Desulfovibrio alaskensis G20 (DA-G20) is utilized as a model for sulfate-reducing bacteria (SRB) that are associated with corrosion issues caused by microorganisms. SRB-based biofilms are thought to be responsible for the billion-dollar-per-year bio-corrosion of metal infrastructure. Understanding the extraction of the bacterial cells' shape and size properties in the SRB-biofilm at different growth stages will assist with the design of anti-corrosion techniques. However, numerous issues affect current approaches, including time-consuming geometric property extraction, low efficiency, and high error rates. This paper proposes BiofilScanner, a Yolact-based deep learning method integrated with invariant moments to address these problems. Our approach efficiently detects and segments bacterial cells in an SRB image while simultaneously invariant moments measure the geometric characteristics of the segmented cells with low errors. The numerical experiments of the proposed method demonstrate that the BiofilmScanner is 2.1x and 6.8x faster than our earlier Mask-RCNN and DLv3+ methods for detecting, segmenting, and measuring the geometric properties of the cell. Furthermore, the BiofilmScanner achieved an F1-score of 85.28% while Mask-RCNN and DLv3+ obtained F1-scores of 77.67% and 75.18%, respectively.

Real-world classifiers can benefit from the option of abstaining from predicting on samples where they have low confidence. Such abstention is particularly useful on samples which are close to the learned decision boundary, or which are outliers with respect to the training sample. These settings have been the subject of extensive but disjoint study in the selective classification (SC) and out-of-distribution (OOD) detection literature. Recent work on selective classification with OOD detection (SCOD) has argued for the unified study of these problems; however, the formal underpinnings of this problem are still nascent, and existing techniques are heuristic in nature. In this paper, we propose new plugin estimators for SCOD that are theoretically grounded, effective, and generalise existing approaches from the SC and OOD detection literature. In the course of our analysis, we formally explicate how na\"{i}ve use of existing SC and OOD detection baselines may be inadequate for SCOD. We empirically demonstrate that our approaches yields competitive SC and OOD detection performance compared to baselines from both literatures.

Numerous examples in the literature proved that deep learning models have the ability to work well with multimodal data. Recently, CLIP has enabled deep learning systems to learn shared latent spaces between images and text descriptions, with outstanding zero- or few-shot results in downstream tasks. In this paper we explore the same idea proposed by CLIP but applied to the speech domain, where the phonetic and acoustic spaces usually coexist. We train a CLIP-based model with the aim to learn shared representations of phonetic and acoustic spaces. The results show that the proposed model is sensible to phonetic changes, with a 91% of score drops when replacing 20% of the phonemes at random, while providing substantial robustness against different kinds of noise, with a 10% performance drop when mixing the audio with 75% of Gaussian noise. We also provide empirical evidence showing that the resulting embeddings are useful for a variety of downstream applications, such as intelligibility evaluation and the ability to leverage rich pre-trained phonetic embeddings in speech generation task. Finally, we discuss potential applications with interesting implications for the speech generation and recognition fields.

Early prediction of Alzheimer's disease (AD) is crucial for timely intervention and treatment. This study aims to use machine learning approaches to analyze longitudinal electronic health records (EHRs) of patients with AD and identify signs and symptoms that can predict AD onset earlier. We used a case-control design with longitudinal EHRs from the U.S. Department of Veterans Affairs Veterans Health Administration (VHA) from 2004 to 2021. Cases were VHA patients with AD diagnosed after 1/1/2016 based on ICD-10-CM codes, matched 1:9 with controls by age, sex and clinical utilization with replacement. We used a panel of AD-related keywords and their occurrences over time in a patient's longitudinal EHRs as predictors for AD prediction with four machine learning models. We performed subgroup analyses by age, sex, and race/ethnicity, and validated the model in a hold-out and "unseen" VHA stations group. Model discrimination, calibration, and other relevant metrics were reported for predictions up to ten years before ICD-based diagnosis. The study population included 16,701 cases and 39,097 matched controls. The average number of AD-related keywords (e.g., "concentration", "speaking") per year increased rapidly for cases as diagnosis approached, from around 10 to over 40, while remaining flat at 10 for controls. The best model achieved high discriminative accuracy (ROCAUC 0.997) for predictions using data from at least ten years before ICD-based diagnoses. The model was well-calibrated (Hosmer-Lemeshow goodness-of-fit p-value = 0.99) and consistent across subgroups of age, sex and race/ethnicity, except for patients younger than 65 (ROCAUC 0.746). Machine learning models using AD-related keywords identified from EHR notes can predict future AD diagnoses, suggesting its potential use for identifying AD risk using EHR notes, offering an affordable way for early screening on large population.

Prognostic and Health Management (PHM) has been widely applied to hardware systems in the electronics and non-electronics domains but has not been explored for software. While software does not decay over time, it can degrade over release cycles. Software health management is confined to diagnostic assessments that identify problems, whereas prognostic assessment potentially indicates when in the future a problem will become detrimental. Relevant research areas such as software defect prediction, software reliability prediction, predictive maintenance of software, software degradation, and software performance prediction, exist, but all of these represent diagnostic models built upon historical data, none of which can predict an RUL for software. This paper addresses the application of PHM concepts to software systems for fault predictions and RUL estimation. Specifically, this paper addresses how PHM can be used to make decisions for software systems such as version update and upgrade, module changes, system reengineering, rejuvenation, maintenance scheduling, budgeting, and total abandonment. This paper presents a method to prognostically and continuously predict the RUL of a software system based on usage parameters (e.g., the numbers and categories of releases) and performance parameters (e.g., response time). The model developed has been validated by comparing actual data, with the results that were generated by predictive models. Statistical validation (regression validation, and k-fold cross validation) has also been carried out. A case study, based on publicly available data for the Bugzilla application is presented. This case study demonstrates that PHM concepts can be applied to software systems and RUL can be calculated to make system management decisions.

Opioid related aberrant behaviors (ORAB) present novel risk factors for opioid overdose. Previously, ORAB have been mainly assessed by survey results and by monitoring drug administrations. Such methods however, cannot scale up and do not cover the entire spectrum of aberrant behaviors. On the other hand, ORAB are widely documented in electronic health record notes. This paper introduces a novel biomedical natural language processing benchmark dataset named ODD, for ORAB Detection Dataset. ODD is an expert-annotated dataset comprising of more than 750 publicly available EHR notes. ODD has been designed to identify ORAB from patients' EHR notes and classify them into nine categories; 1) Confirmed Aberrant Behavior, 2) Suggested Aberrant Behavior, 3) Opioids, 4) Indication, 5) Diagnosed opioid dependency, 6) Benzodiapines, 7) Medication Changes, 8) Central Nervous System-related, and 9) Social Determinants of Health. We explored two state-of-the-art natural language processing (NLP) models (finetuning pretrained language models and prompt-tuning approaches) to identify ORAB. Experimental results show that the prompt-tuning models outperformed the finetuning models in most cateogories and the gains were especially higher among uncommon categories (Suggested aberrant behavior, Diagnosed opioid dependency and Medication change). Although the best model achieved the highest 83.92% on area under precision recall curve, uncommon classes (Suggested Aberrant Behavior, Diagnosed Opioid Dependence, and Medication Change) still have a large room for performance improvement.

The system log generated in a computer system refers to large-scale data that are collected simultaneously and used as the basic data for determining errors, intrusion and abnormal behaviors. The aim of system log anomaly detection is to promptly identify anomalies while minimizing human intervention, which is a critical problem in the industry. Previous studies performed anomaly detection through algorithms after converting various forms of log data into a standardized template using a parser. Particularly, a template corresponding to a specific event should be defined in advance for all the log data using which the information within the log key may get lost. In this study, we propose LAnoBERT, a parser free system log anomaly detection method that uses the BERT model, exhibiting excellent natural language processing performance. The proposed method, LAnoBERT, learns the model through masked language modeling, which is a BERT-based pre-training method, and proceeds with unsupervised learning-based anomaly detection using the masked language modeling loss function per log key during the test process. In addition, we also propose an efficient inference process to establish a practically applicable pipeline to the actual system. Experiments on three well-known log datasets, i.e., HDFS, BGL, and Thunderbird, show that not only did LAnoBERT yield a higher anomaly detection performance compared to unsupervised learning-based benchmark models, but also it resulted in a comparable performance with supervised learning-based benchmark models.

Entity Resolution (ER) is the problem of determining when two entities refer to the same underlying entity. The problem has been studied for over 50 years, and most recently, has taken on new importance in an era of large, heterogeneous 'knowledge graphs' published on the Web and used widely in domains as wide ranging as social media, e-commerce and search. This chapter will discuss the specific problem of named ER in the context of personal knowledge graphs (PKGs). We begin with a formal definition of the problem, and the components necessary for doing high-quality and efficient ER. We also discuss some challenges that are expected to arise for Web-scale data. Next, we provide a brief literature review, with a special focus on how existing techniques can potentially apply to PKGs. We conclude the chapter by covering some applications, as well as promising directions for future research.

Object pose estimation is a core perception task that enables, for example, object grasping and scene understanding. The widely available, inexpensive and high-resolution RGB sensors and CNNs that allow for fast inference based on this modality make monocular approaches especially well suited for robotics applications. We observe that previous surveys on object pose estimation establish the state of the art for varying modalities, single- and multi-view settings, and datasets and metrics that consider a multitude of applications. We argue, however, that those works' broad scope hinders the identification of open challenges that are specific to monocular approaches and the derivation of promising future challenges for their application in robotics. By providing a unified view on recent publications from both robotics and computer vision, we find that occlusion handling, novel pose representations, and formalizing and improving category-level pose estimation are still fundamental challenges that are highly relevant for robotics. Moreover, to further improve robotic performance, large object sets, novel objects, refractive materials, and uncertainty estimates are central, largely unsolved open challenges. In order to address them, ontological reasoning, deformability handling, scene-level reasoning, realistic datasets, and the ecological footprint of algorithms need to be improved.

Identifying Amyotrophic Lateral Sclerosis (ALS) in its early stages is essential for establishing the beginning of treatment, enriching the outlook, and enhancing the overall well-being of those affected individuals. However, early diagnosis and detecting the disease's signs is not straightforward. A simpler and cheaper way arises by analyzing the patient's facial expressions through computational methods. When a patient with ALS engages in specific actions, e.g., opening their mouth, the movement of specific facial muscles differs from that observed in a healthy individual. This paper proposes Facial Point Graphs to learn information from the geometry of facial images to identify ALS automatically. The experimental outcomes in the Toronto Neuroface dataset show the proposed approach outperformed state-of-the-art results, fostering promising developments in the area.