arXiv subjects

Philippe Schwaller

Publications and source records attributed to Philippe Schwaller.

At least 37 records · Page 2Linked to original sources

arXiv2025

Synthelite: Chemist-aligned and feasibility-aware synthesis planning with LLMs

Computer-aided synthesis planning (CASP) has long been envisioned as a complementary tool for synthetic chemists. However, existing frameworks often lack mechanisms to allow interaction with human experts, limiting their ability to integrate chemists' insights. In this work, we introduce Synthelite, a synthesis planning framework that uses large language models (LLMs) to directly propose retrosynthetic transformations. Synthelite can generate end-to-end synthesis routes by harnessing the intrinsic chemical knowledge and reasoning capabilities of LLMs, while allowing expert intervention through natural language prompts. Our experiments demonstrate that Synthelite can flexibly adapt its planning trajectory to diverse user-specified constraints, achieving up to 95\% success rates in both strategy-constrained and starting-material-constrained synthesis tasks. Additionally, Synthelite exhibits the ability to account for chemical feasibility during route design. We envision Synthelite to be both a useful tool and a step toward a paradigm where LLMs are the central orchestrators of synthesis planning.

cs.AI↗

arXiv2025

DynaMate: An Autonomous Agent for Protein-Ligand Molecular Dynamics Simulations

Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug discovery and protein engineering, the technical complexity of MD setup, encompassing parameterization, input preparation, and software configuration, remains a major barrier for widespread and efficient usage. Agentic LLMs have demonstrated their capacity to autonomously execute multi-step scientific processes, and to date, they have not successfully been used to automate protein-ligand MD workflows. Here, we present DynaMate, a modular multi-agent framework that autonomously designs and executes complete MD workflows for both protein and protein-ligand systems, and offers free energy binding affinity calculations with the MM/PB(GB)SA method. The framework integrates dynamic tool use, web search, PaperQA, and a self-correcting behavior. DynaMate comprises three specialized modules, interacting to plan the experiment, perform the simulation, and analyze the results. We evaluated its performance across twelve benchmark systems of varying complexity, assessing success rate, efficiency, and adaptability. DynaMate reliably performed full MD simulations, corrected runtime errors through iterative reasoning, and produced meaningful analyses of protein-ligand interactions. This automated framework paves the way toward standardized, scalable, and time-efficient molecular modeling pipelines for future biomolecular and drug design applications.

cs.AI↗

arXiv2025

SynthStrategy: Extracting and Formalizing Latent Strategic Insights from LLMs in Organic Chemistry

Modern computer-assisted synthesis planning (CASP) systems show promises at generating chemically valid reaction steps but struggle to incorporate strategic considerations such as convergent assembly, protecting group minimization, and optimal ring-forming sequences. We introduce a methodology that leverages Large Language Models to distill synthetic knowledge into code. Our system analyzes synthesis routes and translates strategic principles into Python functions representing diverse strategic and tactical rules, such as strategic functional group interconversions and ring construction strategies. By formalizing this knowledge as verifiable code rather than simple heuristics, we create testable, interpretable representations of synthetic strategy. We release the complete codebase and the USPTO-ST dataset -- synthesis routes annotated with strategic tags. This framework unlocks a novel capability for CASP: natural language-based route retrieval, achieving 75\% Top-3 accuracy on our benchmark. We further validate our library through temporal analysis of historical trends and chemically intuitive route clustering that offers more granular partitioning than common previous methods. This work bridges the tactical-strategic divide in CASP, enabling specification, search, and evaluation of routes by strategic criteria rather than structure alone.

cs.AI↗

arXiv2025

Large language models as uncertainty-calibrated optimizers for experimental discovery

Scientific discovery increasingly depends on efficient experimental optimization to navigate vast design spaces under time and resource constraints. Traditional approaches often require extensive domain expertise and feature engineering. While large language models, with their vast scientific knowledge, circumvent the feature engineering limitations, they lack the calibrated uncertainty estimates required for high-stakes decision making. Hence, current optimization methods force a choice between domain knowledge and reliability, with no principled approach that affords both. In this work, we show that training language models through the uncertainty-aware objectives of traditional optimization methods enables their use as reliable optimizers guided by natural language. By teaching LLMs from experimental outcomes under uncertainty, we transform their overconfidence from a fundamental limitation into a precise calibration mechanism. Applied to Buchwald-Hartwig reactions, a cornerstone of pharmaceutical synthesis, our method nearly doubles the discovery rate of high-yielding reaction conditions, from 24% to 43% in 50 experimental iterations starting from 10 unsuccessful conditions. Across 19 diverse optimization problems spanning organic synthesis, materials science and catalysis, process chemistry, and molecular design, our approach ranks first on average, establishing a new paradigm for reliable, uncertainty-guided optimization with LLMs. Our approach can accelerate discovery by lowering the barrier to using powerful optimization methods, replacing the need for domain-specific feature engineering with more accessible natural language interfaces. These findings highlight that ensuring reliability through principled uncertainty quantification is critical for realizing the full potential of AI-guided experimentation.

cs.LG↗

arXiv2025

LeMat-Bulk: aggregating, and de-duplicating quantum chemistry materials databases

The rapid expansion of materials science databases has driven machine learning-based discovery while also posing challenges in data integration, duplication, and interoperability. Robust standardization and de-duplication methods are needed to address these issues and streamline materials research. We present LeMat-Bulk, a unified dataset combining Materials Project, OQMD, and Alexandria, encompassing over 5.3 million PBE-calculated materials and also representing the largest collection of PBESol and SCAN functional calculations. Our methodology standardizes calculations across databases that utilize different parameters, effectively addressing redundancy and enhancing cross-compatibility. To de-duplicate, we propose a hashing function which we termed the Bonding Algorithm Weisfeiller-Lehman (BAWL). We comprehensively benchmark this fingerprint under atomic noise, lattice strain, and symmetry transformations, demonstrating that it outperforms existing fingerprinting techniques such as SLICES, and CLOUD in robustness while offering greater computational efficiency than similarity-based approaches such as Pymatgen's StructureMatcher. Additionally, the fingerprint facilitates the analysis of functional-dependent trends (PBE, PBESol, SCAN) offering a scalable framework for data-driven materials science.

cond-mat.mtrl-sci↗

arXiv2025

Accelerating inverse materials design using generative diffusion models with reinforcement learning

Diffusion models promise to accelerate material design by directly generating novel structures with desired properties, but existing approaches typically require expensive and substantial labeled data ($>$10,000) and lack adaptability. Here we present MatInvent, a general and efficient reinforcement learning workflow that optimizes diffusion models for goal-directed crystal generation. For single-objective designs, MatInvent rapidly converges to target values within 60 iterations ($\sim$ 1,000 property evaluations) across electronic, magnetic, mechanical, thermal, and physicochemical properties. Furthermore, MatInvent achieves robust optimization in design tasks with multiple conflicting properties, successfully proposing low-supply-chain-risk magnets and high-$κ$ dielectrics. Compared to state-of-the-art methods, MatInvent exhibits superior generation performance under specified property constraints while dramatically reducing the demand for property computation by up to 378-fold. Compatible with diverse diffusion model architectures and property constraints, MatInvent could offer broad applicability in materials discovery.

physics.chem-ph↗

arXiv2025

Lookup multivariate Kolmogorov-Arnold Networks

High-dimensional linear mappings, or linear layers, dominate both the parameter count and the computational cost of most modern deep-learning models. We introduce a general-purpose drop-in replacement, lookup multivariate Kolmogorov-Arnold Networks (lmKANs), which deliver a substantially better trade-off between capacity and inference cost. Our construction expresses a general high-dimensional mapping through trainable low-dimensional multivariate functions. These functions can carry dozens or hundreds of trainable parameters each, and yet it takes only a few multiplications to compute them because they are implemented as spline lookup tables. Empirically, lmKANs reduce inference FLOPs by up to 6.0x while matching the flexibility of MLPs in general high-dimensional function approximation. In another feedforward fully connected benchmark, on the tabular-like dataset of randomly displaced methane configurations, lmKANs enable more than 10x higher H100 throughput at equal accuracy. Within frameworks of Convolutional Neural Networks, lmKAN-based CNNs cut inference FLOPs at matched accuracy by 1.6-2.1x and by 1.7x on the CIFAR-10 and ImageNet-1k datasets, respectively. Our code, including dedicated CUDA kernels, is available online at https://github.com/schwallergroup/lmkan.

cs.LG↗

arXiv2025

Flow-Based Fragment Identification via Binding Site-Specific Latent Representations

Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly and non-specifically. We developed a protein-fragment encoder that relies on a contrastive learning approach to map both molecular fragments and protein surfaces in a shared latent space. The encoder captures interaction-relevant features and allows to perform virtual screening as well as generative design with our new method LatentFrag. In LatentFrag, fragment embeddings and positions are generated conditioned on the protein surface while being chemically realistic by construction. Our expressive fragment and protein representations allow location of protein-fragment interaction sites with high sensitivity and we observe state-of-the-art fragment recovery rates when sampling from the learned distribution of latent fragment embeddings. Our generative method outperforms common methods such as virtual screening at a fraction of its computational cost providing a valuable starting point for fragment hit discovery. We further show the practical utility of LatentFrag and extend the workflow to full ligand design tasks. Together, these approaches contribute to advancing fragment identification and provide valuable tools for fragment-based drug discovery.

q-bio.BM↗

arXiv2025

Swarm Intelligence for Chemical Reaction Optimisation

Chemical reaction optimisation is essential for synthetic chemistry and pharmaceutical development, demanding the extensive exploration of many reaction parameters to achieve efficient and sustainable processes. We report $α$-PSO, a novel nature-inspired metaheuristic algorithm that augments canonical particle swarm optimisation (PSO) with machine learning (ML) for parallel reaction optimisation. Unlike black-box ML approaches that obscure decision-making processes, $α$-PSO uses mechanistically clear optimisation strategies through simple, physically intuitive swarm dynamics directly connected to experimental observables, enabling practitioners to understand the components driving each optimisation decision. We establish a theoretical framework for reaction landscape analysis using local Lipschitz constants to quantify reaction space "roughness", distinguishing between smoothly varying landscapes with predictable surfaces and rough landscapes with many reactivity cliffs. This analysis guides adaptive $α$-PSO parameter selection, optimising performance for different reaction topologies. Systematic evaluation of $α$-PSO across pharmaceutically relevant reaction benchmarks demonstrates competitive performance with state-of-the-art Bayesian optimisation methods, while two prospective high-throughput experimentation (HTE) campaigns showed that $α$-PSO identified optimal reaction conditions more rapidly than Bayesian optimisation. $α$-PSO combines the predictive capability of advanced black-box ML methods with interpretable metaheuristic procedures, offering chemists an effective framework for parallel reaction optimisation that maintains methodological clarity while achieving highly performant experimental outcomes. Alongside our open-source $α$-PSO implementation, we release $989$ new high-quality Pd-catalysed Buchwald-Hartwig and Suzuki reactions.

physics.chem-ph↗

arXiv2025

Molecular Machine Learning in Chemical Process Design

We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in (i) providing highly accurate predictions for properties of pure components and their mixtures, and (ii) exploring the chemical space for new molecular structures. We review current state-of-the-art molecular ML models and discuss research directions that promise further advancements. This includes ML methods, such as graph neural networks and transformers, which can be further advanced through the incorporation of physicochemical knowledge in a hybrid or physics-informed fashion. Then, we consider leveraging molecular ML at the chemical process scale, which is highly desirable yet rather unexplored. We discuss how molecular ML can be integrated into process design and optimization formulations, promising to accelerate the identification of novel molecules and processes. To this end, it will be essential to create molecule and process design benchmarks and practically validate proposed candidates, possibly in collaboration with the chemical industry.

physics.chem-ph↗

arXiv2025

The Rise of Generative AI for Metal-Organic Framework Design and Synthesis

Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches that can autonomously propose and synthesize in the laboratory new porous reticular structures on demand. We outline the progress of employing deep learning models, such as variational autoencoders, diffusion models, and large language model-based agents, that are fueled by the growing amount of available data from the MOF community and suggest novel crystalline materials designs. These generative tools can be combined with high-throughput computational screening and even automated experiments to form accelerated, closed-loop discovery pipelines. The result is a new paradigm for reticular chemistry in which AI algorithms more efficiently direct the search for high-performance MOF materials for clean air and energy applications. Finally, we highlight remaining challenges such as synthetic feasibility, dataset diversity, and the need for further integration of domain knowledge.

cond-mat.mtrl-sci↗

arXiv2025

TempRe: Template generation for single and direct multi-step retrosynthesis

Retrosynthesis planning remains a central challenge in molecular discovery due to the vast and complex chemical reaction space. While traditional template-based methods offer tractability, they suffer from poor scalability and limited generalization, and template-free generative approaches risk generating invalid reactions. In this work, we propose TempRe, a generative framework that reformulates template-based approaches as sequence generation, enabling scalable, flexible, and chemically plausible retrosynthesis. We evaluated TempRe across single-step and multi-step retrosynthesis tasks, demonstrating its superiority over both template classification and SMILES-based generation methods. On the PaRoutes multi-step benchmark, TempRe achieves strong top-k route accuracy. Furthermore, we extend TempRe to direct multi-step synthesis route generation, providing a lightweight and efficient alternative to conventional single-step and search-based approaches. These results highlight the potential of template generative modeling as a powerful paradigm in computer-aided synthesis planning.

cs.LG↗

arXiv2025

Chemical reasoning in LLMs unlocks strategy-aware synthesis planning and reaction mechanism elucidation

While automated chemical tools excel at specific tasks, they have struggled to capture the strategic thinking that characterizes expert chemical reasoning. Here we demonstrate that large language models (LLMs) can serve as powerful tools enabling chemical analysis. When integrated with traditional search algorithms, they enable a new approach to computer-aided synthesis that mirrors human expert thinking. Rather than using LLMs to directly manipulate chemical structures, we leverage their ability to evaluate chemical strategies and guide search algorithms toward chemically meaningful solutions. We demonstrate this paradigm through two fundamental challenges: strategy-aware retrosynthetic planning and mechanism elucidation. In retrosynthetic planning, our system allows chemists to specify desired synthetic strategies in natural language -- from protecting group strategies to global feasibility assessment -- and uses traditional or LLM-guided Monte Carlo Tree Search to find routes that satisfy these constraints. In mechanism elucidation, LLMs guide the search for plausible reaction mechanisms by combining chemical principles with systematic exploration. This approach shows strong performance across diverse chemical tasks, with newer and larger models demonstrating increasingly sophisticated chemical reasoning. Our approach establishes a new paradigm for computer-aided chemistry that combines the strategic understanding of LLMs with the precision of traditional chemical tools, opening possibilities for more intuitive and powerful chemical automation systems.

cs.AI↗

arXiv2025

Position: Intelligent Science Laboratory Requires the Integration of Cognitive and Embodied AI

Scientific discovery has long been constrained by human limitations in expertise, physical capability, and sleep cycles. The recent rise of AI scientists and automated laboratories has accelerated both the cognitive and operational aspects of research. However, key limitations persist: AI systems are often confined to virtual environments, while automated laboratories lack the flexibility and autonomy to adaptively test new hypotheses in the physical world. Recent advances in embodied AI, such as generalist robot foundation models, diffusion-based action policies, fine-grained manipulation learning, and sim-to-real transfer, highlight the promise of integrating cognitive and embodied intelligence. This convergence opens the door to closed-loop systems that support iterative, autonomous experimentation and the possibility of serendipitous discovery. In this position paper, we propose the paradigm of Intelligent Science Laboratories (ISLs): a multi-layered, closed-loop framework that deeply integrates cognitive and embodied intelligence. ISLs unify foundation models for scientific reasoning, agent-based workflow orchestration, and embodied agents for robust physical experimentation. We argue that such systems are essential for overcoming the current limitations of scientific discovery and for realizing the full transformative potential of AI-driven science.

cs.AI↗

arXiv2025

Best Practices for Multi-Fidelity Bayesian Optimization in Materials and Molecular Research

Multi-fidelity Bayesian Optimization (MFBO) is a promising framework to speed up materials and molecular discovery as sources of information of different accuracies are at hand at increasing cost. Despite its potential use in chemical tasks, there is a lack of systematic evaluation of the many parameters playing a role in MFBO. In this work, we provide guidelines and recommendations to decide when to use MFBO in experimental settings. We investigate MFBO methods applied to molecules and materials problems. First, we test two different families of acquisition functions in two synthetic problems and study the effect of the informativeness and cost of the approximate function. We use our implementation and guidelines to benchmark three real discovery problems and compare them against their single-fidelity counterparts. Our results may help guide future efforts to implement MFBO as a routine tool in the chemical sciences.

cs.LG↗

arXiv2025

ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

cs.LG↗

arXiv2025

34 Examples of LLM Applications in Materials Science and Chemistry: Towards Automation, Assistants, Agents, and Accelerated Scientific Discovery

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

cs.LG↗

arXiv2024

Tango*: Constrained synthesis planning using chemically informed value functions

Computer-aided synthesis planning (CASP) has made significant strides in generating retrosynthetic pathways for simple molecules in a non-constrained fashion. Recent work introduces a specialised bidirectional search algorithm with forward and retro expansion to address the starting material-constrained synthesis problem, allowing CASP systems to provide synthesis pathways from specified starting materials, such as waste products or renewable feed-stocks. In this work, we introduce a simple guided search which allows solving the starting material-constrained synthesis planning problem using an existing, uni-directional search algorithm, Retro*. We show that by optimising a single hyperparameter, Tango* outperforms existing methods in terms of efficiency and solve rate. We find the Tango* cost function catalyses strong improvements for the bidirectional DESP methods. Our method also achieves lower wall clock times while proposing synthetic routes of similar length, a common metric for route quality. Finally, we highlight potential reasons for the strong performance of Tango over neural guided search methods

cs.CE↗