arXiv subjects

Pascal Friederich

Publications and source records attributed to Pascal Friederich.

47 records · Page 3Linked to original sources

arXiv2022

On scientific understanding with artificial intelligence

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.

cs.CY↗

arXiv2022

SELFIES and the future of molecular string representations

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.

physics.chem-ph↗

arXiv2022

Charge Transfer Simulations using Hamiltonian Elements and Forces from Neural Networks

The trajectory surface hopping method has been widely used in the simulation of charge transport in organic semiconductors. In the present study, we employ the machine learning (ML) based Hamiltonian to simulate the charge transport in anthracene and pentacene. The neural network (NN) based models are able to predict not just site energies and couplings but also the gradients of the site energy as well as off-diagonal gradients necessary for forces. We train the models on DFTB-quality data for both anthracene and pentacene. By using the obtained models in propagation simulations, we evaluate their performance in reproducing hole mobilities in these materials in terms of both quality and computational cost. The results show that the charge mobilities obtained using the NN-based Hamiltonian are in very good agreements with the charge mobilities computed using the DFTB-based Hamiltonian.

physics.chem-ph↗

arXiv2021

Implementing graph neural networks with TensorFlow-Keras

Graph neural networks are a versatile machine learning architecture that received a lot of attention recently. In this technical report, we present an implementation of convolution and pooling layers for TensorFlow-Keras models, which allows a seamless and flexible integration into standard Keras layers to set up graph models in a functional way. This implies the usage of mini-batches as the first tensor dimension, which can be realized via the new RaggedTensor class of TensorFlow best suited for graphs. We developed the Keras Graph Convolutional Neural Network Python package kgcnn based on TensorFlow-Keras that provides a set of Keras layers for graph networks which focus on a transparent tensor structure passed between layers and an ease-of-use mindset.

cs.LG↗

arXiv2021

Analyzing dynamical disorder for charge transport in organic semiconductors via machine learning

Organic semiconductors are indispensable for today's display technologies in form of organic light emitting diodes (OLEDs) and further optoelectronic applications. However, organic materials do not reach the same charge carrier mobility as inorganic semiconductors, limiting the efficiency of devices. To find or even design new organic semiconductors with higher charge carrier mobility, computational approaches, in particular multiscale models, are becoming increasingly important. However, such models are computationally very costly, especially when large systems and long time scales are required, which is the case to compute static and dynamic energy disorder, i.e. dominant factor to determine charge transport. Here we overcome this drawback by integrating machine learning models into multiscale simulations. This allows us to obtain unprecedented insight into relevant microscopic materials properties, in particular static and dynamic disorder contributions for a series of application-relevant molecules. We find that static disorder and thus the distribution of shallow traps is highly asymmetrical for many materials, impacting widely considered Gaussian disorder models. We furthermore analyse characteristic energy level fluctuation times and compare them to typical hopping rates to evaluate the importance of dynamic disorder for charge transport. We hope that our findings will significantly improve the accuracy of computational methods used to predict application relevant materials properties of organic semiconductors, and thus make these methods applicable for virtual materials design.

cond-mat.soft↗

arXiv2020

Scientific intuition inspired by machine learning generated hypotheses

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.

cs.LG↗

arXiv2020

The influence of impurities on the charge carrier mobility of small molecule organic semiconductors

Amorphous organic semiconductors based on small molecules and polymers are used in many applications, most prominently organic light emitting diodes (OLEDs) and organic solar cells. Impurities and charge traps are omnipresent in most currently available organic semiconductors and limit charge transport and thus device efficiency. The microscopic cause as well as the chemical nature of these traps are presently not well understood. Using a multiscale model we characterize the influence of impurities on the density of states and charge transport in small-molecule amorphous organic semiconductors. We use the model to quantitatively describe the influence of water molecules and water-oxygen complexes on the electron and hole mobilities. These species are seen to impact the shape of the density of states and to act as explicit charge traps within the energy gap. Our results show that trap states introduced by molecular oxygen can be deep enough to limit the electron mobility in widely used materials.

cond-mat.soft↗

arXiv2020

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation

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.

cs.LG↗

arXiv2020

Neural Message Passing on High Order Paths

Graph neural network have achieved impressive results in predicting molecular properties, but they do not directly account for local and hidden structures in the graph such as functional groups and molecular geometry. At each propagation step, GNNs aggregate only over first order neighbours, ignoring important information contained in subsequent neighbours as well as the relationships between those higher order connections. In this work, we generalize graph neural nets to pass messages and aggregate across higher order paths. This allows for information to propagate over various levels and substructures of the graph. We demonstrate our model on a few tasks in molecular property prediction.

cs.LG↗

arXiv2020

Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space

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.

cs.NE↗

arXiv2019

From absorption spectra to charge transfer in PEDOT nanoaggregates with machine learning

Fast and inexpensive characterization of materials properties is a key element to discover novel functional materials. In this work, we suggest an approach employing three classes of Bayesian machine learning (ML) models to correlate electronic absorption spectra of nanoaggregates with the strength of intermolecular electronic couplings in organic conducting and semiconducting materials. As a specific model system, we consider PEDOT:PSS, a cornerstone material for organic electronic applications, and so analyze the couplings between charged dimers of closely packed PEDOT oligomers that are at the heart of the material's unrivaled conductivity. We demonstrate that ML algorithms can identify correlations between the coupling strengths and the electronic absorption spectra. We also show that ML models can be trained to be transferable across a broad range of spectral resolutions, and that the electronic couplings can be predicted from the simulated spectra with an 88 % accuracy when ML models are used as classifiers. Although the ML models employed in this study were trained on data generated by a multi-scale computational workflow, they were able to leverage leverage experimental data.

physics.chem-ph↗