Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM (scCello). We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.

Background: Radiography (X-rays) is the dominant modality in orthopedics, and improving the interpretation of radiographs is clinically relevant. Machine learning (ML) has revolutionized data analysis and has been applied to medicine, with some success, in the form of natural language processing (NLP) and artificial neural networks (ANN). Latent Dirichlet allocation (LDA) is an NLP method that automatically categorizes documents into topics. Successfully applying ML to orthopedic radiography could enable the creation of computer-aided decision systems for use in the clinic. We studied how an automated ML pipeline could classify orthopedic trauma radiographs from radiologist reports. Methods: Wrist and ankle radiographs from Danderyd Hospital in Sweden taken between 2002 and 2015, with radiologist reports. LDA was used to create image labels for radiographs from the radiologist reports. Radiographs and labels were used to train an image recognition ANN. The ANN outcomes were manually reviewed to get an accurate estimate of the method's utility and accuracy. Results: Image Labels generated via LDA could successfully train the ANN. The ANN reached an accuracy between 91% and 60% compared to a gold standard, depending on the label. Conclusions: We found that LDA was unsuited to label orthopedic radiographs from reports with high accuracy. However, despite this, the ANN could learn to detect some features in radiographs with high accuracy. The study also illustrates how ML and ANN can be applied to medical research.

This paper studies a factor modeling-based approach for clustering high-dimensional data generated from a mixture of strongly correlated variables. Statistical modeling with correlated structures pervades modern applications in economics, finance, genomics, wireless sensing, etc., with factor modeling being one of the popular techniques for explaining the common dependence. Standard techniques for clustering high-dimensional data, e.g., naive spectral clustering, often fail to yield insightful results as their performances heavily depend on the mixture components having a weakly correlated structure. To address the clustering problem in the presence of a latent factor model, we propose the Factor Adjusted Spectral Clustering (FASC) algorithm, which uses an additional data denoising step via eliminating the factor component to cope with the data dependency. We prove this method achieves an exponentially low mislabeling rate, with respect to the signal to noise ratio under a general set of assumptions. Our assumption bridges many classical factor models in the literature, such as the pervasive factor model, the weak factor model, and the sparse factor model. The FASC algorithm is also computationally efficient, requiring only near-linear sample complexity with respect to the data dimension. We also show the applicability of the FASC algorithm with real data experiments and numerical studies, and establish that FASC provides significant results in many cases where traditional spectral clustering fails.

As the world increasingly relies on mathematical models for forecasts in different areas, effective communication of uncertainty in time series predictions is important for informed decision making. This study explores how users estimate probabilistic uncertainty in time series predictions under different variants of line charts depicting uncertainty. It examines the role of individual characteristics and the influence of user-reported metrics on uncertainty estimations. By addressing these aspects, this paper aims to enhance the understanding of uncertainty visualization and for improving communication in time series forecast visualizations and the design of prediction data dashboards.As the world increasingly relies on mathematical models for forecasts in different areas, effective communication of uncertainty in time series predictions is important for informed decision making. This study explores how users estimate probabilistic uncertainty in time series predictions under different variants of line charts depicting uncertainty. It examines the role of individual characteristics and the influence of user-reported metrics on uncertainty estimations. By addressing these aspects, this paper aims to enhance the understanding of uncertainty visualization and for improving communication in time series forecast visualizations and the design of prediction data dashboards.

Data scientists often seek to identify the most important features in high-dimensional datasets. This can be done through $L_1$-regularized regression, but this can become inefficient for very high-dimensional datasets. Additionally, high-dimensional regression can leak information about individual datapoints in a dataset. In this paper, we empirically evaluate the established baseline method for feature selection with differential privacy, the two-stage selection technique, and show that it is not stable under sparsity. This makes it perform poorly on real-world datasets, so we consider a different approach to private feature selection. We employ a correlations-based order statistic to choose important features from a dataset and privatize them to ensure that the results do not leak information about individual datapoints. We find that our method significantly outperforms the established baseline for private feature selection on many datasets.

Background: Data quality is vital in software analytics, particularly for machine learning (ML) applications like software defect prediction (SDP). Despite the widespread use of ML in software engineering, the effect of data quality antipatterns on these models remains underexplored. Objective: This study develops a taxonomy of ML-specific data quality antipatterns and assesses their impact on software analytics models' performance and interpretation. Methods: We identified eight types and 14 sub-types of ML-specific data quality antipatterns through a literature review. We conducted experiments to determine the prevalence of these antipatterns in SDP data (RQ1), assess how cleaning order affects model performance (RQ2), evaluate the impact of antipattern removal on performance (RQ3), and examine the consistency of interpretation from models built with different antipatterns (RQ4). Results: In our SDP case study, we identified nine antipatterns. Over 90% of these overlapped at both row and column levels, complicating cleaning prioritization and risking excessive data removal. The order of cleaning significantly impacts ML model performance, with neural networks being more resilient to cleaning order changes than simpler models like logistic regression. Antipatterns such as Tailed Distributions and Class Overlap show a statistically significant correlation with performance metrics when other antipatterns are cleaned. Models built with different antipatterns showed moderate consistency in interpretation results. Conclusion: The cleaning order of different antipatterns impacts ML model performance. Five antipatterns have a statistically significant correlation with model performance when others are cleaned. Additionally, model interpretation is moderately affected by different data quality antipatterns.

This underscores the critical role of information as a precursor to knowledge, rather than knowledge itself (Zins, 2007; Frické, 2009). In digital environments, symbols, letters, words, and phrases have the potential to contribute to knowledge formation, necessitating effective communication and optimal information presentation for Information Systems (IS) success (Delone & McLean, 2003; Venkatesh & Bala, 2008; ISO, 2019). Engagement, defined as the emotional, cognitive, and behavioral connection between users and technological resources, has emerged as a key metric for evaluating user experience (UX), reflecting user interaction depth with a system (O'Brien et al., 2020; Attfield et al., 2011; O'Brien & Cairns, 2016). The digitization of communication through Information and Communication Technologies (ICT) has revolutionized information conveyance, demanding engaging and effective digital content to ensure successful knowledge transmission and user retention (Beaudry, 2005; Dvir, 2018). Information Engagement (IE) has gained prominence, focusing on the quality of user-system interactions and the impact of digital content design on user decision-making and UX (ISO, 2019; O'Brien, 2020). IE is crucial in enhancing user interactions across domains such as education, government, and industry, aiming to foster meaningful user engagement with digital text (Choi et al., 2018; Feng et al., 2020; Han et al., 2022). Failure to achieve IE with digital text hinders content producers, yet overcoming this challenge is complicated by a lack of engaging information experience guidelines (Blythe, 2005; Overbeeke et al., 2003). Limited research on IE development has resulted in a scarcity of systematic approaches for its initiation, sustainment, and improvement (O'Brien, 2017; O'Brien & Toms, 2016).

This paper formulates a new Best-Arm Identification problem in the non-stationary stochastic bandits setting, where the means of all arms are shifted in the same way due to a global influence of the environment. The aim is to identify the unique best arm across environmental change given a fixed total budget. While this setting can be regarded as a special case of Adversarial Bandits or Corrupted Bandits, we demonstrate that existing solutions tailored to those settings do not fully utilise the nature of this global influence, and thus, do not work well in practice (despite their theoretical guarantees). To overcome this issue, in this paper we develop a novel selection policy that is consistent and robust in dealing with global environmental shifts. We then propose an allocation policy, LinLUCB, which exploits information about global shifts across all arms in each environment. Empirical tests depict a significant improvement in our policies against other existing methods.

In this work, we address the question of how to enhance signal-agnostic searches by leveraging multiple testing strategies. Specifically, we consider hypothesis tests relying on machine learning, where model selection can introduce a bias towards specific families of new physics signals. We show that it is beneficial to combine different tests, characterised by distinct choices of hyperparameters, and that performances comparable to the best available test are generally achieved while providing a more uniform response to various types of anomalies. Focusing on the New Physics Learning Machine, a methodology to perform a signal-agnostic likelihood-ratio test, we explore a number of approaches to multiple testing, such as combining p-values and aggregating test statistics.

The analysis and detection of communities in network structures are becoming increasingly relevant for understanding social behavior. One of the principal challenges in this field is the complexity of existing algorithms. The Girvan-Newman algorithm, which uses the betweenness metric as a measure of node similarity, is one of the most representative algorithms in this area. This study employs the same method to evaluate the relevance of using local similarity metrics for community detection. A series of local metrics were tested on a set of networks constructed using the Girvan-Newman basic algorithm. The efficacy of these metrics was evaluated by applying the base algorithm to several real networks with varying community sizes, using modularity and NMI. The results indicate that approaches based on local similarity metrics have significant potential for community detection.