Understanding the spatial architecture of the tumor microenvironment (TME) is critical to advance precision oncology. We present ProteinPNet, a novel framework based on prototypical part networks that discovers TME motifs from spatial proteomics data. Unlike traditional post-hoc explanability models, ProteinPNet directly learns discriminative, interpretable, faithful spatial prototypes through supervised training. We validate our approach on synthetic datasets with ground truth motifs, and further test it on a real-world lung cancer spatial proteomics dataset. ProteinPNet consistently identifies biologically meaningful prototypes aligned with different tumor subtypes. Through graphical and morphological analyses, we show that these prototypes capture interpretable features pointing to differences in immune infiltration and tissue modularity. Our results highlight the potential of prototype-based learning to reveal interpretable spatial biomarkers within the TME, with implications for mechanistic discovery in spatial omics.

Quantum error correction is essential for fault-tolerant quantum computing. However, standard methods relying on active measurements may introduce additional errors. Autonomous quantum error correction (AQEC) circumvents this by utilizing engineered dissipation and drives in bosonic systems, but identifying practical encoding remains challenging due to stringent Knill-Laflamme conditions. In this work, we utilize curriculum learning enabled deep reinforcement learning to discover Bosonic codes under approximate AQEC framework to resist both single-photon and double-photon losses. We present an analytical solution of solving the master equation under approximation conditions, which can significantly accelerate the training process of reinforcement learning. The agent first identifies an encoded subspace surpassing the breakeven point through rapid exploration within a constrained evolutionary time-frame, then strategically fine-tunes its policy to sustain this performance advantage over extended temporal horizons. We find that the two-phase trained agent can discover the optimal set of codewords, i.e., the Fock states $\ket{4}$ and $\ket{7}$ considering the effect of both single-photon and double-photon loss. We identify that the discovered code surpasses the breakeven threshold over a longer evolution time and achieve the state-of-art performance. We also analyze the robustness of the code against the phase damping and amplitude damping noise. Our work highlights the potential of curriculum learning enabled deep reinforcement learning in discovering the optimal quantum error correct code especially in early fault-tolerant quantum systems.

Research in Neuroscience, as in many scientific disciplines, is undergoing a renaissance based on deep learning.

The application of causal discovery to diseases like Alzheimer's (AD) is limited by the static graph assumptions of most methods; such models cannot account for an evolving pathophysiology, modulated by a latent disease pseudotime. We propose to apply an existing latent variable model to real-world AD data, inferring a pseudotime that orders patients along a data-driven disease trajectory independent of chronological age, then learning how causal relationships evolve. Pseudotime outperformed age in predicting diagnosis (AUC 0.82 vs 0.59). Incorporating minimal, disease-agnostic background knowledge substantially improved graph accuracy and orientation. Our framework reveals dynamic interactions between novel (NfL, GFAP) and established AD markers, enabling practical causal discovery despite violated assumptions.

Machine-learned force fields (MLFFs), especially pre-trained foundation models, are transforming computational materials science by enabling ab initio-level accuracy at molecular dynamics scales. Yet their rapid rise raises a key question: should researchers train specialist models from scratch, fine-tune generalist foundation models, or use hybrid approaches? The trade-offs in data efficiency, accuracy, cost, and robustness to out-of-distribution failure remain unclear. We introduce a benchmarking framework using defect migration pathways, evaluated through nudged elastic band trajectories, as diagnostic probes that test both interpolation and extrapolation. Using Cr-doped Sb2Te3 as a representative two-dimensional material, we benchmark multiple training paradigms within the MACE architecture across equilibrium, kinetic (atomic migration), and mechanical (interlayer sliding) tasks. Fine-tuned models substantially outperform from-scratch and zero-shot approaches for kinetic properties but show partial loss of long-range physics. Representational analysis reveals distinct, non-overlapping latent encodings, indicating that different training strategies learn different aspects of system physics. This framework provides practical guidelines for MLFF development and establishes migration-based probes as efficient diagnostics linking performance to learned representations, guiding future uncertainty-aware active learning.

Computational drug repurposing for rare diseases is especially challenging when no prior associations exist between drugs and target diseases. Therefore, knowledge graph completion and message-passing GNNs have little reliable signal to learn and propagate, resulting in poor performance. We present RareAgent, a self-evolving multi-agent system that reframes this task from passive pattern recognition to active evidence-seeking reasoning. RareAgent organizes task-specific adversarial debates in which agents dynamically construct evidence graphs from diverse perspectives to support, refute, or entail hypotheses. The reasoning strategies are analyzed post hoc in a self-evolutionary loop, producing textual feedback that refines agent policies, while successful reasoning paths are distilled into transferable heuristics to accelerate future investigations. Comprehensive evaluations reveal that RareAgent improves the indication AUPRC by 18.1% over reasoning baselines and provides a transparent reasoning chain consistent with clinical evidence.

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p $<$ 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

The optical transparent layers, which are trained with an online training approach, backpropagating the error to the analytical model of the system, are passive and kept the same across different steps of denoising.

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.