Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data.

Understanding the intricate motivations behind human actions is paramount in developing sophisticated systems capable of nuanced behavior analysis.

Understanding the intricate motivations behind human actions is paramount in developing sophisticated systems capable of nuanced behavior analysis.

Personality traits have long been studied as predictors of human behavior.Recent advances in Large Language Models (LLMs) suggest similar patterns may emerge in artificial systems, with advanced LLMs displaying consistent behavioral tendencies resembling human traits like agreeableness and self-regulation. Understanding these patterns is crucial, yet prior work primarily relied on simplified self-reports and heuristic prompting, with little behavioral validation. In this study, we systematically characterize LLM personality across three dimensions: (1) the dynamic emergence and evolution of trait profiles throughout training stages; (2) the predictive validity of self-reported traits in behavioral tasks; and (3) the impact of targeted interventions, such as persona injection, on both self-reports and behavior. Our findings reveal that instructional alignment (e.g., RLHF, instruction tuning) significantly stabilizes trait expression and strengthens trait correlations in ways that mirror human data. However, these self-reported traits do not reliably predict behavior, and observed associations often diverge from human patterns. While persona injection successfully steers self-reports in the intended direction, it exerts little or inconsistent effect on actual behavior. By distinguishing surface-level trait expression from behavioral consistency, our findings challenge assumptions about LLM personality and underscore the need for deeper evaluation in alignment and interpretability.

--Retinal microvascular imaging is increasingly recognised as a non-invasive method for evaluating systemic vascular and metabolic health. However, the association between lipidomics and retinal vasculature remains inadequate. This study investigates the relationships between serum lipid subclasses, free fatty acids (F A), diacylglycerols (DAG), triacylglycerols (T AG), and cholesteryl esters (CE), and retinal microvascular characteristics in a large population-based cohort. Using Spearman correlation analysis, we examined the interconnection between lipid subclasses and ten retinal microvascular traits, applying the Benjamini-Hochberg false discovery rate (BH-FDR) to adjust for statistical significance. Results indicated that F A were linked to retinal vessel twisti-ness, while CE correlated with the average widths of arteries and veins. Conversely, DAG and T AG showed negative correlations with the width and complexity of arterioles and venules. These findings suggest that retinal vascular architecture reflects distinct circulating lipid profiles, supporting its role as a non-invasive marker of systemic metabolic health. This study is the first to integrate deep-learning (DL)-derived retinal traits with lipidomic subclasses in a healthy cohort, thereby providing insights into microvascular structural changes independent of disease status or treatment effects.

Postural sway assessment is important for detecting balance problems and identifying people at risk of falls. Force plates (FP) are considered the gold standard postural sway assessment method in laboratory conditions, but their lack of portability and requirement of high-level expertise limit their widespread usage. This study evaluates the reliability and validity of a novel Balance Mat (BM) device, a low-cost portable alternative that uses optical fibre technology. The research includes two studies: a robot study and a human study. In the robot study, a UR10 robotic arm was used to obtain controlled sway patterns to assess the reliability and sensitivity of the BM. In the human study, 51 healthy young participants performed balance tasks on the BM in combination with an FP to evaluate the BM's validity. Sway metrics such as sway mean, sway absolute mean, sway root mean square (RMS), sway path, sway range, and sway velocity were calculated from both BM and FP and compared. Reliability was evaluated using the intra-class correlation coefficient (ICC), where values greater than 0.9 were considered excellent and values between 0.75 and 0.9 were considered good. Results from the robot study demonstrated good to excellent ICC values in both single and double-leg stances. The human study showed moderate to strong correlations for sway path and range. Using Bland-Altman plots for agreement analysis revealed proportional bias between the BM and the FP where the BM overestimated sway metrics compared to the FP. Calibration was used to improve the agreement between the devices. The device demonstrated consistent sway measurement across varied stance conditions, establishing both reliability and validity following appropriate calibration.

Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior knowledge of enzyme catalysis to rationally modulate general protein-molecule features that are misaligned with catalytic patterns. To address this issue, we introduce a two-stage progressive framework, OmniESI, for enzyme-substrate interaction prediction through conditional deep learning. By decomposing the modeling of enzyme-substrate interactions into a two-stage progressive process, OmniESI incorporates two conditional networks that respectively emphasize enzymatic reaction specificity and crucial catalysis-related interactions, facilitating a gradual feature modulation in the latent space from general protein-molecule domain to catalysis-aware domain. On top of this unified architecture, OmniESI can adapt to a variety of downstream tasks, including enzyme kinetic parameter prediction, enzyme-substrate pairing prediction, enzyme mutational effect prediction, and enzymatic active site annotation. Under the multi-perspective performance evaluation of in-distribution and out-of-distribution settings, OmniESI consistently delivered superior performance than state-of-the-art specialized methods across seven benchmarks. More importantly, the proposed conditional networks were shown to internalize the fundamental patterns of catalytic efficiency while significantly improving prediction performance, with only negligible parameter increases (0.16%), as demonstrated by ablation studies on key components. Overall, OmniESI represents a unified predictive approach for enzyme-substrate interactions, providing an effective tool for catalytic mechanism cracking and enzyme engineering with strong generalization and broad applicability.

This paper introduces an Unmanned Aerial Vehicle - enabled content management architecture that is suitable for critical content access in communities of users that are communication-isolated during diverse types of disaster scenarios. The proposed architecture leverages a hybrid network of stationary anchor UAVs and mobile Micro-UAVs for ubiquitous content dissemination. The anchor UAVs are equipped with both vertical and lateral communication links, and they serve local users, while the mobile micro-ferrying UAVs extend coverage across communities with increased mobility. The focus is on developing a content dissemination system that dynamically learns optimal caching policies to maximize content availability. The core innovation is an adaptive content dissemination framework based on distributed Federated Multi-Armed Bandit learning. The goal is to optimize UAV content caching decisions based on geo-temporal content popularity and user demand variations. A Selective Caching Algorithm is also introduced to reduce redundant content replication by incorporating inter-UAV information sharing. This method strategically preserves the uniqueness in user preferences while amalgamating the intelligence across a distributed learning system. This approach improves the learning algorithm's ability to adapt to diverse user preferences. Functional verification and performance evaluation confirm the proposed architecture's utility across different network sizes, UAV swarms, and content popularity patterns.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: \textit{de novo} molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at \url{https://github.com/pluskal-lab/MassSpecGym}.