Neurological conditions, such as Alzheimer's Disease, are challenging to diagnose, particularly in the early stages where symptoms closely resemble healthy controls. Existing brain network analysis methods primarily focus on graph-based models that rely solely on imaging data, which may overlook important non-imaging factors and limit the model's predictive power and interpretability. In this paper, we present BrainPrompt, an innovative framework that enhances Graph Neural Networks (GNNs) by integrating Large Language Models (LLMs) with knowledge-driven prompts, enabling more effective capture of complex, non-imaging information and external knowledge for neurological disease identification. BrainPrompt integrates three types of knowledge-driven prompts: (1) ROI-level prompts to encode the identity and function of each brain region, (2) subject-level prompts that incorporate demographic information, and (3) disease-level prompts to capture the temporal progression of disease. By leveraging these multi-level prompts, BrainPrompt effectively harnesses knowledge-enhanced multi-modal information from LLMs, enhancing the model's capability to predict neurological disease stages and meanwhile offers more interpretable results. We evaluate BrainPrompt on two resting-state functional Magnetic Resonance Imaging (fMRI) datasets from neurological disorders, showing its superiority over state-of-the-art methods. Additionally, a biomarker study demonstrates the framework's ability to extract valuable and interpretable information aligned with domain knowledge in neuroscience.

Drug discovery requires a tremendous amount of time and cost. Computational drug-target interaction prediction, a significant part of this process, can reduce these requirements by narrowing the search space for wet lab experiments. In this survey, we provide comprehensive details of graph machine learning-based methods in predicting drug-target interaction, as they have shown promising results in this field. These details include the overall framework, main contribution, datasets, and their source codes. The selected papers were mainly published from 2020 to 2024. Prior to discussing papers, we briefly introduce the datasets commonly used with these methods and measurements to assess their performance. Finally, future challenges and some crucial areas that need to be explored are discussed.

We introduce SLiM-Gym, a Python package for integrating reinforcement learning (RL) with forward-time population genetic simulations. Wright-Fisher evolutionary dynamics offer a tractable framework for modeling populations across discrete generations, yet applying RL to these systems requires a compatible training environment. SLiM-Gym connects the standardized RL interface provided by Gymnasium with the high-fidelity evolutionary simulations of SLiM, allowing agents to interact with evolving populations in real time. This framework enables the development and evaluation of RL-based strategies for understanding evolutionary processes.

The de novo design of proteins refers to creating proteins with specific structures and functions that do not naturally exist. In recent years, the accumulation of high-quality protein structure and sequence data and technological advancements have paved the way for the successful application of generative artificial intelligence (AI) models in protein design. These models have surpassed traditional approaches that rely on fragments and bioinformatics. They have significantly enhanced the success rate of de novo protein design, and reduced experimental costs, leading to breakthroughs in the field. Among various generative AI models, diffusion models have yielded the most promising results in protein design. In the past two to three years, more than ten protein design models based on diffusion models have emerged. Among them, the representative model, RFDiffusion, has demonstrated success rates in 25 protein design tasks that far exceed those of traditional methods, and other AI-based approaches like RFjoint and hallucination. This review will systematically examine the application of diffusion models in generating protein backbones and sequences. We will explore the strengths and limitations of different models, summarize successful cases of protein design using diffusion models, and discuss future development directions.

Existing depression screening predominantly relies on standardized questionnaires (e.g., PHQ-9, BDI), which suffer from high misdiagnosis rates (18-34% in clinical studies) due to their static, symptom-counting nature and susceptibility to patient recall bias. This paper presents an AI-powered depression prevention system that leverages large language models (LLMs) to analyze real-time conversational cues--including subtle emotional expressions (e.g., micro-sentiment shifts, self-referential language patterns)--for more accurate and dynamic mental state assessment. Our system achieves three key innovations: (1) Continuous monitoring through natural dialogue, detecting depression-indicative linguistic features (anhedonia markers, hopelessness semantics) with 89% precision (vs. 72% for PHQ-9); (2) Adaptive risk stratification that updates severity levels based on conversational context, reducing false positives by 41% compared to scale-based thresholds; and (3) Personalized intervention strategies tailored to users' emotional granularity, demonstrating 2.3x higher adherence rates than generic advice. Clinical validation with 450 participants shows the system identifies 92% of at-risk cases missed by traditional scales, while its explainable AI interface bridges the gap between automated analysis and clinician judgment. This work establishes conversational AI as a paradigm shift from episodic scale-dependent diagnosis to continuous, emotionally intelligent mental health monitoring.

Background: Morbid obesity is associated with metabolic alterations and the onset of type 2 diabetes. Patients who undergo a malabsorptive bariatric surgery show an important improvement in several clinical variables and a modification in the gut microbiota balance. In this study, we aimed to identify bacteria related to changes in the body mass index of patients who underwent a bariatric surgery and their relationship with nutrients intake. Results: There were differences in bacterial diversity in the gut microbiota of patients that underwent a bariatric surgery. The Shannon and Simpson indexes decrease after the surgery (p < 0.001) and the beta diversity indexes (Bray-Curtis, Weighted and Unweighted UniFrac) showed differences when comparing pre- and post-surgery (p = 0.001). The abundance of a species in the genus Coprococcus correlated positively with the intake of magnesium and thiamin in post-surgery individuals (rho = 0.816, pFDR = 0.029 and rho = 0.812, pFDR = 0.029, respectively) and was related to BMI in both groups (p = 0.043 pre-surgery and p = 0.036 post-surgery). The abundances of several bacteria belonging to the order Clostridiales, as well as an enrichment of vitamin B1 (thiamin) biosynthesis, sugar degradation, acetate production and some amino acids biosynthesis were higher before the surgery. Conclusions: The abundance of a species of the genus Coprococcus that showed inverse relationships with BMI in pre-surgery and post-surgery patients correlates with the intake of magnesium and thiamin in individuals that underwent a malabsorptive bariatric surgery. It indicates that the well-established beneficial effects of bariatric surgery on BMI may be amplified by modulating the intake of micronutrients and its effect on the gut bacterial.

We propose a model of the functional architecture of curvature sensible cells in the visual cortex that associates curvature with scale. The feature space of orientation and position is naturally enhanced via its oriented prolongation, yielding a 4-dimensional manifold endowed with a canonical Engel structure. This structure encodes position, orientation, signed curvature, and scale. We associate an open submanifold of the prolongation with the quasi-regular representation of the similitude group SIM (2), and find left-invariant generators for the Engel structure. Finally, we use the generators of the Engel structure to characterize curvature-sensitive receptive profiles .

The ability to make zero-shot predictions about the fitness consequences of protein sequence changes with pre-trained machine learning models enables many practical applications. Such models can be applied for downstream tasks like genetic variant interpretation and protein engineering without additional labeled data. The advent of capable protein structure prediction tools has led to the availability of orders of magnitude more precomputed predicted structures, giving rise to powerful structure-based fitness prediction models. Through our experiments, we assess several modeling choices for structure-based models and their effects on downstream fitness prediction. Zero-shot fitness prediction models can struggle to assess the fitness landscape within disordered regions of proteins, those that lack a fixed 3D structure. We confirm the importance of matching protein structures to fitness assays and find that predicted structures for disordered regions can be misleading and affect predictive performance. Lastly, we evaluate an additional structure-based model on the ProteinGym substitution benchmark and show that simple multi-modal ensembles are strong baselines.

Decoding behavior, such as movement, from multiscale brain networks remains a central objective in neuroscience. Over the past decades, artificial intelligence and machine learning have played an increasingly significant role in elucidating the neural mechanisms underlying motor function. The advancement of brain-monitoring technologies, capable of capturing complex neuronal signals with high spatial and temporal resolution, necessitates the development and application of more sophisticated machine learning models for behavioral decoding. In this study, we employ a hybrid deep learning framework, an attention-based CNN-BiLSTM model, to decode skilled and complex forelimb movements using signals obtained from in vivo two-photon calcium imaging. Our findings demonstrate that the intricate movements of both ipsilateral and contralateral forelimbs can be accurately decoded from unilateral M1 neuronal ensembles. These results highlight the efficacy of advanced hybrid deep learning models in capturing the spatiotemporal dependencies of neuronal networks activity linked to complex movement execution.

How can we make sense of large-scale recordings of neural activity across learning? Theories of neural network learning with their origins in statistical physics offer a potential answer: for a given task, there are often a small set of summary statistics that are sufficient to predict performance as the network learns. Here, we review recent advances in how summary statistics can be used to build theoretical understanding of neural network learning. We then argue for how this perspective can inform the analysis of neural data, enabling better understanding of learning in biological and artificial neural networks.

In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of unlabeled and labeled time-consistent galled trees. We present a new derivation via the symbolic method of the number of unlabeled time-consistent galled trees with a fixed number of leaves and a fixed number of galls. We also derive new generating functions and asymptotics for labeled time-consistent galled trees.

Understanding the dynamics of excitation patterns in neural fields is an important topic in neuroscience. Neural field equations are mathematical models that describe the excitation dynamics of interacting neurons to perform the theoretical analysis. Although many analyses of neural field equations focus on the effect of neuronal interactions on the flat surface, the geometric constraint of the dynamics is also an attractive topic when modeling organs such as the brain. This paper reports pattern dynamics in a neural field equation defined on spheroids as model curved surfaces. We treat spot solutions as localized patterns and discuss how the geometric properties of the curved surface change their properties. To analyze spot patterns on spheroids with small flattening, we first construct exact stationary spot solutions on the spherical surface and reveal their stability. We then extend the analysis to show the existence and stability of stationary spot solutions in the spheroidal case. One of our theoretical results is the derivation of a stability criterion for stationary spot solutions localized at poles on oblate spheroids. The criterion determines whether a spot solution remains at a pole or moves away. Finally, we conduct numerical simulations to discuss the dynamics of spot solutions with the insight of our theoretical predictions. Our results show that the dynamics of spot solutions depend on the curved surface and the coordination of neural interactions.

Understanding nonlinear social contagion dynamics on dynamical networks, such as opinion formation, is crucial for gaining new insights into consensus and polarization. Similar to threshold-dependent complex contagions, the nonlinearity in adoption rates poses challenges for mean-field approximations. To address this theoretical gap, we focus on nonlinear binary-opinion dynamics on dynamical networks and analytically derive local configurations, specifically the distribution of opinions within any given focal individual's neighborhood. This exact local configuration of opinions, combined with network degree distributions, allows us to obtain exact solutions for consensus times and evolutionary trajectories. Our counterintuitive results reveal that neither biased assimilation (i.e., nonlinear adoption rates) nor preferences in local network rewiring -- such as in-group bias (preferring like-minded individuals) and the Matthew effect (preferring social hubs) -- can significantly slow down consensus. Among these three social factors, we find that biased assimilation is the most influential in accelerating consensus. Furthermore, our analytical method efficiently and precisely predicts the evolutionary trajectories of adoption curves arising from nonlinear contagion dynamics. Our work paves the way for enabling analytical predictions for general nonlinear contagion dynamics beyond opinion formation.

In neuroscience research, achieving single-neuron matching across different imaging modalities is critical for understanding the relationship between neuronal structure and function. However, modality gaps and limited annotations present significant challenges. We propose a few-shot metric learning method with a dual-channel attention mechanism and a pretrained vision transformer to enable robust cross-modal neuron identification. The local and global channels extract soma morphology and fiber context, respectively, and a gating mechanism fuses their outputs. To enhance the model's fine-grained discrimination capability, we introduce a hard sample mining strategy based on the MultiSimilarityMiner algorithm, along with the Circle Loss function. Experiments on two-photon and fMOST datasets demonstrate superior Top-K accuracy and recall compared to existing methods. Ablation studies and t-SNE visualizations validate the effectiveness of each module. The method also achieves a favorable trade-off between accuracy and training efficiency under different fine-tuning strategies. These results suggest that the proposed approach offers a promising technical solution for accurate single-cell level matching and multimodal neuroimaging integration.

Modeling the joint distribution of the data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic capabilities reaching beyond purely generative or predictive models. However, training joint models presents daunting architectural and optimization challenges. Here, we propose Hyformer, a transformer-based joint model that successfully blends the generative and predictive functionalities, using an alternating attention mask together with a unified pre-training scheme. We show that Hyformer rivals other joint models, as well as state-of-the-art molecule generation and property prediction models. Additionally, we show the benefits of joint modeling in downstream tasks of molecular representation learning, hit identification and antimicrobial peptide design.

Dissolution Dynamic Nuclear Polarisation (dDNP) is an experimental technique that increases the sensitivity of magnetic resonance experiments by more than a factor of $10^5$, permitting isotopically-labelled molecules to be transiently visible in MRI scans with their biochemical fates spatially resolvable over time following injection into a patient. dDNP requires a source of unpaired electrons to be in contact with the isotope-labelled nuclei, cooled to temperatures close to absolute zero, and spin-pumped into a given state by microwave irradiation. At present, these electrons are typically provided by chemical radicals which require removal by filtration prior to injection into humans. Alternative sources include UV irradiation, requiring storing samples in liquid nitrogen, or cobalt-60 gamma irradiation, which requires days and generates polarisation two to three orders of magnitude lower than chemical radicals. In this study, we present ultra-high dose rate electron beam irradiation as a novel alternative for generating non-persistent radicals in glycerol/alanine mixtures. These radicals are stable for months at room temperature, are present at concentrations dependent on irradiation dose, and generate comparable nuclear polarisation to the typically used trityl radicals (20%) through a novel mechanism. The process of their generation inherently sterilises samples, and they enable the imaging of alanine metabolism in vivo using dDNP. This new method of generating radicals for dDNP offers the potential to report on relevant biological processes while being translatable to the clinic.