Mario Krenn

Alston Lo, Robert Pollice, AkshatKumar Nigam et al.

String-based molecular representations play a crucial role in cheminformatics applications, and with the growing success of deep learning in chemistry, have been readily adopted into machine learning pipelines. However, traditional string-based representations such as SMILES are often prone to syntactic and semantic errors when produced by generative models. To address these problems, a novel representation, SELF-referencIng Embedded Strings (SELFIES), was proposed that is inherently 100% robust, alongside an accompanying open-source implementation. Since then, we have generalized SELFIES to support a wider range of molecules and semantic constraints and streamlined its underlying grammar. We have implemented this updated representation in subsequent versions of \selfieslib, where we have also made major advances with respect to design, efficiency, and supported features. Hence, we present the current status of \selfieslib (version 2.1.1) in this manuscript.

Mario Krenn, Robert Pollice, Si Yue Guo et al.

Imagine an oracle that correctly predicts the outcome of every particle physics experiment, the products of every chemical reaction, or the function of every protein. Such an oracle would revolutionize science and technology as we know them. However, as scientists, we would not be satisfied with the oracle itself. We want more. We want to comprehend how the oracle conceived these predictions. This feat, denoted as scientific understanding, has frequently been recognized as the essential aim of science. Now, the ever-growing power of computers and artificial intelligence poses one ultimate question: How can advanced artificial systems contribute to scientific understanding or achieve it autonomously? We are convinced that this is not a mere technical question but lies at the core of science. Therefore, here we set out to answer where we are and where we can go from here. We first seek advice from the philosophy of science to understand scientific understanding. Then we review the current state of the art, both from literature and by collecting dozens of anecdotes from scientists about how they acquired new conceptual understanding with the help of computers. Those combined insights help us to define three dimensions of android-assisted scientific understanding: The android as a I) computational microscope, II) resource of inspiration and the ultimate, not yet existent III) agent of understanding. For each dimension, we explain new avenues to push beyond the status quo and unleash the full power of artificial intelligence's contribution to the central aim of science. We hope our perspective inspires and focuses research towards androids that get new scientific understanding and ultimately bring us closer to true artificial scientists.

Mario Krenn, Lorenzo Buffoni, Bruno Coutinho et al.

A tool that could suggest new personalized research directions and ideas by taking insights from the scientific literature could significantly accelerate the progress of science. A field that might benefit from such an approach is artificial intelligence (AI) research, where the number of scientific publications has been growing exponentially over the last years, making it challenging for human researchers to keep track of the progress. Here, we use AI techniques to predict the future research directions of AI itself. We develop a new graph-based benchmark based on real-world data -- the Science4Cast benchmark, which aims to predict the future state of an evolving semantic network of AI. For that, we use more than 100,000 research papers and build up a knowledge network with more than 64,000 concept nodes. We then present ten diverse methods to tackle this task, ranging from pure statistical to pure learning methods. Surprisingly, the most powerful methods use a carefully curated set of network features, rather than an end-to-end AI approach. It indicates a great potential that can be unleashed for purely ML approaches without human knowledge. Ultimately, better predictions of new future research directions will be a crucial component of more advanced research suggestion tools.

Tareq Jaouni, Sören Arlt, Carlos Ruiz-Gonzalez et al.

Despite their promise to facilitate new scientific discoveries, the opaqueness of neural networks presents a challenge in interpreting the logic behind their findings. Here, we use a eXplainable-AI (XAI) technique called $inception$ or $deep$ $dreaming$, which has been invented in machine learning for computer vision. We use this technique to explore what neural networks learn about quantum optics experiments. Our story begins by training deep neural networks on the properties of quantum systems. Once trained, we "invert" the neural network -- effectively asking how it imagines a quantum system with a specific property, and how it would continuously modify the quantum system to change a property. We find that the network can shift the initial distribution of properties of the quantum system, and we can conceptualize the learned strategies of the neural network. Interestingly, we find that, in the first layers, the neural network identifies simple properties, while in the deeper ones, it can identify complex quantum structures and even quantum entanglement. This is in reminiscence of long-understood properties known in computer vision, which we now identify in a complex natural science task. Our approach could be useful in a more interpretable way to develop new advanced AI-based scientific discovery techniques in quantum physics.

Sören Arlt, Xuemei Gu, Mario Krenn

Artificial intelligence (AI) is used in numerous fields of science, yet the initial research questions and targets are still almost always provided by human researchers. AI-generated creative ideas in science are rare and often vague, so that it remains a human task to execute them. Automating idea generation and implementation in one coherent system would significantly shift the role of humans in the scientific process. Here we present AI-Mandel, an LLM agent that can generate and implement ideas in quantum physics. AI-Mandel formulates ideas from the literature and uses a domain-specific AI tool to turn them into concrete experiment designs that can readily be implemented in laboratories. The generated ideas by AI-Mandel are often scientifically interesting - for two of them we have already written independent scientific follow-up papers. The ideas include new variations of quantum teleportation, primitives of quantum networks in indefinite causal orders, and new concepts of geometric phases based on closed loops of quantum information transfer. AI-Mandel is a prototypical demonstration of an AI physicist that can generate and implement concrete, actionable ideas. Building such a system is not only useful to accelerate science, but it also reveals concrete open challenges on the path to human-level artificial scientists.

Xuemei Gu, Mario Krenn

The exponential growth in scientific publications poses a severe challenge for human researchers. It forces attention to more narrow sub-fields, which makes it challenging to discover new impactful research ideas and collaborations outside one's own field. While there are ways to predict a scientific paper's future citation counts, they need the research to be finished and the paper written, usually assessing impact long after the idea was conceived. Here we show how to predict the impact of onsets of ideas that have never been published by researchers. For that, we developed a large evolving knowledge graph built from more than 21 million scientific papers. It combines a semantic network created from the content of the papers and an impact network created from the historic citations of papers. Using machine learning, we can predict the dynamic of the evolving network into the future with high accuracy (AUC values beyond 0.9 for most experiments), and thereby the impact of new research directions. We envision that the ability to predict the impact of new ideas will be a crucial component of future artificial muses that can inspire new impactful and interesting scientific ideas.

Giovanni Acampora, Andris Ambainis, Natalia Ares et al.

This white paper discusses and explores the various points of intersection between quantum computing and artificial intelligence (AI). It describes how quantum computing could support the development of innovative AI solutions. It also examines use cases of classical AI that can empower research and development in quantum technologies, with a focus on quantum computing and quantum sensing. The purpose of this white paper is to provide a long-term research agenda aimed at addressing foundational questions about how AI and quantum computing interact and benefit one another. It concludes with a set of recommendations and challenges, including how to orchestrate the proposed theoretical work, align quantum AI developments with quantum hardware roadmaps, estimate both classical and quantum resources - especially with the goal of mitigating and optimizing energy consumption - advance this emerging hybrid software engineering discipline, and enhance European industrial competitiveness while considering societal implications.

Felix Frohnert, Xuemei Gu, Mario Krenn et al.

As the field of quantum physics evolves, researchers naturally form subgroups focusing on specialized problems. While this encourages in-depth exploration, it can limit the exchange of ideas across structurally similar problems in different subfields. To encourage cross-talk among these different specialized areas, data-driven approaches using machine learning have recently shown promise to uncover meaningful connections between research concepts, promoting cross-disciplinary innovation. Current state-of-the-art approaches represent concepts using knowledge graphs and frame the task as a link prediction problem, where connections between concepts are explicitly modeled. In this work, we introduce a novel approach based on dynamic word embeddings for concept combination prediction. Unlike knowledge graphs, our method captures implicit relationships between concepts, can be learned in a fully unsupervised manner, and encodes a broader spectrum of information. We demonstrate that this representation enables accurate predictions about the co-occurrence of concepts within research abstracts over time. To validate the effectiveness of our approach, we provide a comprehensive benchmark against existing methods and offer insights into the interpretability of these embeddings, particularly in the context of quantum physics research. Our findings suggest that this representation offers a more flexible and informative way of modeling conceptual relationships in scientific literature.

Philipp Schmidt, Sören Arlt, Carlos Ruiz-Gonzalez et al.

Generative Artificial Intelligence (AI) models can propose solutions to scientific problems beyond human capability. To truly make conceptual contributions, researchers need to be capable of understanding the AI-generated structures and extracting the underlying concepts and ideas. When algorithms provide little explanatory reasoning alongside the output, scientists have to reverse-engineer the fundamental insights behind proposals based solely on examples. This task can be challenging as the output is often highly complex and thus not immediately accessible to humans. In this work we show how transferring part of the analysis process into an immersive Virtual Reality (VR) environment can assist researchers in developing an understanding of AI-generated solutions. We demonstrate the usefulness of VR in finding interpretable configurations of abstract graphs, representing Quantum Optics experiments. Thereby, we can manually discover new generalizations of AI-discoveries as well as new understanding in experimental quantum optics. Furthermore, it allows us to customize the search space in an informed way - as a human-in-the-loop - to achieve significantly faster subsequent discovery iterations. As concrete examples, with this technology, we discover a new resource-efficient 3-dimensional entanglement swapping scheme, as well as a 3-dimensional 4-particle Greenberger-Horne-Zeilinger-state analyzer. Our results show the potential of VR for increasing a human researcher's ability to derive knowledge from graph-based generative AI that, which is a common abstract data representation used in diverse fields of science.

Carlos Ruiz-Gonzalez, Sören Arlt, Sebastian Lehner et al.

Physics simulators are essential in science and engineering, enabling the analysis, control, and design of complex systems. In experimental sciences, they are increasingly used to automate experimental design, often via combinatorial search and optimization. However, as the setups grow more complex, the computational cost of traditional, CPU-based simulators becomes a major limitation. Here, we show how neural surrogate models can significantly reduce reliance on such slow simulators while preserving accuracy. Taking the design of interferometric gravitational wave detectors as a representative example, we train a neural network to surrogate the gravitational wave physics simulator Finesse, which was developed by the LIGO community. Despite that small changes in physical parameters can change the output by orders of magnitudes, the model rapidly predicts the quality and feasibility of candidate designs, allowing an efficient exploration of large design spaces. Our algorithm loops between training the surrogate, inverse designing new experiments, and verifying their properties with the slow simulator for further training. Assisted by auto-differentiation and GPU parallelism, our method proposes high-quality experiments much faster than direct optimization. Solutions that our algorithm finds within hours outperform designs that take five days for the optimizer to reach. Though shown in the context of gravitational wave detectors, our framework is broadly applicable to other domains where simulator bottlenecks hinder optimization and discovery.

Sören Arlt, Haonan Duan, Felix Li et al.

Artificial Intelligence (AI) can solve complex scientific problems beyond human capabilities, but the resulting solutions offer little insight into the underlying physical principles. One prominent example is quantum physics, where computers can discover experiments for the generation of specific quantum states, but it is unclear how finding general design concepts can be automated. Here, we address this challenge by training a transformer-based language model to create human-readable Python code, which solves an entire class of problems in a single pass. This strategy, which we call meta-design, enables scientists to gain a deeper understanding and extrapolate to larger experiments without additional optimization. To demonstrate the effectiveness of our approach, we uncover previously unknown experimental generalizations of important quantum states, e.g. from condensed matter physics. The underlying methodology of meta-design can naturally be extended to fields such as materials science or engineering.

Mario Krenn, Jonas Landgraf, Thomas Foesel et al.

In recent years, the dramatic progress in machine learning has begun to impact many areas of science and technology significantly. In the present perspective article, we explore how quantum technologies are benefiting from this revolution. We showcase in illustrative examples how scientists in the past few years have started to use machine learning and more broadly methods of artificial intelligence to analyze quantum measurements, estimate the parameters of quantum devices, discover new quantum experimental setups, protocols, and feedback strategies, and generally improve aspects of quantum computing, quantum communication, and quantum simulation. We highlight open challenges and future possibilities and conclude with some speculative visions for the next decade.

Mario Krenn, Qianxiang Ai, Senja Barthel et al.

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings -- most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100\% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chemistry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.

Alba Cervera-Lierta, Mario Krenn, Alán Aspuru-Guzik

Logic Artificial Intelligence (AI) is a subfield of AI where variables can take two defined arguments, True or False, and are arranged in clauses that follow the rules of formal logic. Several problems that span from physical systems to mathematical conjectures can be encoded into these clauses and solved by checking their satisfiability (SAT). In contrast to machine learning approaches where the results can be approximations or local minima, Logic AI delivers formal and mathematically exact solutions to those problems. In this work, we propose the use of logic AI for the design of optical quantum experiments. We show how to map into a SAT problem the experimental preparation of an arbitrary quantum state and propose a logic-based algorithm, called Klaus, to find an interpretable representation of the photonic setup that generates it. We compare the performance of Klaus with the state-of-the-art algorithm for this purpose based on continuous optimization. We also combine both logic and numeric strategies to find that the use of logic AI significantly improves the resolution of this problem, paving the path to developing more formal-based approaches in the context of quantum physics experiments.

Daniel Flam-Shepherd, Tony Wu, Xuemei Gu et al.

Quantum physics experiments produce interesting phenomena such as interference or entanglement, which are core properties of numerous future quantum technologies. The complex relationship between the setup structure of a quantum experiment and its entanglement properties is essential to fundamental research in quantum optics but is difficult to intuitively understand. We present a deep generative model of quantum optics experiments where a variational autoencoder is trained on a dataset of quantum optics experimental setups. In a series of computational experiments, we investigate the learned representation of our Quantum Optics Variational Auto Encoder (QOVAE) and its internal understanding of the quantum optics world. We demonstrate that the QOVAE learns an interpretable representation of quantum optics experiments and the relationship between experiment structure and entanglement. We show the QOVAE is able to generate novel experiments for highly entangled quantum states with specific distributions that match its training data. The QOVAE can learn to generate specific entangled states and efficiently search the space of experiments that produce highly entangled quantum states. Importantly, we are able to interpret how the QOVAE structures its latent space, finding curious patterns that we can explain in terms of quantum physics. The results demonstrate how we can use and understand the internal representations of deep generative models in a complex scientific domain. The QOVAE and the insights from our investigations can be immediately applied to other physical systems.

Luca A. Thiede, Mario Krenn, AkshatKumar Nigam et al.

Computer-aided design of molecules has the potential to disrupt the field of drug and material discovery. Machine learning, and deep learning, in particular, have been topics where the field has been developing at a rapid pace. Reinforcement learning is a particularly promising approach since it allows for molecular design without prior knowledge. However, the search space is vast and efficient exploration is desirable when using reinforcement learning agents. In this study, we propose an algorithm to aid efficient exploration. The algorithm is inspired by a concept known in the literature as curiosity. We show on three benchmarks that a curious agent finds better performing molecules. This indicates an exciting new research direction for reinforcement learning agents that can explore the chemical space out of their own motivation. This has the potential to eventually lead to unexpected new molecules that no human has thought about so far.

Cynthia Shen, Mario Krenn, Sagi Eppel et al.

Computer-based de-novo design of functional molecules is one of the most prominent challenges in cheminformatics today. As a result, generative and evolutionary inverse designs from the field of artificial intelligence have emerged at a rapid pace, with aims to optimize molecules for a particular chemical property. These models 'indirectly' explore the chemical space; by learning latent spaces, policies, distributions or by applying mutations on populations of molecules. However, the recent development of the SELFIES string representation of molecules, a surjective alternative to SMILES, have made possible other potential techniques. Based on SELFIES, we therefore propose PASITHEA, a direct gradient-based molecule optimization that applies inceptionism techniques from computer vision. PASITHEA exploits the use of gradients by directly reversing the learning process of a neural network, which is trained to predict real-valued chemical properties. Effectively, this forms an inverse regression model, which is capable of generating molecular variants optimized for a certain property. Although our results are preliminary, we observe a shift in distribution of a chosen property during inverse-training, a clear indication of PASITHEA's viability. A striking property of inceptionism is that we can directly probe the model's understanding of the chemical space it was trained on. We expect that extending PASITHEA to larger datasets, molecules and more complex properties will lead to advances in the design of new functional molecules as well as the interpretation and explanation of machine learning models.

Pascal Friederich, Mario Krenn, Isaac Tamblyn et al.

Machine learning with application to questions in the physical sciences has become a widely used tool, successfully applied to classification, regression and optimization tasks in many areas. Research focus mostly lies in improving the accuracy of the machine learning models in numerical predictions, while scientific understanding is still almost exclusively generated by human researchers analysing numerical results and drawing conclusions. In this work, we shift the focus on the insights and the knowledge obtained by the machine learning models themselves. In particular, we study how it can be extracted and used to inspire human scientists to increase their intuitions and understanding of natural systems. We apply gradient boosting in decision trees to extract human interpretable insights from big data sets from chemistry and physics. In chemistry, we not only rediscover widely know rules of thumb but also find new interesting motifs that tell us how to control solubility and energy levels of organic molecules. At the same time, in quantum physics, we gain new understanding on experiments for quantum entanglement. The ability to go beyond numerics and to enter the realm of scientific insight and hypothesis generation opens the door to use machine learning to accelerate the discovery of conceptual understanding in some of the most challenging domains of science.

Mario Krenn, Manuel Erhard, Anton Zeilinger

The design of new devices and experiments in science and engineering has historically relied on the intuitions of human experts. This credo, however, has changed. In many disciplines, computer-inspired design processes, also known as inverse-design, have augmented the capability of scientists. Here we visit different fields of physics in which computer-inspired designs are applied. We will meet vastly diverse computational approaches based on topological optimization, evolutionary strategies, deep learning, reinforcement learning or automated reasoning. Then we draw our attention specifically on quantum physics. In the quest for designing new quantum experiments, we face two challenges: First, quantum phenomena are unintuitive. Second, the number of possible configurations of quantum experiments explodes combinatorially. To overcome these challenges, physicists began to use algorithms for computer-designed quantum experiments. We focus on the most mature and \textit{practical} approaches that scientists used to find new complex quantum experiments, which experimentalists subsequently have realized in the laboratories. The underlying idea is a highly-efficient topological search, which allows for scientific interpretability. In that way, some of the computer-designs have led to the discovery of new scientific concepts and ideas -- demonstrating how computer algorithm can genuinely contribute to science by providing unexpected inspirations. We discuss several extensions and alternatives based on optimization and machine learning techniques, with the potential of accelerating the discovery of practical computer-inspired experiments or concepts in the future. Finally, we discuss what we can learn from the different approaches in the fields of physics, and raise several fascinating possibilities for future research.

Thomas Adler, Manuel Erhard, Mario Krenn et al.

We demonstrate how machine learning is able to model experiments in quantum physics. Quantum entanglement is a cornerstone for upcoming quantum technologies such as quantum computation and quantum cryptography. Of particular interest are complex quantum states with more than two particles and a large number of entangled quantum levels. Given such a multiparticle high-dimensional quantum state, it is usually impossible to reconstruct an experimental setup that produces it. To search for interesting experiments, one thus has to randomly create millions of setups on a computer and calculate the respective output states. In this work, we show that machine learning models can provide significant improvement over random search. We demonstrate that a long short-term memory (LSTM) neural network can successfully learn to model quantum experiments by correctly predicting output state characteristics for given setups without the necessity of computing the states themselves. This approach not only allows for faster search but is also an essential step towards automated design of multiparticle high-dimensional quantum experiments using generative machine learning models.

AkshatKumar Nigam, Pascal Friederich, Mario Krenn et al.

Challenges in natural sciences can often be phrased as optimization problems. Machine learning techniques have recently been applied to solve such problems. One example in chemistry is the design of tailor-made organic materials and molecules, which requires efficient methods to explore the chemical space. We present a genetic algorithm (GA) that is enhanced with a neural network (DNN) based discriminator model to improve the diversity of generated molecules and at the same time steer the GA. We show that our algorithm outperforms other generative models in optimization tasks. We furthermore present a way to increase interpretability of genetic algorithms, which helped us to derive design principles.

Mario Krenn, Anton Zeilinger

The vast and growing number of publications in all disciplines of science cannot be comprehended by a single human researcher. As a consequence, researchers have to specialize in narrow sub-disciplines, which makes it challenging to uncover scientific connections beyond the own field of research. Thus access to structured knowledge from a large corpus of publications could help pushing the frontiers of science. Here we demonstrate a method to build a semantic network from published scientific literature, which we call SemNet. We use SemNet to predict future trends in research and to inspire new, personalized and surprising seeds of ideas in science. We apply it in the discipline of quantum physics, which has seen an unprecedented growth of activity in recent years. In SemNet, scientific knowledge is represented as an evolving network using the content of 750,000 scientific papers published since 1919. The nodes of the network correspond to physical concepts, and links between two nodes are drawn when two physical concepts are concurrently studied in research articles. We identify influential and prize-winning research topics from the past inside SemNet thus confirm that it stores useful semantic knowledge. We train a deep neural network using states of SemNet of the past, to predict future developments in quantum physics research, and confirm high quality predictions using historic data. With the neural network and theoretical network tools we are able to suggest new, personalized, out-of-the-box ideas, by identifying pairs of concepts which have unique and extremal semantic network properties. Finally, we consider possible future developments and implications of our findings.

Mario Krenn, Florian Häse, AkshatKumar Nigam et al.

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

Alexey A. Melnikov, Hendrik Poulsen Nautrup, Mario Krenn et al.

How useful can machine learning be in a quantum laboratory? Here we raise the question of the potential of intelligent machines in the context of scientific research. A major motivation for the present work is the unknown reachability of various entanglement classes in quantum experiments. We investigate this question by using the projective simulation model, a physics-oriented approach to artificial intelligence. In our approach, the projective simulation system is challenged to design complex photonic quantum experiments that produce high-dimensional entangled multiphoton states, which are of high interest in modern quantum experiments. The artificial intelligence system learns to create a variety of entangled states, and improves the efficiency of their realization. In the process, the system autonomously (re)discovers experimental techniques which are only now becoming standard in modern quantum optical experiments - a trait which was not explicitly demanded from the system but emerged through the process of learning. Such features highlight the possibility that machines could have a significantly more creative role in future research.