Abstract--Directed evolution is an iterative laboratory process of designing proteins with improved function by iteratively synthesizing new protein variants and evaluating their desired property with expensive and time-consuming biochemical screening. Machine learning methods can help select informative or promising variants for screening to increase their quality and reduce the amount of necessary screening. In this paper, we present a novel method for machine-learning-assisted directed evolution of proteins which combines Bayesian optimization with informative representation of protein variants extracted from a pre-trained protein language model. We demonstrate that the new representation based on the sequence embeddings significantly improves the performance of Bayesian optimization yielding better results with the same number of conducted screening in total. At the same time, our method outperforms the state-of-the-art machine-learning-assisted directed evolution methods with regression objective. Protein engineering (PE) is the process of designing proteins with desired properties, such as improved stability, catalytic function, or specific binding affinity [1]. PE can be leveraged in industrial applications, environmental applications, medicine, nanobiotechnology, and other fields [1]. Because the functional properties of proteins are determined by their sequence of amino acids [2], the task of PE translates to finding a sequence of amino acids with the desired properties/function.

This work presents a fully quantum approach to support vector machine (SVM) learning by integrating gate-based quantum kernel methods with quantum annealing-based optimization. We explore the construction of quantum kernels using various feature maps and qubit configurations, evaluating their suitability through Kernel-Target Alignment (KTA). The SVM dual problem is reformulated as a Quadratic Unconstrained Binary Optimization (QUBO) problem, enabling its solution via quantum annealers. Our experiments demonstrate that a high degree of alignment in the kernel and an appropriate regularization parameter lead to competitive performance, with the best model achieving an F1-score of 90%. These results highlight the feasibility of an end-to-end quantum learning pipeline and the potential of hybrid quantum architectures in quantum high-performance computing (QHPC) contexts.

Music adversarial attacks have garnered significant interest in the field of Music Information Retrieval (MIR). In this paper, we present Music Adversarial Inpainting Attack (MAIA), a novel adversarial attack framework that supports both white-box and black-box attack scenarios. MAIA begins with an importance analysis to identify critical audio segments, which are then targeted for modification. Utilizing generative inpainting models, these segments are reconstructed with guidance from the output of the attacked model, ensuring subtle and effective adversarial perturbations. We evaluate MAIA on multiple MIR tasks, demonstrating high attack success rates in both white-box and black-box settings while maintaining minimal perceptual distortion. Additionally, subjective listening tests confirm the high audio fidelity of the adversarial samples. Our findings highlight vulnerabilities in current MIR systems and emphasize the need for more robust and secure models.

Electronic Health Records (EHRs) provide a rich, longitudinal view of patient health and hold significant potential for advancing clinical decision support, risk prediction, and data-driven healthcare research. However, most artificial intelligence (AI) models for EHRs are designed for narrow, single-purpose tasks, limiting their generalizability and utility in real-world settings. Here, we present CEHR-XGPT, a general-purpose foundation model for EHR data that unifies three essential capabilities - feature representation, zero-shot prediction, and synthetic data generation - within a single architecture. To support temporal reasoning over clinical sequences, CEHR-XGPT incorporates a novel time-token-based learning framework that explicitly encodes patients' dynamic timelines into the model structure. CEHR-XGPT demonstrates strong performance across all three tasks and generalizes effectively to external datasets through vocabulary expansion and fine-tuning. Its versatility enables rapid model development, cohort discovery, and patient outcome forecasting without the need for task-specific retraining.

To avoid the featuri zation bottleneck of traditional descriptors, we also leverage GNNs to generate fast, latent-space approximations of MatMiner (ℓ-MM) and Orbital Field Matrix (ℓ-OFM) features. Finally, we augment this feature set with new descriptors derived via symbolic regression. This multifac eted strategy aims to create a more robust, accurate, and versatile featurizer that capitalizes on the distinct strengths of each approach to be useful for a wider range of dataset sizes. To simplify the generation of all those features, a package was developed named MatterVial standing for MATerials fea T uR e E xtraction Via I nterpretable Artificial L earning, which, besides producing all latent-space features from the GNN models, aids i n obtaining the interpretable chemical descriptors that correlate to these high-level features. This is achieved through techniques such as SHapley Additive exPlanations (SHAP) analysi s in surrogate models and symbolic regression via Sure Independence Screening and Sparsifying Operator (SISSO) to obtain an approximate formula from the most important features. Our re sults demonstrate an overall improvement in all analyzed datasets compare d with the baseline MatMiner featurizer. In addition, it surpassed the performance of the individua l GNN models in several cases, indicating that the combination of traditional and l atent-space features leads to a more robust generalization.

There is growing interest in understanding how people interact with large language models (LLMs) and whether such models elicit dependency or even addictive behaviour. Validated tools to assess the extent to which individuals may become dependent on LLMs are scarce and primarily build on classic behavioral addiction symptoms, adapted to the context of LLM use. We view this as a conceptual limitation, as the LLM-human relationship is more nuanced and warrants a fresh and distinct perspective. To address this gap, we developed and validated a new 12-item questionnaire to measure LLM dependency, referred to as LLM-D12. The scale was based on the authors' prior theoretical work, with items developed accordingly and responses collected from 526 participants in the UK. Exploratory and confirmatory factor analyses, performed on separate halves of the total sample using a split-sample approach, supported a two-factor structure: Instrumental Dependency (six items) and Relationship Dependency (six items). Instrumental Dependency reflects the extent to which individuals rely on LLMs to support or collaborate in decision-making and cognitive tasks. Relationship Dependency captures the tendency to perceive LLMs as socially meaningful, sentient, or companion-like entities. The two-factor structure demonstrated excellent internal consistency and clear discriminant validity. External validation confirmed both the conceptual foundation and the distinction between the two subscales. The psychometric properties and structure of our LLM-D12 scale were interpreted in light of the emerging view that dependency on LLMs does not necessarily indicate dysfunction but may still reflect reliance levels that could become problematic in certain contexts.

Autoregressive pre-trained models combined with decoding methods have achieved impressive performance on complex reasoning tasks. While mainstream decoding strategies such as beam search can generate plausible candidate sets, they often lack provable coverage guarantees, and struggle to effectively balance search efficiency with the need for versatile trajectories, particularly those involving long-tail sequences that are essential in certain real-world applications. To address these limitations, we propose \textsc{CoVeR}, a novel model-free decoding strategy wihtin the conformal prediction framework that simultaneously maintains a compact search space and ensures high coverage probability over desirable trajectories. Theoretically, we establish a PAC-style generalization bound, guaranteeing that \textsc{CoVeR} asymptotically achieves a coverage rate of at least $1 - α$ for any target level $α\in (0,1)$.

Digital maps play a crucial role in various applications such as navigation, fleet management, and ride-sharing, necessitating their accuracy and currency, which require timely updates. While the majority of geospatial databases (GDBs) provide high-quality information, their data is (i) limited to specific regions and/or (ii) missing some entities, even in their covered areas. Map conflation is the process of augmentation of a GDB using another GDB to conflate missing spatial features. Existing map conflation methods suffer from two main limitations: (1) They are designed for the conflation of linear objects (e.g., road networks) and cannot simply be extended to non-linear objects, thus missing information about most entities in the map. (2) They are heuristic algorithmic approaches that are based on pre-defined rules, unable to learn entities matching in a data-driven manner. To address these limitations, we design KRAFT, a learning based approach consisting of three parts: (1) Knowledge Graph Construction - where each GDB is represented by a knowledge graph, (2) Map Matching - where we use a knowledge graph alignment method as well as a geospatial feature encoder to match entities in obtained knowledge graphs, and (3) Map Merging - where we merge matched entities in the previous modules in a consistent manner, using a mixed integer linear programming formulation that fully merges the GDBs without adding any inconsistencies. Our experimental evaluation shows that not only does KRAFT achieve outstanding performance compared to state-of-the-art and baseline methods in map conflation tasks, but each of its modules (e.g., Map Matching and Map Merging) also separately outperforms traditional matching and merging methods.

Differential privacy (DP) is the standard for privacy-preserving analysis, and introduces a fundamental trade-off between privacy guarantees and model performance. Selecting the optimal balance is a critical challenge that can be framed as a multi-objective optimization (MOO) problem where one first discovers the set of optimal trade-offs (the Pareto front) and then learns a decision-maker's preference over them. While a rich body of work on interactive MOO exists, the standard approach -- modeling the objective functions with generic surrogates and learning preferences from simple pairwise feedback -- is inefficient for DP because it fails to leverage the problem's unique structure: a point on the Pareto front can be generated directly by maximizing accuracy for a fixed privacy level. Motivated by this property, we first derive the shape of the trade-off theoretically, which allows us to model the Pareto front directly and efficiently. To address inefficiency in preference learning, we replace pairwise comparisons with a more informative interaction. In particular, we present the user with hypothetical trade-off curves and ask them to pick their preferred trade-off. Our experiments on differentially private logistic regression and deep transfer learning across six real-world datasets show that our method converges to the optimal privacy-accuracy trade-off with significantly less computational cost and user interaction than baselines.

Sampling from unnormalized target distributions, e.g. Boltzmann distributions $μ_{\text{target}}(x) \propto \exp(-E(x)/T)$, is fundamental to many scientific applications yet computationally challenging due to complex, high-dimensional energy landscapes. Existing approaches applying modern generative models to Boltzmann distributions either require large datasets of samples drawn from the target distribution or, when using only energy evaluations for training, cannot efficiently leverage the expressivity of advanced architectures like continuous normalizing flows that have shown promise for molecular sampling. To address these shortcomings, we introduce Energy-Weighted Flow Matching (EWFM), a novel training objective enabling continuous normalizing flows to model Boltzmann distributions using only energy function evaluations. Our objective reformulates conditional flow matching via importance sampling, allowing training with samples from arbitrary proposal distributions. Based on this objective, we develop two algorithms: iterative EWFM (iEWFM), which progressively refines proposals through iterative training, and annealed EWFM (aEWFM), which additionally incorporates temperature annealing for challenging energy landscapes. On benchmark systems, including challenging 55-particle Lennard-Jones clusters, our algorithms demonstrate sample quality competitive with state-of-the-art energy-only methods while requiring up to three orders of magnitude fewer energy evaluations.