices has many applications, e.g., emergency response and tracking. State-of-the-art computer vision techniques rely on large Deep Neural Networks (DNNs) that are usually too power-hungry to be deployed on resource-constrained edge devices. Many techniques improve DNN efficiency of DNNs by compromising accuracy. However, the accuracy and efficiency of these techniques cannot be adapted for diverse edge applications with different hardware constraints and accuracy requirements. This paper demonstrates that a recent, efficient tree-based DNN architecture, called the hierarchical DNN, can be converted into a Directed Acyclic Graph-based (DAG) architecture to provide tunable accuracy-efficiency tradeoff options. We …

Robustar: Interactive Toolbox Supporting Precise Data Annotation For Robust Vision Learning, Chonghan Chen, Haohan Wang, Leyang Hu, Yuhao Zhang, Shuguang Lyu, Jingcheng Wu, Xinnuo Li, Linjing Sun, Eric Xing

Machine Learning Faculty Publications

We introduce the initial release of our software Robustar, which aims to improve the robustness of vision classification machine learning models through a data-driven perspective. Building upon the recent understanding that the lack of machine learning model’s robustness is the tendency of the model’s learning of spurious features, we aim to solve this problem from its root at the data perspective by removing the spurious features from the data before training. In particular, we introduce a software that helps the users to better prepare the data for training image classification models by allowing the users to annotate the spurious features …

Action-Sufficient State Representation Learning For Control With Structural Constraints, Biwei Huang, Chaochao Lu, Liu Leqi, Josã© Miguel Hernã¡Ndez-Lobato, Clark Glymour, Bernhard Schã¶Lkopf, Kun Zhang

Machine Learning Faculty Publications

Perceived signals in real-world scenarios are usually high-dimensional and noisy, and finding and using their representation that contains essential and sufficient information required by downstream decision-making tasks will help improve computational efficiency and generalization ability in the tasks. In this paper, we focus on partially observable environments and propose to learn a minimal set of state representations that capture sufficient information for decision-making, termed Action-Sufficient state Representations (ASRs). We build a generative environment model for the structural relationships among variables in the system and present a principled way to characterize ASRs based on structural constraints and the goal of maximizing …

Imagining New Futures Beyond Predictive Systems In Child Welfare: A Qualitative Study With Impacted Stakeholders, Logan Stapleton, Min Hun Lee, Diana Qing, Marya Wright, Alexandra Chouldechova, Ken Holstein, Zhiwei Steven Wu, Haiyi Zhu

Research Collection School Of Computing and Information Systems

Child welfare agencies across the United States are turning to datadriven predictive technologies (commonly called predictive analytics) which use government administrative data to assist workers’ decision-making. While some prior work has explored impacted stakeholders’ concerns with current uses of data-driven predictive risk models (PRMs), less work has asked stakeholders whether such tools ought to be used in the first place. In this work, we conducted a set of seven design workshops with 35 stakeholders who have been impacted by the child welfare system or who work in it to understand their beliefs and concerns around PRMs, and to engage them …

Real Time Call-Flagging System To Respond To Suicidal Ideation In Call Centers, Vishnu Menon, Joseph Carrigan, Charles Floeder, Thomas Walton, Devin Mcguire

Honors Theses

The 2021-2022 Signature Performance Design Studio team developed a live audio call-flagging system that enables faster responses and new response pathways to veteran crises by call service representatives and their management team. Using a custom made deep learning model, live audio streaming server, and Teams broadcasting add-on, the system empowers Signature Performance call service representatives to make quicker and more well informed decisions to provide veteran’s the best care possible.

Industrial Digital Twins At The Nexus Of Nextg Wireless Networks And Computational Intelligence: A Survey, Shah Zeb, Aamir Mahmood, Syed Ali Hassan, Md. Jalil Piran, Mikael Gidlund, Mohsen Guizani

Machine Learning Faculty Publications

By amalgamating recent communication and control technologies, computing and data analytics techniques, and modular manufacturing, Industry 4.0 promotes integrating cyber–physical worlds through cyber–physical systems (CPS) and digital twin (DT) for monitoring, optimization, and prognostics of industrial processes. A DT enables interaction with the digital image of the industrial physical objects/processes to simulate, analyze, and control their real-time operation. DT is rapidly diffusing in numerous industries with the interdisciplinary advances in the industrial Internet of things (IIoT), edge and cloud computing, machine learning, artificial intelligence, and advanced data analytics. However, the existing literature lacks in identifying and discussing the role and …

Reinforcement Learning With Deep Q-Networks, Caleb Cassady

Masters Theses & Specialist Projects

In the past decade, machine learning strategies centered on the use of Deep Neural Networks (DNNs) have caught the interest of researchers due to their success in complicated classification and prediction problems. More recently, these DNNs have been applied to reinforcement learning tasks with state of- the-art results using Deep Q-Networks (DQNs) based on the Q-Learning algorithm. However, the DQN training process is different from standard DNNs and poses significant challenges for certain reinforcement learning environments. This paper examines some of these challenges, compares proposed solutions, and offers novel solutions based on previous research. Experiment implementation available at https://github.com/caleb98/dqlearning.

Moving Toward Personalized Law, Cary Coglianese

All Faculty Scholarship

Rules operate as a tool of governance by making generalizations, thereby cutting down on government officials’ need to make individual determinations. But because they are generalizations, rules can result in inefficient or perverse outcomes due to their over- and under-inclusiveness. With the aid of advances in machine-learning algorithms, however, it is becoming increasingly possible to imagine governments shifting away from a predominant reliance on general rules and instead moving toward increased reliance on precise individual determinations—or on “personalized law,” to use the term Omri Ben-Shahar and Ariel Porat use in the title of their 2021 book. Among the various technological, …

Machine Learning To Predict Sports-Related Concussion Recovery Using Clinical Data, Yan Chu, Gregory Knell, Riley P. Brayton, Scott O. Burkhart, Xiaoqian Jiang, Shayan Shams

Faculty Research, Scholarly, and Creative Activity

Objectives
Sport-related concussions (SRCs) are a concern for high school athletes. Understanding factors contributing to SRC recovery time may improve clinical management. However, the complexity of the many clinical measures of concussion data precludes many traditional methods. This study aimed to answer the question, what is the utility of modeling clinical concussion data using machine-learning algorithms for predicting SRC recovery time and protracted recovery?
Methods
This was a retrospective case series of participants aged 8 to 18 years with a diagnosis of SRC. A 6-part measure was administered to assess pre-injury risk factors, initial injury severity, and post-concussion symptoms, including …

Land-Surface Parameters For Spatial Predictive Mapping And Modeling, Aaron E. Maxwell, Charles Shobe

Faculty & Staff Scholarship

Land-surface parameters derived from digital land surface models (DLSMs) (for example, slope, surface curvature, topographic position, topographic roughness, aspect, heat load index, and topographic moisture index) can serve as key predictor variables in a wide variety of mapping and modeling tasks relating to geomorphic processes, landform delineation, ecological and habitat characterization, and geohazard, soil, wetland, and general thematic mapping and modeling. However, selecting features from the large number of potential derivatives that may be predictive for a specific feature or process can be complicated, and existing literature may offer contradictory or incomplete guidance. The availability of multiple data sources and …

Understanding Deep Learning - Challenges And Prospects, Niha Adnan, Fahad Umer

Department of Surgery

The developments in Artificial Intelligence have been on the rise since its advent. The advancements in this field have been the innovative research area across a wide range of industries, making its incorporation in dentistry inevitable. Artificial Intelligence techniques are making serious progress in the diagnostic and treatment planning aspects of dental clinical practice. This will ultimately help in the elimination of subjectivity and human error that are often part of radiographic interpretations, and will improve the overall efficiency of the process. The various types of Artificial Intelligence algorithms that exist today make the understanding of their application quite complex. …

Assessing Feature Representations For Instance-Based Cross-Domain Anomaly Detection In Cloud Services Univariate Time Series Data, Rahul Agrahari, Matthew Nicholson, Clare Conran, Haythem Assem, John D. Kelleher

Articles

In this paper, we compare and assess the efficacy of a number of time-series instance feature representations for anomaly detection. To assess whether there are statistically significant differences between different feature representations for anomaly detection in a time series, we calculate and compare confidence intervals on the average performance of different feature sets across a number of different model types and cross-domain time-series datasets. Our results indicate that the catch22 time-series feature set augmented with features based on rolling mean and variance performs best on average, and that the difference in performance between this feature set and the next best …

Post-Quantum Secure Identity-Based Encryption Scheme Using Random Integer Lattices For Iot-Enabled Ai Applications, Dharminder Dharminder, Ashok Kumar Das, Sourav Saha, Basudeb Bera, Athanasios V. Vasilakos

VMASC Publications

Identity-based encryption is an important cryptographic system that is employed to ensure confidentiality of a message in communication. This article presents a provably secure identity based encryption based on post quantum security assumption. The security of the proposed encryption is based on the hard problem, namely Learning with Errors on integer lattices. This construction is anonymous and produces pseudo random ciphers. Both public-key size and ciphertext-size have been reduced in the proposed encryption as compared to those for other relevant schemes without compromising the security. Next, we incorporate the constructed identity based encryption (IBE) for Internet of Things (IoT) applications, …

Part I - Ai And Data As Medical Devices, W. Nicholson Price Ii

Other Publications

It may seem counterintuitive to open a book on medical devices with chapters on software and data, but these are the frontiers of new medical device regulation and law. Physical devices are still crucial to medicine, but they – and medical practice as a whole – are embedded in and permeated by networks of software and caches of data. Those software systems are often mindbogglingly complex and largely inscrutable, involving artificial intelligence and machine learning. Ensuring that such software works effectively and safely remains a substantial challenge for regulators and policymakers. Each of the three chapters in this part examines …

Security Concerns On Machine Learning Solutions For 6g Networks In Mmwave Beam Prediction, Ferhat Ozgur Catak, Murat Kuzlu, Evren Catak, Umit Cali, Devrim Unal

Engineering Technology Faculty Publications

6G – sixth generation – is the latest cellular technology currently under development for wireless communication systems. In recent years, machine learning (ML) algorithms have been applied widely in various fields, such as healthcare, transportation, energy, autonomous cars, and many more. Those algorithms have also been used in communication technologies to improve the system performance in terms of frequency spectrum usage, latency, and security. With the rapid developments of ML techniques, especially deep learning (DL), it is critical to consider the security concern when applying the algorithms. While ML algorithms offer significant advantages for 6G networks, security concerns on artificial …

Deeply Learning Deep Inelastic Scattering Kinematics, Markus Diefenthaler, Abdullah Farhat, Andrii Verbytskyi, Yuesheng Xu

Mathematics & Statistics Faculty Publications

We study the use of deep learning techniques to reconstruct the kinematics of the neutral current deep inelastic scattering (DIS) process in electron–proton collisions. In particular, we use simulated data from the ZEUS experiment at the HERA accelerator facility, and train deep neural networks to reconstruct the kinematic variables Q² and x. Our approach is based on the information used in the classical construction methods, the measurements of the scattered lepton, and the hadronic final state in the detector, but is enhanced through correlations and patterns revealed with the simulated data sets. We show that, with the appropriate selection …

Algorithm Vs. Algorithm, Cary Coglianese, Alicia Lai

All Faculty Scholarship

Critics raise alarm bells about governmental use of digital algorithms, charging that they are too complex, inscrutable, and prone to bias. A realistic assessment of digital algorithms, though, must acknowledge that government is already driven by algorithms of arguably greater complexity and potential for abuse: the algorithms implicit in human decision-making. The human brain operates algorithmically through complex neural networks. And when humans make collective decisions, they operate via algorithms too—those reflected in legislative, judicial, and administrative processes. Yet these human algorithms undeniably fail and are far from transparent. On an individual level, human decision-making suffers from memory limitations, fatigue, …

Antitrust By Algorithm, Cary Coglianese, Alicia Lai

All Faculty Scholarship

Technological innovation is changing private markets around the world. New advances in digital technology have created new opportunities for subtle and evasive forms of anticompetitive behavior by private firms. But some of these same technological advances could also help antitrust regulators improve their performance in detecting and responding to unlawful private conduct. We foresee that the growing digital complexity of the marketplace will necessitate that antitrust authorities increasingly rely on machine-learning algorithms to oversee market behavior. In making this transition, authorities will need to meet several key institutional challenges—building organizational capacity, avoiding legal pitfalls, and establishing public trust—to ensure successful …

From Negative To Positive Algorithm Rights, Cary Coglianese, Kat Hefter

All Faculty Scholarship

Artificial intelligence, or “AI,” is raising alarm bells. Advocates and scholars propose policies to constrain or even prohibit certain AI uses by governmental entities. These efforts to establish a negative right to be free from AI stem from an understandable motivation to protect the public from arbitrary, biased, or unjust applications of algorithms. This movement to enshrine protective rights follows a familiar pattern of suspicion that has accompanied the introduction of other technologies into governmental processes. Sometimes this initial suspicion of a new technology later transforms into widespread acceptance and even a demand for its use. In this paper, we …