Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high-throughput. These efforts have facilitated understanding of compound mechanism-of-action (MOA), drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.

Recent years have seen rapid development of descriptor generation based on representation learning of extremely diverse molecules, especially those that apply natural language processing (NLP) models to SMILES, a literal representation of molecular structure. However, little research has been done on how these models understand chemical structure. To address this black box, we investigated the relationship between the learning progress of SMILES and chemical structure using a representative NLP model, the Transformer. We show that while the Transformer learns partial structures of molecules quickly, it requires extended training to understand overall structures. Consistently, the accuracy of molecular property predictions using descriptors generated from models at different learning steps was similar from the beginning to the end of training. Furthermore, we found that the Transformer requires particularly long training to learn chirality and sometimes stagnates with low performance due to misunderstanding of enantiomers. These findings are expected to deepen the understanding of NLP models in chemistry.

The US government has reportedly approved AI-based memory loss prediction software for the first time. Darmiyan, a San Francisco-based brain imaging analytics company, says the FDA has granted De Novo approval for its product BrainSee. The software platform assigns "an objective score that predicts the likelihood of progression from aMCI to Alzheimer's dementia within 5 years," according to the medical company. Fierce Biotech first reported the announcement. Darmiyan says BrainSee can predict memory loss progression using clinical brain MRIs and cognitive tests, which are already standard for patients worried about early signs of decline.

Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the pharmaceutical industry. Our survey offers a comprehensive overview of state-of-the-art methods in molecule design, particularly focusing on \emph{de novo} drug design, which incorporates (deep) graph learning techniques. We categorize these methods into three distinct groups: \emph{i)} \emph{all-at-once}, \emph{ii)} \emph{fragment-based}, and \emph{iii)} \emph{node-by-node}. Additionally, we introduce some key public datasets and outline the commonly used evaluation metrics for both the generation and optimization of molecules. In the end, we discuss the existing challenges in this field and suggest potential directions for future research.

This study investigates the complexity of regulatory affairs in the medical device industry, a critical factor influencing market access and patient care. Through qualitative research, we sought expert insights to understand the factors contributing to this complexity. The study involved semi-structured interviews with 28 professionals from medical device companies, specializing in various aspects of regulatory affairs. These interviews were analyzed using open coding and Natural Language Processing (NLP) techniques. The findings reveal key sources of complexity within the regulatory landscape, divided into five domains: (A) Regulatory language complexity, (B) Intricacies within the regulatory process, (C) Global-level complexities, (D) Database-related considerations, and (E) Product-level issues. The participants highlighted the need for strategies to streamline regulatory compliance, enhance interactions between regulatory bodies and industry players, and develop adaptable frameworks for rapid technological advancements. Emphasizing interdisciplinary collaboration and increased transparency, the study concludes that these elements are vital for establishing coherent and effective regulatory procedures in the medical device sector.

We propose a new large-scale molecular model, named AdaMR, which stands for Adjustable Molecular Representation for Unified Pre-training Strategy. Unlike recent large-scale molecular models that use a single molecular encoding, AdaMR employs a granularity-adjustable molecular encoder, learning molecular representations at both the atomic and substructure levels. For the pretraining process, we designed a task for molecular canonicalization, which involves transforming multiple generic molecular representations into canonical representations. By adjusting the granularity of molecular encoding, the trained model can improve the effects on multiple downstream tasks, such as model attribute prediction and molecule generation. Substructure-level molecular representation retains information of specific atom groups or arrangements that determine chemical properties and have similar functions, which is beneficial for tasks like property prediction. Meanwhile, atomic-level representation, combined with generative molecular canonicalization pre-training tasks, enhances the validity, novelty, and uniqueness in generative tasks. These features of AdaMR demonstrate its strong performance in numerous downstream tasks. We use different molecular properties prediction tasks on six different datasets on MoleculeNet and two generative tasks on ZINC250K dataset to evaluate our proposed molecular encoding and pre-training methods, and obtain state-of-the-art (SOTA) results on five of these tasks.

Fox News contributor Dr. Marc Siegel weighs in on how artificial intelligence can change the patient-doctor relationship on'America's Newsroom.' If you received medical care any time this year, there's a good chance you had a close encounter with artificial intelligence. Widely regarded as the breakout year for AI, 2023 ushered in a whole crop of new and improved tech tools, many of which have impacted the health and wellness space. "2023 has been a landmark year for AI in health care, witnessing groundbreaking advancements that have reshaped medical practices and paved the way for a future where health care is more personalized, efficient and accessible," Dr. Harvey Castro, a Dallas, Texas-based board-certified emergency medicine physician and national speaker on AI in health care, told Fox News Digital. WHAT IS ARTIFICIAL INTELLIGENCE (AI)?

External control arms (ECA) can inform the early clinical development of experimental drugs and provide efficacy evidence for regulatory approval in non-randomized settings. However, the main challenge of implementing ECA lies in accessing real-world data or historical clinical trials. Indeed, data sharing is often not feasible due to privacy considerations related to data leaving the original collection centers, along with pharmaceutical companies' competitive motives. In this paper, we leverage a privacy-enhancing technology called federated learning (FL) to remove some of the barriers to data sharing. We introduce a federated learning inverse probability of treatment weighted (IPTW) method for time-to-event outcomes called FedECA which eases the implementation of ECA by limiting patients' data exposure. We show with extensive experiments that FedECA outperforms its closest competitor, matching-adjusted indirect comparison (MAIC), in terms of statistical power and ability to balance the treatment and control groups. To encourage the use of such methods, we publicly release our code which relies on Substra, an open-source FL software with proven experience in privacy-sensitive contexts.

The recent outbreak of the MPox virus has resulted in a tremendous increase in the usage of Twitter. Prior works in this area of research have primarily focused on the sentiment analysis and content analysis of these Tweets, and the few works that have focused on topic modeling have multiple limitations. This paper aims to address this research gap and makes two scientific contributions to this field. First, it presents the results of performing Topic Modeling on 601,432 Tweets about the 2022 Mpox outbreak that were posted on Twitter between 7 May 2022 and 3 March 2023. The results indicate that the conversations on Twitter related to Mpox during this time range may be broadly categorized into four distinct themes - Views and Perspectives about Mpox, Updates on Cases and Investigations about Mpox, Mpox and the LGBTQIA+ Community, and Mpox and COVID-19. Second, the paper presents the findings from the analysis of these Tweets. The results show that the theme that was most popular on Twitter (in terms of the number of Tweets posted) during this time range was Views and Perspectives about Mpox. This was followed by the theme of Mpox and the LGBTQIA+ Community, which was followed by the themes of Mpox and COVID-19 and Updates on Cases and Investigations about Mpox, respectively. Finally, a comparison with related studies in this area of research is also presented to highlight the novelty and significance of this research work.

The fundamental goal of small molecule discovery is to generate chemicals with target functionality. While this often proceeds through structure-based methods, we set out to investigate the practicality of orthogonal methods that leverage the extensive corpus of chemical literature. We hypothesize that a sufficiently large text-derived chemical function dataset would mirror the actual landscape of chemical functionality. Such a landscape would implicitly capture complex physical and biological interactions given that chemical function arises from both a molecule's structure and its interacting partners. To evaluate this hypothesis, we built a Chemical Function (CheF) dataset of patent-derived functional labels. This dataset, comprising 631K molecule-function pairs, was created using an LLM- and embedding-based method to obtain functional labels for approximately 100K molecules from their corresponding 188K unique patents. We carry out a series of analyses demonstrating that the CheF dataset contains a semantically coherent textual representation of the functional landscape congruent with chemical structural relationships, thus approximating the actual chemical function landscape. We then demonstrate that this text-based functional landscape can be leveraged to identify drugs with target functionality using a model able to predict functional profiles from structure alone. We believe that functional label-guided molecular discovery may serve as an orthogonal approach to traditional structure-based methods in the pursuit of designing novel functional molecules.