Agentic AI "scientists" now use language models to search the literature, run analyses, and generate hypotheses. We evaluate KOSMOS, an autonomous AI scientist, on three problems in radiation biology using simple random-gene null benchmarks. Hypothesis 1: baseline DNA damage response (DDR) capacity across cell lines predicts the p53 transcriptional response after irradiation (GSE30240). Hypothesis 2: baseline expression of OGT and CDO1 predicts the strength of repressed and induced radiation-response modules in breast cancer cells (GSE59732). Hypothesis 3: a 12-gene expression signature predicts biochemical recurrence-free survival after prostate radiotherapy plus androgen deprivation therapy (GSE116918). The DDR-p53 hypothesis was not supported: DDR score and p53 response were weakly negatively correlated (Spearman rho = -0.40, p = 0.76), indistinguishable from random five-gene scores. OGT showed only a weak association (r = 0.23, p = 0.34), whereas CDO1 was a clear outlier (r = 0.70, empirical p = 0.0039). The 12-gene signature achieved a concordance index of 0.61 (p = 0.017) but a non-unique effect size. Overall, KOSMOS produced one well-supported discovery, one plausible but uncertain result, and one false hypothesis, illustrating that AI scientists can generate useful ideas but require rigorous auditing against appropriate null models.

Understanding the decision of large deep learning models is a critical challenge for building transparent and trustworthy systems. Although the current post hoc explanation methods offer valuable insights into feature importance, they are inherently disconnected from the model training process, limiting their faithfulness and utility. In this work, we introduce a novel differentiable approach to global ex-plainability by design, integrating feature importance estimation directly into model training. Central to our method is the ScoresActivation function, a feature-ranking mechanism embedded within the learning pipeline. This integration enables models to prioritize features according to their contribution to predictive performance in a differentiable and end-to-end trainable manner. Evaluations across benchmark datasets show that our approach yields globally faithful, stable feature rankings aligned with SHAP values and ground-truth feature importance, while maintaining high predictive performance. Moreover, feature scoring is 150 times faster than the classical SHAP method, requiring only 2 seconds during training compared to SHAP's 300 seconds for feature ranking in the same configuration. Our method also improves classification accuracy by 11.24% with 10 features (5 relevant) and 29.33% with 16 features (5 relevant, 11 irrelevant), demonstrating robustness to irrelevant inputs.

A classifier using byte n-grams as features is the only approach we have found fast enough to meet requirements in size (sub 2 MB), speed (multiple GB/s), and latency (sub 10 ms) for deployment in numerous malware detection scenarios. However, we've consistently found that 6-8 grams achieve the best accuracy on our production deployments but have been unable to deploy regularly updated models due to the high cost of finding the top-k most frequent n-grams over terabytes of executable programs. Because the Zipfian distribution well models the distribution of n-grams, we exploit its properties to develop a new top-k n-gram extractor that is up to $35\times$ faster than the previous best alternative. Using our new Zipf-Gramming algorithm, we are able to scale up our production training set and obtain up to 30\% improvement in AUC at detecting new malware. We show theoretically and empirically that our approach will select the top-k items with little error and the interplay between theory and engineering required to achieve these results.

This paper describes the experiences and lessons learned after the deployment of a country-scale environmental digital twin on the island of Cyprus for three years. This digital twin, called GAEA, contains 27 environmental geospatial services and is suitable for urban planners, policymakers, farmers, property owners, real-estate and forestry professionals, as well as insurance companies and banks that have properties in their portfolio. This paper demonstrates the power, potential, current and future challenges of geospatial analytics and environmental digital twins on a large scale.

Microbial Fuel Cells (MFCs) offer a promising pathway for sustainable energy generation by converting organic matter into electricity through microbial processes. A key factor influencing MFC performance is the anode structure, where design and material properties play a crucial role. Existing predictive models struggle to capture the complex geometric dependencies necessary to optimize these structures. To solve this problem, we propose KANGURA: Kolmogorov-Arnold Network-Based Geometry-Aware Learning with Unified Representation Attention. KANGURA introduces a new approach to three-dimensional (3D) machine learning modeling. It formulates prediction as a function decomposition problem, where Kolmogorov-Arnold Network (KAN)- based representation learning reconstructs geometric relationships without a conventional multi- layer perceptron (MLP). To refine spatial understanding, geometry-disentangled representation learning separates structural variations into interpretable components, while unified attention mechanisms dynamically enhance critical geometric regions. Experimental results demonstrate that KANGURA outperforms over 15 state-of-the-art (SOTA) models on the ModelNet40 benchmark dataset, achieving 92.7% accuracy, and excels in a real-world MFC anode structure problem with 97% accuracy. This establishes KANGURA as a robust framework for 3D geometric modeling, unlocking new possibilities for optimizing complex structures in advanced manufacturing and quality-driven engineering applications.

Human Immunodeficiency Virus (HIV) has posed a major global health challenge for decades, and forecasting HIV diagnoses continues to be a critical area of research. However, capturing the complex spatial and temporal dependencies of HIV transmission remains challenging. Conventional Message Passing Neural Network (MPNN) models rely on a fixed binary adjacency matrix that only encodes geographic adjacency, which is unable to represent interactions between non-contiguous counties. Our study proposes a deep learning architecture Mobility-Aware Transformer-Message Passing Neural Network (MAT-MPNN) framework to predict county-level HIV diagnosis rates across California, Florida, and the New England region. The model combines temporal features extracted by a Transformer encoder with spatial relationships captured through a Mobility Graph Generator (MGG). The MGG improves conventional adjacency matrices by combining geographic and demographic information. Compared with the best-performing hybrid baseline, the Transformer MPNN model, MAT-MPNN reduced the Mean Squared Prediction Error (MSPE) by 27.9% in Florida, 39.1% in California, and 12.5% in New England, and improved the Predictive Model Choice Criterion (PMCC) by 7.7%, 3.5%, and 3.9%, respectively. MAT-MPNN also achieved better results than the Spatially Varying Auto-Regressive (SVAR) model in Florida and New England, with comparable performance in California. These results demonstrate that applying mobility-aware dynamic spatial structures substantially enhances predictive accuracy and calibration in spatiotemporal epidemiological prediction.

Real - time crash detection is essential for developing proactive safety management strategy and enhancing overall traffic efficien cy . To address the limitations associated with trajectory acquisition and vehicle tracki ng, road segment maps recording the individual - level traffic dynamic data were di rectly served in crash detection. A novel two - stage trajectory - free crash detection framework, was present to generate the rational future road segment map and identify crashe s. The first - stage diffusion - based segment map generation model, Mapfusion, conducts a noisy - to - normal process that progressively adds noise to the road segment map until the map is corrupted to pure Gaussian noise. The denoising process is guided by seque ntial embedding c omponent s capturing the temporal dynamics of segment map sequence s . Furthermore, the generation model is designed to incorporate background context through ControlNet to enhance generation control. Crash detection is achieved by comparing the monitored segment map with the generat ions f rom diffusion model in second stage . Trained on non - crash vehicle motion data, Mapfusion successfully generates realistic road segment evolution maps based on learned motion patterns and remains robust across different sampling intervals . Experiments on real - world crashes indicate the effectiveness of the proposed two - stage method in accurately detecting crashes .

Avoiding bias and understanding the real-world consequences of AI-supported decision-making are critical to address fairness and assign accountability. Existing approaches often focus either on technical aspects, such as datasets and models, or on high-level socio-ethical considerations - rarely capturing how these elements interact in practice. In this paper, we apply an information flow-based modeling framework to a real-world recruitment process that integrates automated candidate matching with human decision-making. Through semi-structured stakeholder interviews and iterative modeling, we construct a multi-level representation of the recruitment pipeline, capturing how information is transformed, filtered, and interpreted across both algorithmic and human components. We identify where biases may emerge, how they can propagate through the system, and what downstream impacts they may have on candidates. This case study illustrates how information flow modeling can support structured analysis of fairness risks, providing transparency across complex socio-technical systems.

Proteins perform essential biological functions, and accurate classification of their sequences is critical for understanding structure-function relationships, enzyme mechanisms, and molecular interactions. This study presents a deep learning-based framework for functional group classification of protein sequences derived from the Protein Data Bank (PDB). Four architectures were implemented: Convolutional Neural Network (CNN), Bidirectional Long Short-Term Memory (BiLSTM), CNN-BiLSTM hybrid, and CNN with Attention. Each model was trained using k-mer integer encoding to capture both local and long-range dependencies. Among these, the CNN achieved the highest validation accuracy of 91.8%, demonstrating the effectiveness of localized motif detection. Explainable AI techniques, including Grad-CAM and Integrated Gradients, were applied to interpret model predictions and identify biologically meaningful sequence motifs. The discovered motifs, enriched in histidine, aspartate, glutamate, and lysine, represent amino acid residues commonly found in catalytic and metal-binding regions of transferase enzymes. These findings highlight that deep learning models can uncover functionally relevant biochemical signatures, bridging the gap between predictive accuracy and biological interpretability in protein sequence analysis.

Backdoor attacks pose a serious threat to the security of large language models (LLMs), causing them to exhibit anomalous behavior under specific trigger conditions. The design of backdoor triggers has evolved from fixed triggers to dynamic or implicit triggers. This increased flexibility in trigger design makes it challenging for defenders to identify their specific forms accurately. Most existing backdoor defense methods are limited to specific types of triggers or rely on an additional clean model for support. To address this issue, we propose a backdoor detection method based on attention similarity, enabling backdoor detection without prior knowledge of the trigger. Our study reveals that models subjected to backdoor attacks exhibit unusually high similarity among attention heads when exposed to triggers. Based on this observation, we propose an attention safety alignment approach combined with head-wise fine-tuning to rectify potentially contaminated attention heads, thereby effectively mitigating the impact of backdoor attacks. Extensive experimental results demonstrate that our method significantly reduces the success rate of backdoor attacks while preserving the model's performance on downstream tasks.