In this methods article, we provide a flexible but easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning, together with a tutorial on how to use it. The package \texttt{adabmDCA 2.0} is available in different programming languages (C++, Julia, Python) usable on different architectures (single-core and multi-core CPU, GPU) using a common front-end interface. In addition to several learning protocols for dense and sparse generative DCA models, it allows to directly address common downstream tasks like residue-residue contact prediction, mutational-effect prediction, scoring of sequence libraries and generation of artificial sequences for sequence design. It is readily applicable to protein and RNA sequence data.

Reinforcement Learning (RL) (Sutton and Barto, We tackle average-reward infinite-horizon 2018) tackles the sequential decision-making problem POMDPs with an unknown transition model of an agent interacting with an unknown or partially but a known observation model, a setting known environment with the goal of maximizing the that has been previously addressed in two long-term sum of rewards. The RL agent should tradeoff limiting ways: (i) frequentist methods relying between exploring the environment to learn its on suboptimal stochastic policies having structure and exploiting the estimates to compute a a minimum probability of choosing each action, policy that maximizes the reward. This problem has and (ii) Bayesian approaches employing been successfully addressed in past works under the the optimal policy class but requiring MDP formulation (Bartlett and Tewari, 2009; Jaksch strong assumptions about the consistency et al., 2010; Zanette and Brunskill, 2019). MDPs assume of employed estimators. Our work removes full observability of the state space but this assumption these limitations by proving convenient estimation is often violated in many real-world scenarios guarantees for the transition model such as robotics or finance, where only a partial and introducing an optimistic algorithm that observation of the environment is available. In this leverages the optimal class of deterministic case, it is more appropriate to model the problem using belief-based policies. We introduce modifications Partially-Observable MDPs (Sondik, 1978).

We address the problem of best policy identification in preference-based reinforcement learning (PbRL), where learning occurs from noisy binary preferences over trajectory pairs rather than explicit numerical rewards. This approach is useful for post-training optimization of generative AI models during multi-turn user interactions, where preference feedback is more robust than handcrafted reward models. In this setting, learning is driven by both an offline preference dataset -- collected from a rater of unknown 'competence' -- and online data collected with pure exploration. Since offline datasets may exhibit out-of-distribution (OOD) biases, principled online data collection is necessary. To address this, we propose Posterior Sampling for Preference Learning ($\mathsf{PSPL}$), a novel algorithm inspired by Top-Two Thompson Sampling, that maintains independent posteriors over the true reward model and transition dynamics. We provide the first theoretical guarantees for PbRL in this setting, establishing an upper bound on the simple Bayesian regret of $\mathsf{PSPL}$. Since the exact algorithm can be computationally impractical, we also provide an approximate version that outperforms existing baselines.

Large language models (LLMs) have significantly facilitated human life, and prompt engineering has improved the efficiency of these models. However, recent years have witnessed a rise in prompt engineering-empowered attacks, leading to issues such as privacy leaks, increased latency, and system resource wastage. Though safety fine-tuning based methods with Reinforcement Learning from Human Feedback (RLHF) are proposed to align the LLMs, existing security mechanisms fail to cope with fickle prompt attacks, highlighting the necessity of performing security detection on prompts. In this paper, we jointly consider prompt security, service latency, and system resource optimization in Edge-Cloud LLM (EC-LLM) systems under various prompt attacks. To enhance prompt security, a vector-database-enabled lightweight attack detector is proposed. We formalize the problem of joint prompt detection, latency, and resource optimization into a multi-stage dynamic Bayesian game model. The equilibrium strategy is determined by predicting the number of malicious tasks and updating beliefs at each stage through Bayesian updates. The proposed scheme is evaluated on a real implemented EC-LLM system, and the results demonstrate that our approach offers enhanced security, reduces the service latency for benign users, and decreases system resource consumption compared to state-of-the-art algorithms.

Lung cancer is a major issue in worldwide public health, requiring early diagnosis using stable techniques. This work begins a thorough investigation of the use of machine learning (ML) methods for precise classification of lung cancer stages. A cautious analysis is performed to overcome overfitting issues in model performance, taking into account minimum child weight and learning rate. A set of machine learning (ML) models including XGBoost (XGB), LGBM, Adaboost, Logistic Regression (LR), Decision Tree (DT), Random Forest (RF), CatBoost, and k-Nearest Neighbor (k-NN) are run methodically and contrasted. Furthermore, the correlation between features and targets is examined using the deep neural network (DNN) model and thus their capability in detecting complex patternsis established. It is argued that several ML models can be capable of classifying lung cancer stages with great accuracy. In spite of the complexity of DNN architectures, traditional ML models like XGBoost, LGBM, and Logistic Regression excel with superior performance. The models perform better than the others in lung cancer prediction on the complete set of comparative metrics like accuracy, precision, recall, and F-1 score

To generate accurate and reliable predictions, modern AI systems need to combine data from multiple modalities, such as text, images, audio, spreadsheets, and time series. Multi-modal data introduces new opportunities and challenges for disentangling uncertainty: it is commonly assumed in the machine learning community that epistemic uncertainty can be reduced by collecting more data, while aleatoric uncertainty is irreducible. However, this assumption is challenged in modern AI systems when information is obtained from different modalities. This paper introduces an innovative data acquisition framework where uncertainty disentanglement leads to actionable decisions, allowing sampling in two directions: sample size and data modality. The main hypothesis is that aleatoric uncertainty decreases as the number of modalities increases, while epistemic uncertainty decreases by collecting more observations. We provide proof-of-concept implementations on two multi-modal datasets to showcase our data acquisition framework, which combines ideas from active learning, active feature acquisition and uncertainty quantification.

In MOO, there is usually not a single optimal solution, but a range of so-called Pareto optimal or non-dominated Many real-world black-box optimization problems solutions with different trade-offs. A widely adopted approach have multiple conflicting objectives. Rather aims to search for a good representation of these than attempting to approximate the entire set of Pareto-optimal solutions by maximizing their hypervolume. Pareto-optimal solutions, interactive preference Two prominent methods stand out in this regard: ParEGO learning, i.e., optimization with a decision maker (Knowles, 2006), which employs random augmented Chebyshev in the loop, allows to focus the search on the scalarizations for optimization in each iteration, and most relevant subset. However, few previous studies expected hypervolume maximization (Yang et al., 2019; have exploited the fact that utility functions Daulton et al., 2020), which directly maximizes the hypervolume are usually monotonic.

Antibiotics are often grouped by their mechanisms of action, such as blocking protein synthesis, disrupting folate biosynthesis, changing cell wall construction, compromising the cell membrane integrity and affecting DNA replication [93, 25]. These antibiotics, whether created in labs or found in nature, serve as the primary defence against bacterial infections. However, bacteria employ a series of strategies in response to resist these antibiotics, including inactivating antibiotics through enzymatic degradation, altering the antibiotic target, modifying cell membrane permeability, and using efflux pumps to maintain intracellular antibiotic concentrations of antibiotics below inhibitory levels [25]. Moreover, the gene transfer of antibiotic-resistant bacteria (ARB) further aggravates this challenge [92].

Autonomous systems are increasingly expected to operate in the presence of adversaries, though an adversary may infer sensitive information simply by observing a system, without even needing to interact with it. Therefore, in this work we present a deceptive decision-making framework that not only conceals sensitive information, but in fact actively misleads adversaries about it. We model autonomous systems as Markov decision processes, and we consider adversaries that attempt to infer their reward functions using inverse reinforcement learning. To counter such efforts, we present two regularization strategies for policy synthesis problems that actively deceive an adversary about a system's underlying rewards. The first form of deception is ``diversionary'', and it leads an adversary to draw any false conclusion about what the system's reward function is. The second form of deception is ``targeted'', and it leads an adversary to draw a specific false conclusion about what the system's reward function is. We then show how each form of deception can be implemented in policy optimization problems, and we analytically bound the loss in total accumulated reward that is induced by deception. Next, we evaluate these developments in a multi-agent sequential decision-making problem with one real agent and multiple decoys. We show that diversionary deception can cause the adversary to believe that the most important agent is the least important, while attaining a total accumulated reward that is $98.83\%$ of its optimal, non-deceptive value. Similarly, we show that targeted deception can make any decoy appear to be the most important agent, while still attaining a total accumulated reward that is $99.25\%$ of its optimal, non-deceptive value.

Energy-based models (EBMs) offer a flexible framework for parameterizing probability distributions using neural networks. However, learning EBMs by exact maximum likelihood estimation (MLE) is generally intractable, due to the need to compute the partition function (normalization constant). In this paper, we propose a novel formulation for approximately learning probabilistic EBMs in combinatorially-large discrete spaces, such as sets or permutations. Our key idea is to jointly learn both an energy model and its log-partition, both parameterized as a neural network. Our approach not only provides a novel tractable objective criterion to learn EBMs by stochastic gradient descent (without relying on MCMC), but also a novel means to estimate the log-partition function on unseen data points. On the theoretical side, we show that our approach recovers the optimal MLE solution when optimizing in the space of continuous functions. Furthermore, we show that our approach naturally extends to the broader family of Fenchel-Young losses, allowing us to obtain the first tractable method for optimizing the sparsemax loss in combinatorially-large spaces. We demonstrate our approach on multilabel classification and label ranking.