Ligand strain energy, the energy difference between the bound and unbound conformations of a ligand, is an important component of structure-based small molecule drug design. A large majority of observed ligands in protein-small molecule co-crystal structures bind in low-strain conformations, making strain energy a useful filter for structure-based drug design. In this work we present a tool for calculating ligand strain with a high accuracy. StrainRelief uses a MACE Neural Network Potential (NNP), trained on a large database of Density Functional Theory (DFT) calculations to estimate ligand strain of neutral molecules with quantum accuracy. We show that this tool estimates strain energy differences relative to DFT to within 1.4 kcal/mol, more accurately than alternative NNPs. These results highlight the utility of NNPs in drug discovery, and provide a useful tool for drug discovery teams.

NLP models trained with differential privacy (DP) usually adopt the DP-SGD framework, and privacy guarantees are often reported in terms of the privacy budget $\epsilon$. However, $\epsilon$ does not have any intrinsic meaning, and it is generally not possible to compare across variants of the framework. Work in image processing has therefore explored how to empirically calibrate noise across frameworks using Membership Inference Attacks (MIAs). However, this kind of calibration has not been established for NLP. In this paper, we show that MIAs offer little help in calibrating privacy, whereas reconstruction attacks are more useful. As a use case, we define a novel kind of directional privacy based on the von Mises-Fisher (VMF) distribution, a metric DP mechanism that perturbs angular distance rather than adding (isotropic) Gaussian noise, and apply this to NLP architectures. We show that, even though formal guarantees are incomparable, empirical privacy calibration reveals that each mechanism has different areas of strength with respect to utility-privacy trade-offs.

Fire and smoke phenomena pose a significant threat to the natural environment, ecosystems, and global economy, as well as human lives and wildlife. In this particular circumstance, there is a demand for more sophisticated and advanced technologies to implement an effective strategy for early detection, real-time monitoring, and minimizing the overall impacts of fires on ecological balance and public safety. Recently, the rapid advancement of Artificial Intelligence (AI) and Computer Vision (CV) frameworks has substantially revolutionized the momentum for developing efficient fire management systems. However, these systems extensively rely on the availability of adequate and high-quality fire and smoke data to create proficient Machine Learning (ML) methods for various tasks, such as detection and monitoring. Although fire and smoke datasets play a critical role in training, evaluating, and testing advanced Deep Learning (DL) models, a comprehensive review of the existing datasets is still unexplored. For this purpose, we provide an in-depth review to systematically analyze and evaluate fire and smoke datasets collected over the past 20 years. We investigate the characteristics of each dataset, including type, size, format, collection methods, and geographical diversities. We also review and highlight the unique features of each dataset, such as imaging modalities (RGB, thermal, infrared) and their applicability for different fire management tasks (classification, segmentation, detection). Furthermore, we summarize the strengths and weaknesses of each dataset and discuss their potential for advancing research and technology in fire management. Ultimately, we conduct extensive experimental analyses across different datasets using several state-of-the-art algorithms, such as ResNet-50, DeepLab-V3, and YoloV8.

Biological signals, such as electroencephalograms (EEGs) and electrocardiograms (ECGs), play a pivotal role in numerous clinical practices, such as diagnosing brain and cardiac arrhythmic diseases. Existing methods for biosignal classification rely on Attention-based frameworks with dense Feed Forward layers, which lead to inefficient learning, high computational overhead, and suboptimal performance. In this work, we introduce BioMamba, a Spectro-Temporal Embedding strategy applied to the Bidirectional Mamba framework with Sparse Feed Forward layers to enable effective learning of biosignal sequences. By integrating these three key components, BioMamba effectively addresses the limitations of existing methods. Extensive experiments demonstrate that BioMamba significantly outperforms state-of-the-art methods with marked improvement in classification performance. The advantages of the proposed BioMamba include (1) Reliability: BioMamba consistently delivers robust results, confirmed across six evaluation metrics. (2) Efficiency: We assess both model and training efficiency, the BioMamba demonstrates computational effectiveness by reducing model size and resource consumption compared to existing approaches. (3) Generality: With the capacity to effectively classify a diverse set of tasks, BioMamba demonstrates adaptability and effectiveness across various domains and applications.

As large language models (LLMs) become increasingly capable, ensuring that their self-generated explanations are faithful to their internal decision-making process is critical for safety and oversight. In this work, we conduct a comprehensive counterfactual faithfulness analysis across 62 models from 8 families, encompassing both pretrained and instruction-tuned variants and significantly extending prior studies of counterfactual tests. We introduce phi-CCT, a simplified variant of the Correlational Counterfactual Test, which avoids the need for token probabilities while explaining most of the variance of the original test. Our findings reveal clear scaling trends: larger models are consistently more faithful on our metrics. However, when comparing instruction-tuned and human-imitated explanations, we find that observed differences in faithfulness can often be attributed to explanation verbosity, leading to shifts along the true-positive/false-positive Pareto frontier. While instruction-tuning and prompting can influence this trade-off, we find limited evidence that they fundamentally expand the frontier of explanatory faithfulness beyond what is achievable with pretrained models of comparable size. Our analysis highlights the nuanced relationship between instruction-tuning, verbosity, and the faithful representation of model decision processes.

Inpatient pathways demand complex clinical decision-making based on comprehensive patient information, posing critical challenges for clinicians. Despite advancements in large language models (LLMs) in medical applications, limited research focused on artificial intelligence (AI) inpatient pathways systems, due to the lack of large-scale inpatient datasets. Moreover, existing medical benchmarks typically concentrated on medical question-answering and examinations, ignoring the multifaceted nature of clinical decision-making in inpatient settings. To address these gaps, we first developed the Inpatient Pathway Decision Support (IPDS) benchmark from the MIMIC-IV database, encompassing 51,274 cases across nine triage departments and 17 major disease categories alongside 16 standardized treatment options. Then, we proposed the Multi-Agent Inpatient Pathways (MAP) framework to accomplish inpatient pathways with three clinical agents, including a triage agent managing the patient admission, a diagnosis agent serving as the primary decision maker at the department, and a treatment agent providing treatment plans. Additionally, our MAP framework includes a chief agent overseeing the inpatient pathways to guide and promote these three clinician agents. Extensive experiments showed our MAP improved the diagnosis accuracy by 25.10% compared to the state-of-the-art LLM HuatuoGPT2-13B. It is worth noting that our MAP demonstrated significant clinical compliance, outperforming three board-certified clinicians by 10%-12%, establishing a foundation for inpatient pathways systems.

We investigate the impact of robot appearance on users' spoken behavior during real-world interactions by comparing a human-like android, ERICA, with a less anthropomorphic humanoid, TELECO. Analyzing data from 42 participants at SIGDIAL 2024, we extracted linguistic features such as disfluencies and syntactic complexity from conversation transcripts. The results showed moderate effect sizes, suggesting that participants produced fewer disfluencies and employed more complex syntax when interacting with ERICA. Further analysis involving training classification models like Na\"ive Bayes, which achieved an F1-score of 71.60\%, and conducting feature importance analysis, highlighted the significant role of disfluencies and syntactic complexity in interactions with robots of varying human-like appearances. Discussing these findings within the frameworks of cognitive load and Communication Accommodation Theory, we conclude that designing robots to elicit more structured and fluent user speech can enhance their communicative alignment with humans.

An important goal in cancer research is the survival prognosis of a patient based on a minimal panel of genomic and molecular markers such as genes or proteins. Purely data-driven models without any biological knowledge can produce non-interpretable results. We propose a penalized semiparametric Bayesian Cox model with graph-structured selection priors for sparse identification of multi-omics features by making use of a biologically meaningful graph via a Markov random field (MRF) prior to capturing known relationships between multi-omics features. Since the fixed graph in the MRF prior is for the prior probability distribution, it is not a hard constraint to determine variable selection, so the proposed model can verify known information and has the potential to identify new and novel biomarkers for drawing new biological knowledge. Our simulation results show that the proposed Bayesian Cox model with graph-based prior knowledge results in more trustable and stable variable selection and non-inferior survival prediction, compared to methods modeling the covariates independently without any prior knowledge. The results also indicate that the performance of the proposed model is robust to a partially correct graph in the MRF prior, meaning that in a real setting where not all the true network information between covariates is known, the graph can still be useful. The proposed model is applied to the primary invasive breast cancer patients data in The Cancer Genome Atlas project.

Comprehensive forecasts of space tourism demand are crucial for businesses to optimize strategies and customer experiences in this burgeoning industry. Traditional methods struggle to capture the complex factors influencing an individual's decision to travel to space. In this paper, we propose an explainable and trustworthy artificial intelligence framework to address the challenge of predicting space tourism demand by following the National Institute of Standards and Technology guidelines. We develop a novel machine learning network, called SpaceNet, capable of learning wide-range dependencies in data and allowing us to analyze the relationships between various factors such as age, income, and risk tolerance. We investigate space travel demand in the US, categorizing it into four types: no travel, moon travel, suborbital, and orbital travel. To this end, we collected 1860 data points in many states and cities with different ages and then conducted our experiment with the data. From our experiments, the SpaceNet achieves an average ROC-AUC of 0.82 $\pm$ 0.088, indicating strong classification performance. Our investigation demonstrated that travel price, age, annual income, gender, and fatality probability are important features in deciding whether a person wants to travel or not. Beyond demand forecasting, we use explainable AI to provide interpretation for the travel-type decisions of an individual, offering insights into the factors driving interest in space travel, which is not possible with traditional classification methods. This knowledge enables businesses to tailor marketing strategies and optimize service offerings in this rapidly evolving market. To the best of our knowledge, this is the first work to implement an explainable and interpretable AI framework for investigating the factors influencing space tourism.

Despite extensive research efforts focused on OOD detection on images, OOD detection on nodes in graph learning remains underexplored. The dependence among graph nodes hinders the trivial adaptation of existing approaches on images that assume inputs to be i.i.d. sampled, since many unique features and challenges specific to graphs are not considered, such as the heterophily issue. Recently, GNNSafe, which considers node dependence, adapted energy-based detection to the graph domain with state-of-the-art performance, however, it has two serious issues: 1) it derives node energy from classification logits without specifically tailored training for modeling data distribution, making it less effective at recognizing OOD data; 2) it highly relies on energy propagation, which is based on homophily assumption and will cause significant performance degradation on heterophilic graphs, where the node tends to have dissimilar distribution with its neighbors. To address the above issues, we suggest training EBMs by MLE to enhance data distribution modeling and remove energy propagation to overcome the heterophily issues. However, training EBMs via MLE requires performing MCMC sampling on both node feature and node neighbors, which is challenging due to the node interdependence and discrete graph topology. To tackle the sampling challenge, we introduce DeGEM, which decomposes the learning process into two parts: a graph encoder that leverages topology information for node representations and an energy head that operates in latent space. Extensive experiments validate that DeGEM, without OOD exposure during training, surpasses previous state-of-the-art methods, achieving an average AUROC improvement of 6.71% on homophilic graphs and 20.29% on heterophilic graphs, and even outperform methods trained with OOD exposure. Our code is available at: https://github.com/draym28/DeGEM.