Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys considered candidate PFMs is key because it determines the most stable arrangement of atoms within the alloy, directly influencing its phase stability, structural integrity, and thermo-mechanical properties. However, since the search space grows exponentially with the number of atoms considered, obtaining such MECs using computationally expensive first-principles DFT calculations often results in a cumbersome task. To escape the above compromise between physical fidelity and computational efficiency, we have developed a novel physics-based data-driven approach that combines Monte Carlo sampling, first-principles DFT calculations, and Machine Learning to accelerate the discovery of MECs in multi-component alloys. More specifically, we have leveraged well-established Cluster Expansion (CE) techniques with Local Outlier Factor models to establish strategies that enhance the reliability of the CE method. In this work, we demonstrated the capabilities of the proposed approach for the particular case of a tungsten-based quaternary high-entropy alloy. However, the method is applicable to other types of alloys and enables a wide range of applications.

Deep learning has the potential to revolutionize quantum chemistry as it is ideally suited to learn representations for structured data and speed up the exploration of chemical space. While convolutional neural networks have proven to be the first choice for images, audio and video data, the atoms in molecules are not restricted to a grid. Instead, their precise locations contain essential physical information, that would get lost if discretized. Thus, we propose to use continuousfilter convolutional layers to be able to model local correlations without requiring the data to lie on a grid. We apply those layers in SchNet: a novel deep learning architecture modeling quantum interactions in molecules. We obtain a joint model for the total energy and interatomic forces that follows fundamental quantumchemical principles. Our architecture achieves state-of-the-art performance for benchmarks of equilibrium molecules and molecular dynamics trajectories. Finally, we introduce a more challenging benchmark with chemical and structural variations that suggests the path for further work.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which directly incorporates functional group information into the representations. This strategic reduction in tokenization granularity is intentionally aligned with key drivers of functional properties (i.e., functional groups), enhancing the model's understanding of chemical language. By expanding the chemical lexicon, FARM more effectively bridges SMILES and natural language, ultimately advancing the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research. Artificial intelligence (AI) has emerged as a transformative tool in accelerating scientific discovery, particularly in drug development. However, one of the central challenges in this field is the scarcity of large labeled datasets required for traditional supervised learning methods. This has shifted the focus towards self-supervised pre-trained models that can extract meaningful patterns from vast amounts of unlabeled molecular data (Shen & Nicolaou, 2019). As a result, the development of robust foundation models for molecular representations is now more critical than ever. Despite significant advancements in other domains, such as natural language processing (NLP) and computer vision, there is still no dominant foundation model tailored to molecular representation in drug discovery (Zhang et al., 2023b). This paper begins to address this pressing gap by introducing an innovative approach that leverages functional group (FG)-aware tokenization in the context of both sequence-based and graph-based molecular representations.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

In the last few years, the formulation of real-world optimization problems and their efficient solution via metaheuristic algorithms has been a catalyst for a myriad of research studies. In spite of decades of historical advancements on the design and use of metaheuristics, large difficulties still remain in regards to the understandability, algorithmic design uprightness, and performance verifiability of new technical achievements. A clear example stems from the scarce replicability of works dealing with metaheuristics used for optimization, which is often infeasible due to ambiguity and lack of detail in the presentation of the methods to be reproduced. Additionally, in many cases, there is a questionable statistical significance of their reported results. This work aims at providing the audience with a proposal of good practices which should be embraced when conducting studies about metaheuristics methods used for optimization in order to provide scientific rigor, value and transparency. To this end, we introduce a step by step methodology covering every research phase that should be followed when addressing this scientific field. Specifically, frequently overlooked yet crucial aspects and useful recommendations will be discussed in regards to the formulation of the problem, solution encoding, implementation of search operators, evaluation metrics, design of experiments, and considerations for real-world performance, among others. Finally, we will outline important considerations, challenges, and research directions for the success of newly developed optimization metaheuristics in their deployment and operation over real-world application environments.

Large language models (LLMs) have proven to be remarkably efficient, both across a wide range of natural language processing tasks and well beyond them. However, a comprehensive theoretical analysis of the origins of their impressive performance remains elusive. In this paper, we approach this challenging task by drawing an equivalence between generic autoregressive language models with vocabulary of size $T$ and context window of size $K$ and Markov chains defined on a finite state space of size $\mathcal{O}(T^K)$. We derive several surprising findings related to the existence of a stationary distribution of Markov chains that capture the inference power of LLMs, their speed of convergence to it, and the influence of the temperature on the latter. We then prove pre-training and in-context generalization bounds and show how the drawn equivalence allows us to enrich their interpretation. Finally, we illustrate our theoretical guarantees with experiments on several recent LLMs to highlight how they capture the behavior observed in practice.

Mechanisms are designed to perform functions in various fields. Often, there is no unique mechanism that performs a well-defined function. For example, vehicle suspensions are designed to improve driving performance and ride comfort, but different types are available depending on the environment. This variability in design makes performance comparison difficult. Additionally, the traditional design process is multi-step, gradually reducing the number of design candidates while performing costly analyses to meet target performance. Recently, AI models have been used to reduce the computational cost of FEA. However, there are limitations in data availability and different analysis environments, especially when transitioning from low-fidelity to high-fidelity analysis. In this paper, we propose a multi-fidelity design framework aimed at recommending optimal types and designs of mechanical mechanisms. As an application, vehicle suspension systems were selected, and several types were defined. For each type, mechanism parameters were generated and converted into 3D CAD models, followed by low-fidelity rigid body dynamic analysis under driving conditions. To effectively build a deep learning-based multi-fidelity surrogate model, the results of the low-fidelity analysis were analyzed using DBSCAN and sampled at 5% for high-cost flexible body dynamic analysis. After training the multi-fidelity model, a multi-objective optimization problem was formulated for the performance metrics of each suspension type. Finally, we recommend the optimal type and design based on the input to optimize ride comfort-related performance metrics. To validate the proposed methodology, we extracted basic design rules of Pareto solutions using data mining techniques. We also verified the effectiveness and applicability by comparing the results with those obtained from a conventional deep learning-based design process.

In this paper, we present a novel approach to coal mining question answering (QA) using large language models (LLMs) combined with tailored prompt engineering techniques. Coal mining is a complex, high-risk industry where accurate, context-aware information is critical for safe and efficient operations. Current QA systems struggle to handle the technical and dynamic nature of mining-related queries. To address these challenges, we propose a multi-turn prompt engineering framework designed to guide LLMs, such as GPT-4, in answering coal mining questions with higher precision and relevance. By breaking down complex queries into structured components, our approach allows LLMs to process nuanced technical information more effectively. We manually curated a dataset of 500 questions from real-world mining scenarios and evaluated the system's performance using both accuracy (ACC) and GPT-4-based scoring metrics. Experiments comparing ChatGPT, Claude2, and GPT-4 across baseline, chain-of-thought (CoT), and multi-turn prompting methods demonstrate that our method significantly improves both accuracy and contextual relevance, with an average accuracy improvement of 15-18\% and a notable increase in GPT-4 scores. The results show that our prompt-engineering approach provides a robust, adaptable solution for domain-specific question answering in high-stakes environments like coal mining.

In order to train agents that can quickly adapt to new objectives or reward functions, efficient unsupervised representation learning in sequential decision-making environments can be important. Frameworks such as the Exogenous Block Markov Decision Process (Ex-BMDP) have been proposed to formalize this representation-learning problem (Efroni et al., 2022b). In the Ex-BMDP framework, the agent's high-dimensional observations of the environment have two latent factors: a controllable factor, which evolves deterministically within a small state space according to the agent's actions, and an exogenous factor, which represents time-correlated noise, and can be highly complex. The goal of the representation learning problem is to learn an encoder that maps from observations into the controllable latent space, as well as the dynamics of this space. Efroni et al. (2022b) has shown that this is possible with a sample complexity that depends only on the size of the controllable latent space, and not on the size of the noise factor. However, this prior work has focused on the episodic setting, where the controllable latent state resets to a specific start state after a finite horizon. By contrast, if the agent can only interact with the environment in a single continuous trajectory, prior works have not established sample-complexity bounds. We propose STEEL, the first provably sample-efficient algorithm for learning the controllable dynamics of an Ex-BMDP from a single trajectory, in the function approximation setting. STEEL has a sample complexity that depends only on the sizes of the controllable latent space and the encoder function class, and (at worst linearly) on the mixing time of the exogenous noise factor. We prove that STEEL is correct and sample-efficient, and demonstrate STEEL on two toy problems. Code is available at: https://github.com/midi-lab/steel.