Patterns最新文献

How to select the “best” embryo for transfer is a long-standing question in clinical in vitro fertilization (IVF). Wang et al. proposed a multi-modal self-supervised learning framework for human embryo selection with a high accuracy and generalization ability.

Street names are omnipresent but hold an often-overlooked symbolic function of representing societal power balances, rendering women largely invisible. With this embroidered T-shirt, we aim to bring attention to this gendered imbalance and create a conversation starter around the topic of equality.

Imputation of missing features in spatial transcriptomics is urgently needed due to technological limitations. However, most existing computational methods suffer from moderate accuracy and cannot estimate the reliability of the imputation. To fill this research gap, we introduce a computational model, TransImpute, that imputes the missing feature modality in spatial transcriptomics by mapping it from single-cell reference data. We derive a set of attributes that can accurately predict imputation uncertainty, enabling us to select reliably imputed genes. In addition, we introduce a spatial autocorrelation metric as a regularization to avoid overestimating spatial patterns. Multiple datasets from various platforms demonstrate that our approach significantly improves the reliability of downstream analyses in detecting spatial variable genes and interacting ligand-receptor pairs. Therefore, TransImpute offers a reliable approach to spatial analysis of missing features for both matched and unseen modalities, such as nascent RNAs.

A vast amount of single-cell RNA sequencing (SC) data have been accumulated via various studies and consortiums, but the lack of spatial information limits its analysis of complex biological activities. To bridge this gap, we introduce CellContrast, a computational method for reconstructing spatial relationships among SC cells from spatial transcriptomics (ST) reference. By adopting a contrastive learning framework and training with ST data, CellContrast projects gene expressions into a hidden space where proximate cells share similar representation values. We performed extensive benchmarking on diverse platforms, including SeqFISH, Stereo-seq, 10X Visium, and MERSCOPE, on mouse embryo and human breast cells. The results reveal that CellContrast substantially outperforms other related methods, facilitating accurate spatial reconstruction of SC. We further demonstrate CellContrast’s utility by applying it to cell-type co-localization and cell-cell communication analysis with real-world SC samples, proving the recovered cell locations empower more discoveries and mitigate potential false positives.

Artificial intelligence (AI) is considered one of the most revolutionary technological developments today. But can it replace teachers in education? A new proposal in São Paulo, Brazil, suggests this might be possible, but it raises significant concerns about educational quality and equity.

Rapid advances in human brain organoid technologies have prompted the question of their consciousness. Although brain organoids resemble many facets of the brain, their shortcomings strongly suggest that they do not fit any of the operational definitions of consciousness. As organoids gain internal processing systems through statistical learning and closed loop algorithms, interact with the external world, and become embodied through fusion with other organ systems, questions of biosynthetic consciousness will arise.

Reconstructing neuronal morphology is vital for classifying neurons and mapping brain connectivity. However, it remains a significant challenge due to its complex structure, dense distribution, and low image contrast. In particular, AI-assisted methods often yield numerous errors that require extensive manual intervention. Therefore, reconstructing hundreds of neurons is already a daunting task for general research projects. A key issue is the lack of specialized training for challenging regions due to inadequate data and training methods. This study extracted 2,800 challenging neuronal blocks and categorized them into multiple density levels. Furthermore, we enhanced images using an axial continuity-based network that improved three-dimensional voxel resolution while reducing the difficulty of neuron recognition. Comparing the pre- and post-enhancement results in automatic algorithms using fluorescence micro-optical sectioning tomography (fMOST) data, we observed a significant increase in the recall rate. Our study not only enhances the throughput of reconstruction but also provides a fundamental dataset for tangled neuron reconstruction.

To make explainable artificial intelligence (XAI) systems trustworthy, understanding harmful effects is important. In this paper, we address an important yet unarticulated type of negative effect in XAI. We introduce explainability pitfalls (EPs), unanticipated negative downstream effects from AI explanations manifesting even when there is no intention to manipulate users. EPs are different from dark patterns, which are intentionally deceptive practices. We articulate the concept of EPs by demarcating it from dark patterns and highlighting the challenges arising from uncertainties around pitfalls. We situate and operationalize the concept using a case study that showcases how, despite best intentions, unsuspecting negative effects, such as unwarranted trust in numerical explanations, can emerge. We propose proactive and preventative strategies to address EPs at three interconnected levels: research, design, and organizational. We discuss design and societal implications around reframing AI adoption, recalibrating stakeholder empowerment, and resisting the “move fast and break things” mindset.

Many problems in biology require looking for a “needle in a haystack,” corresponding to a binary classification where there are a few positives within a much larger set of negatives, which is referred to as a class imbalance. The receiver operating characteristic (ROC) curve and the associated area under the curve (AUC) have been reported as ill-suited to evaluate prediction performance on imbalanced problems where there is more interest in performance on the positive minority class, while the precision-recall (PR) curve is preferable. We show via simulation and a real case study that this is a misinterpretation of the difference between the ROC and PR spaces, showing that the ROC curve is robust to class imbalance, while the PR curve is highly sensitive to class imbalance. Furthermore, we show that class imbalance cannot be easily disentangled from classifier performance measured via PR-AUC.