Daily Papers

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

In this work, we describe strategies and provide case-study activities that can be used to examine the properties of superposition, entanglement, tagging, complementarity, and measurement in quantum curricula geared for teacher training. Having a solid foundation in these conceptual ideas is critical for educators who will be adopting quantum ideas within the classroom. Yet they are some of the most difficult concepts to master. We show how one can systematically develop these conceptual foundations with thought experiments on light and with thought experiments that employ the Stern-Gerlach experiment. We emphasize the importance of computer animations in aiding the instruction on these concepts.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of ``slow thinking" into multimodal large language models (MLLMs). Contrary to existing methods that rely on direct or fast thinking, our key idea is to construct long chains of thought (CoT) consisting of atomic actions in a step-by-step manner, guiding MLLMs to perform complex reasoning. To this end, we design a novel AtomThink framework composed of three key modules: (i) a CoT annotation engine that automatically generates high-quality CoT annotations to address the lack of high-quality visual mathematical data; (ii) an atomic step fine-tuning strategy that jointly optimizes an MLLM and a policy reward model (PRM) for step-wise reasoning; and (iii) four different search strategies that can be applied with the PRM to complete reasoning. Additionally, we propose AtomMATH, a large-scale multimodal dataset of long CoTs, and an atomic capability evaluation metric for mathematical tasks. Extensive experimental results show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving approximately 50\% relative accuracy gains on MathVista and 120\% on MathVerse. To support the advancement of multimodal slow-thinking models, we will make our code and dataset publicly available on https://github.com/Quinn777/AtomThink.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab-initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses, and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory static and relaxation trajectories of sim 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

The sequential process of conceptualization and instantiation is essential to generalizable commonsense reasoning as it allows the application of existing knowledge to unfamiliar scenarios. However, existing works tend to undervalue the step of instantiation and heavily rely on pre-built concept taxonomies and human annotations to collect both types of knowledge, resulting in a lack of instantiated knowledge to complete reasoning, high cost, and limited scalability. To tackle these challenges, we introduce CANDLE, a distillation framework that iteratively performs contextualized conceptualization and instantiation over commonsense knowledge bases by instructing large language models to generate both types of knowledge with critic filtering. By applying CANDLE to ATOMIC, we construct a comprehensive knowledge base comprising six million conceptualizations and instantiated commonsense knowledge triples. Both types of knowledge are firmly rooted in the original ATOMIC dataset, and intrinsic evaluations demonstrate their exceptional quality and diversity. Empirical results indicate that distilling CANDLE on student models provides benefits across four downstream tasks. Our code, data, and models are publicly available at https://github.com/HKUST-KnowComp/CANDLE.

In contrast to entropy, which increases monotonically, the "complexity" or "interestingness" of closed systems seems intuitively to increase at first and then decrease as equilibrium is approached. For example, our universe lacked complex structures at the Big Bang and will also lack them after black holes evaporate and particles are dispersed. This paper makes an initial attempt to quantify this pattern. As a model system, we use a simple, two-dimensional cellular automaton that simulates the mixing of two liquids ("coffee" and "cream"). A plausible complexity measure is then the Kolmogorov complexity of a coarse-grained approximation of the automaton's state, which we dub the "apparent complexity." We study this complexity measure, and show analytically that it never becomes large when the liquid particles are non-interacting. By contrast, when the particles do interact, we give numerical evidence that the complexity reaches a maximum comparable to the "coffee cup's" horizontal dimension. We raise the problem of proving this behavior analytically.

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

The Four-Element Theory is a fundamental framework in criminal law, defining the constitution of crime through four dimensions: Subject, Object, Subjective aspect, and Objective aspect. This theory is widely referenced in legal reasoning, and many Large Language Models (LLMs) attempt to incorporate it when handling legal tasks. However, current approaches rely on LLMs' internal knowledge to incorporate this theory, often lacking completeness and representativeness. To address this limitation, we introduce JUREX-4E, an expert-annotated knowledge base covering 155 criminal charges. It is structured through a progressive hierarchical annotation framework that prioritizes legal source validity and employs diverse legal interpretation methods to ensure comprehensiveness and authority. We evaluate JUREX-4E on the Similar Charge Distinction task and apply it to Legal Case Retrieval, demonstrating its effectiveness in improving LLM performance. Experimental results validate the high quality of JUREX-4E and its substantial impact on downstream legal tasks, underscoring its potential for advancing legal AI applications. Code: https://github.com/THUlawtech/JUREX

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

Quantum Computing is a new and exciting field at the intersection of mathematics, computer science and physics. It concerns a utilization of quantum mechanics to improve the efficiency of computation. Here we present a gentle introduction to some of the ideas in quantum computing. The paper begins by motivating the central ideas of quantum mechanics and quantum computation with simple toy models. From there we move on to a formal presentation of the small fraction of (finite dimensional) quantum mechanics that we will need for basic quantum computation. Central notions of quantum architecture (qubits and quantum gates) are described. The paper ends with a presentation of one of the simplest quantum algorithms: Deutsch's algorithm. Our presentation demands neither advanced mathematics nor advanced physics.

Rydberg atom arrays have emerged as a powerful platform to simulate a number of exotic quantum ground states and phase transitions. To verify these capabilities numerically, we develop a versatile quantum Monte Carlo sampling technique which operates in the reduced Hilbert space generated by enforcing the constraint of a Rydberg blockade. We use the framework of stochastic series expansion and show that in the restricted space, the configuration space of operator strings can be understood as a hard rod gas in d+1 dimensions. We use this mapping to develop cluster algorithms which can be visualized as various non-local movements of rods. We study the efficiency of each of our updates individually and collectively. To elucidate the utility of the algorithm, we show that it can efficiently generate the phase diagram of a Rydberg atom array, to temperatures much smaller than all energy scales involved, on a Kagom\'e link lattice. This is of broad interest as the presence of a Z_2 spin liquid has been hypothesized recently.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model -- and its qualitative and at times quantitative accuracy -- on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, and chemical reactions. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.

Conceptual combination is a cognitive process that merges basic concepts, enabling the creation of complex expressions. During this process, the properties of combination (e.g., the whiteness of a peeled apple) can be inherited from basic concepts, newly emerge, or be canceled. However, previous studies have evaluated a limited set of properties and have not examined the generative process. To address this gap, we introduce the Conceptual Combination with Property Type dataset (CCPT), which consists of 12.3K annotated triplets of noun phrases, properties, and property types. Using CCPT, we establish three types of tasks to evaluate LLMs for conceptual combination thoroughly. Our key findings are threefold: (1) Our automatic metric grading property emergence and cancellation closely corresponds with human judgments. (2) LLMs, including OpenAI's o1, struggle to generate noun phrases which possess given emergent properties. (3) Our proposed method, inspired by cognitive psychology model that explains how relationships between concepts are formed, improves performances in all generative tasks. The dataset and experimental code are available at https://github.com/seokwon99/CCPT.git.

Recent advancements in large language models (LLMs) have led to significant improvements in various natural language processing tasks, but it is still challenging for LLMs to perform knowledge-intensive complex question answering due to LLMs' inefficacy in reasoning planning and the hallucination problem. A typical solution is to employ retrieval-augmented generation (RAG) coupled with chain-of-thought (CoT) reasoning, which decomposes complex questions into chain-like sub-questions and applies iterative RAG at each sub-question. However, prior works exhibit sub-optimal reasoning planning and overlook dynamic knowledge retrieval from heterogeneous sources. In this paper, we propose AtomR, a novel heterogeneous knowledge reasoning framework that conducts multi-source reasoning at the atomic level. Drawing inspiration from the graph modeling of knowledge, AtomR leverages large language models (LLMs) to decompose complex questions into combinations of three atomic knowledge operators, significantly enhancing the reasoning process at both the planning and execution stages. We also introduce BlendQA, a novel evaluation benchmark tailored to assess complex heterogeneous knowledge reasoning. Experiments show that AtomR significantly outperforms state-of-the-art baselines across three single-source and two multi-source reasoning benchmarks, with notable performance gains of 9.4% on 2WikiMultihop and 9.5% on BlendQA.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Large language models (LLMs) have shown remarkable performances across a wide range of tasks. However, the mechanisms by which these models encode tasks of varying complexities remain poorly understood. In this paper, we explore the hypothesis that LLMs process concepts of varying complexities in different layers, introducing the idea of "Concept Depth" to suggest that more complex concepts are typically acquired in deeper layers. Specifically, we categorize concepts based on their level of abstraction, defining them in the order of increasing complexity within factual, emotional, and inferential tasks. We conduct extensive probing experiments using layer-wise representations across various LLM families (Gemma, LLaMA, QWen) on various datasets spanning the three domains of tasks. Our findings reveal that models could efficiently conduct probing for simpler tasks in shallow layers, and more complex tasks typically necessitate deeper layers for accurate understanding. Additionally, we examine how external factors, such as adding noise to the input and quantizing the model weights, might affect layer-wise representations. Our findings suggest that these factors can impede the development of a conceptual understanding of LLMs until deeper layers are explored. We hope that our proposed concept and experimental insights will enhance the understanding of the mechanisms underlying LLMs. Our codes are available at https://github.com/Luckfort/CD.

Identifying and predicting the factors that contribute to the success of interdisciplinary research is crucial for advancing scientific discovery. However, there is a lack of methods to quantify the integration of new ideas and technological advancements in astronomical research and how these new technologies drive further scientific breakthroughs. Large language models, with their ability to extract key concepts from vast literature beyond keyword searches, provide a new tool to quantify such processes. In this study, we extracted concepts in astronomical research from 297,807 publications between 1993 and 2024 using large language models, resulting in a set of 24,939 concepts. These concepts were then used to form a knowledge graph, where the link strength between any two concepts was determined by their relevance through the citation-reference relationships. By calculating this relevance across different time periods, we quantified the impact of numerical simulations and machine learning on astronomical research. The knowledge graph demonstrates two phases of development: a phase where the technology was integrated and another where the technology was explored in scientific discovery. The knowledge graph reveals that despite machine learning has made much inroad in astronomy, there is currently a lack of new concept development at the intersection of AI and Astronomy, which may be the current bottleneck preventing machine learning from further transforming the field of astronomy.

Discovering novel high-entropy alloys (HEAs) with desirable properties is challenging due to the vast compositional space and complex phase formation mechanisms. Efficient exploration of this space requires a strategic approach that integrates heterogeneous knowledge sources. Here, we propose a framework that systematically combines knowledge extracted from computational material datasets with domain knowledge distilled from scientific literature using large language models (LLMs). A central feature of this approach is the explicit consideration of element substitutability, identifying chemically similar elements that can be interchanged to potentially stabilize desired HEAs. Dempster-Shafer theory, a mathematical framework for reasoning under uncertainty, is employed to model and combine substitutabilities based on aggregated evidence from multiple sources. The framework predicts the phase stability of candidate HEA compositions and is systematically evaluated on both quaternary alloy systems, demonstrating superior performance compared to baseline machine learning models and methods reliant on single-source evidence in cross-validation experiments. By leveraging multi-source knowledge, the framework retains robust predictive power even when key elements are absent from the training data, underscoring its potential for knowledge transfer and extrapolation. Furthermore, the enhanced interpretability of the methodology offers insights into the fundamental factors governing HEA formation. Overall, this work provides a promising strategy for accelerating HEA discovery by integrating computational and textual knowledge sources, enabling efficient exploration of vast compositional spaces with improved generalization and interpretability.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

Integer sequences are of central importance to the modeling of concepts admitting complete finitary descriptions. We introduce a novel view on the learning of such concepts and lay down a set of benchmarking tasks aimed at conceptual understanding by machine learning models. These tasks indirectly assess model ability to abstract, and challenge them to reason both interpolatively and extrapolatively from the knowledge gained by observing representative examples. To further aid research in knowledge representation and reasoning, we present FACT, the Finitary Abstraction Comprehension Toolkit. The toolkit surrounds a large dataset of integer sequences comprising both organic and synthetic entries, a library for data pre-processing and generation, a set of model performance evaluation tools, and a collection of baseline model implementations, enabling the making of the future advancements with ease.

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

In this work, we explore two classes of density dependent relativistic mean-field models, their predictions of proton fractions at high densities and neutron star structure. We have used a metamodelling approach to these relativistic density functionals. We have generated a large ensemble of models with these classes and then applied constraints from theoretical and experimental nuclear physics and astrophysical observations. We find that both models produce similar equations of state and neutron star mass-radius sequences. But, their underlying compositions, denoted by the proton fraction in this case, are vastly different. This reinstates previous findings that information on composition gets masqueraded in beta-equilibrium. Additional observations of non-equilibrium phenomena are necessary to pin it down.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Colloids play an important role in fundamental science as well as in nature and technology. They have had a strong impact on the fundamental understanding of statistical physics. For example, colloids have helped to obtain a better understanding of collective phenomena, ranging from phase transitions and glass formation to the swarming of active Brownian particles. Yet the success of colloidal systems hinges crucially on the specific physical and chemical properties of the colloidal particles, i.e. particles with the appropriate characteristics must be available. Here we present an idea to create particles with freely selectable properties. The properties might depend, for example, on the presence of other particles (hence mimicking specific pair or many-body interactions), previous configurations (hence introducing some memory or feedback), or a directional bias (hence changing the dynamics). Without directly interfering with the sample, each particle is fully controlled and can receive external commands through a predefined algorithm that can take into account any input parameters. This is realized with computer-controlled colloids, which we term cybloids - short for cybernetic colloids. The potential of cybloids is illustrated by programming a time-delayed external potential acting on a single colloid and interaction potentials for many colloids. Both an attractive harmonic potential and an annular potential are implemented. For a single particle, this programming can cause subdiffusive behavior or lend activity. For many colloids, the programmed interaction potential allows to select a crystal structure at wish. Beyond these examples, we discuss further opportunities which cybloids offer.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

Although quantum simulation can give insight into elusive or intractable physical phenomena, many quantum simulators are unavoidably limited in the models they mimic. Such is also the case for atom arrays interacting via Rydberg states - a platform potentially capable of simulating any kind of spin exchange model, albeit with currently unattainable experimental capabilities. Here, we propose a new route towards simulating generic spin exchange Hamiltonians in atom arrays, using Floquet engineering with both global and local control. To demonstrate the versatility and applicability of our approach, we numerically investigate the generation of several spin exchange models which have yet to be realized in atom arrays, using only previously-demonstrated experimental capabilities. Our proposed scheme can be readily explored in many existing setups, providing a path to investigate a large class of exotic quantum spin models.

Physics is based on probabilities as fundamental entities of a mathematical description. Expectation values of observables are computed according to the classical statistical rule. The overall probability distribution for one world covers all times. The quantum formalism arises once one focuses on the evolution of the time-local probabilistic information. Wave functions or the density matrix allow the formulation of a general linear evolution law for classical statistics. The quantum formalism for classical statistics is a powerful tool which allows us to implement for generalized Ising models the momentum observable with the associated Fourier representation. The association of operators to observables permits the computation of expectation values in terms of the density matrix by the usual quantum rule. We show that probabilistic cellular automata are quantum systems in a formulation with discrete time steps and real wave functions. With a complex structure the evolution operator for automata can be expressed in terms of a Hamiltonian involving fermionic creation and annihilation operators. The time-local probabilistic information amounts to a subsystem of the overall probabilistic system which is correlated with its environment consisting of the past and future. Such subsystems typically involve probabilistic observables for which only a probability distribution for their possible measurement values is available. Incomplete statistics does not permit to compute classical correlation functions for arbitrary subsystem-observables. Bell's inequalities are not generally applicable.

Solar photospheric abundances and CI-chondrite compositions are reviewed and updated to obtain representative solar system abundances of the elements and their isotopes. The new photospheric abundances obtained here lead to higher solar metallicity. Full 3D NLTE photospheric analyses are only available for 11 elements. A quality index for analyses is introduced. For several elements, uncertainties remain large. Protosolar mass fractions are H (X = 0.7060), He (Y = 0.2753), and for metals Li to U (Z = 0.0187). The protosolar (C+N)/H agrees within 13% with the ratio for the solar core from the Borexino experiment. Elemental abundances in CI-chondrites were screened by analytical methods, sample sizes, and evaluated using concentration frequency distributions. Aqueously mobile elements (e.g., alkalis, alkaline earths, etc.) often deviate from normal distributions indicating mobilization and/or sequestration into carbonates, phosphates, and sulfates. Revised CI-chondrite abundances of non-volatile elements are similar to earlier estimates. The moderately volatile elements F and Sb are higher than before, as are C, Br and I, whereas the CI-abundances of Hg and N are now significantly lower. The solar system nuclide distribution curves of s-process elements agree within 4% with s-process predictions of Galactic chemical evolution models. P-process nuclide distributions are assessed. No obvious correlation of CI-chondritic to solar elemental abundance ratios with condensation temperatures is observed, nor is there one for ratios of CI-chondrites/solar wind abundances.

We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our domain is human life, both its everyday concerns and its major milestones. We have limited the initial scope of the modeled concepts to only established human universals: spacetime (places, events) plus social (people, groups, organizations). The inclusion criteria for modeled concepts are pragmatic, beginning with universality and utility. We compare and contrast previous work such as Schema.org and Cyc--as well as attempts at a synthesis of knowledge graphs and language models--noting how LLMs already encode internally much of the commonsense tacit knowledge that took decades to capture in the Cyc project. We also make available code-generated software libraries for the 12 most popular programming languages, enabling the direct use of ontology concepts in software engineering. We emphasize simplicity and developer experience in promoting AI interoperability.

We describe a method, based on Jennifer Nado's definition of classification procedures as targets of conceptual engineering, that implements such procedures using a large language model. We then apply this method using data from the Wikidata knowledge graph to evaluate concept definitions from two paradigmatic conceptual engineering projects: the International Astronomical Union's redefinition of PLANET and Haslanger's ameliorative analysis of WOMAN. We discuss implications of this work for the theory and practice of conceptual engineering. The code and data can be found on GitHub.

The advent of artificial intelligence (AI) has enabled a comprehensive exploration of materials for various applications. However, AI models often prioritize frequently encountered materials in the scientific literature, limiting the selection of suitable candidates based on inherent physical and chemical properties. To address this imbalance, we have generated a dataset of 1,494,017 natural language-material paragraphs based on combined OQMD, Materials Project, JARVIS, COD and AFLOW2 databases, which are dominated by ab initio calculations and tend to be much more evenly distributed on the periodic table. The generated text narratives were then polled and scored by both human experts and ChatGPT-4, based on three rubrics: technical accuracy, language and structure, and relevance and depth of content, showing similar scores but with human-scored depth of content being the most lagging. The merger of multi-modality data sources and large language model (LLM) holds immense potential for AI frameworks to help the exploration and discovery of solid-state materials for specific applications.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

We explore the integration of Kolmogorov Networks (KANs) into molecular dynamics (MD) simulations to improve interatomic potentials. We propose that widely used potentials, such as the Lennard-Jones (LJ) potential, the embedded atom model (EAM), and artificial neural network (ANN) potentials, can be interpreted within the KAN framework. Specifically, we demonstrate that the descriptors for ANN potentials, typically constructed using polynomials, can be redefined using KAN's non-linear functions. By employing linear or cubic spline interpolations for these KAN functions, we show that the computational cost of evaluating ANN potentials and their derivatives is reduced.

This topical review article gives an overview of the interplay between quantum information theory and thermodynamics of quantum systems. We focus on several trending topics including the foundations of statistical mechanics, resource theories, entanglement in thermodynamic settings, fluctuation theorems and thermal machines. This is not a comprehensive review of the diverse field of quantum thermodynamics; rather, it is a convenient entry point for the thermo-curious information theorist. Furthermore this review should facilitate the unification and understanding of different interdisciplinary approaches emerging in research groups around the world.

I propose a version of quantum mechanics featuring a discrete and finite number of states that is plausibly a model of the real world. The model is based on standard unitary quantum theory of a closed system with a finite-dimensional Hilbert space. Given certain simple conditions on the spectrum of the Hamiltonian, Schr\"odinger evolution is periodic, and it is straightforward to replace continuous time with a discrete version, with the result that the system only visits a discrete and finite set of state vectors. The biggest challenges to the viability of such a model come from cosmological considerations. The theory may have implications for questions of mathematical realism and finitism.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

The ability to summarize and organize knowledge into abstract concepts is key to learning and reasoning. Many industrial applications rely on the consistent and systematic use of concepts, especially when dealing with decision-critical knowledge. However, we demonstrate that, when methodically questioned, large language models (LLMs) often display and demonstrate significant inconsistencies in their knowledge. Computationally, the basic aspects of the conceptualization of a given domain can be represented as Is-A hierarchies in a knowledge graph (KG) or ontology, together with a few properties or axioms that enable straightforward reasoning. We show that even simple ontologies can be used to reveal conceptual inconsistencies across several LLMs. We also propose strategies that domain experts can use to evaluate and improve the coverage of key domain concepts in LLMs of various sizes. In particular, we have been able to significantly enhance the performance of LLMs of various sizes with openly available weights using simple knowledge-graph (KG) based prompting strategies.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

All current formulations of thermodynamics invoke some form of coarse-graining or ensembles as the supposed link between their own laws and the microscopic laws of motion. They deal only with ensemble-averages, expectation values, macroscopic limits, infinite heat baths, etc., not with the details of physical variables of individual microscopic systems. They are consistent with the laws of motion for finite systems only in certain approximations, which improve with increasing scale, given various assumptions about initial conditions which are neither specified precisely nor even thought to hold exactly in nature. Here I propose a new formulation of the zeroth, first and second laws, improving upon the axiomatic approach to thermodynamics (Carath\'eodory, 1909; Lieb & Yngvason, 1999), via the principles of the recently proposed constructor theory. Specifically, I provide a non-approximative, scale-independent formulation of 'adiabatic accessibility'; this in turn provides a non-approximative, scale-independent distinction between work and heat and reveals an unexpected connection between information theory and the first law of thermodynamics (not just the second). It also achieves the long-sought unification of the axiomatic approach with Kelvin's.

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

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.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Conceptual knowledge is fundamental to human cognition and knowledge bases. However, existing knowledge probing works only focus on evaluating factual knowledge of pre-trained language models (PLMs) and ignore conceptual knowledge. Since conceptual knowledge often appears as implicit commonsense behind texts, designing probes for conceptual knowledge is hard. Inspired by knowledge representation schemata, we comprehensively evaluate conceptual knowledge of PLMs by designing three tasks to probe whether PLMs organize entities by conceptual similarities, learn conceptual properties, and conceptualize entities in contexts, respectively. For the tasks, we collect and annotate 24k data instances covering 393 concepts, which is COPEN, a COnceptual knowledge Probing bENchmark. Extensive experiments on different sizes and types of PLMs show that existing PLMs systematically lack conceptual knowledge and suffer from various spurious correlations. We believe this is a critical bottleneck for realizing human-like cognition in PLMs. COPEN and our codes are publicly released at https://github.com/THU-KEG/COPEN.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

The intricate relationship between electrons and the crystal lattice is a linchpin in condensed matter, traditionally described by the Fr\"ohlich model encompassing the lowest-order lattice-electron coupling. Recently developed quantum acoustics, emphasizing the wave nature of lattice vibrations, has enabled the exploration of previously uncharted territories of electron-lattice interaction not accessible with conventional tools such as perturbation theory. In this context, our agenda here is two-fold. First, we showcase the application of machine learning methods to categorize various interaction regimes within the subtle interplay of electrons and the dynamical lattice landscape. Second, we shed light on a nebulous region of electron dynamics identified by the machine learning approach and then attribute it to transient localization, where strong lattice vibrations result in a momentary Anderson prison for electronic wavepackets, which are later released by the evolution of the lattice. Overall, our research illuminates the spectrum of dynamics within the Fr\"ohlich model, such as transient localization, which has been suggested as a pivotal factor contributing to the mysteries surrounding strange metals. Furthermore, this paves the way for utilizing time-dependent perspectives in machine learning techniques for designing materials with tailored electron-lattice properties.

In geometrically frustrated magnetic systems, weak interactions or slight changes to the structure can tip the delicate balance of exchange interactions, sending the system into a different ground state. Brochantite, Cu_4SO_4(OH)_6, has a copper sublattice composed of distorted triangles, making it a likely host for frustrated magnetism, but exhibits stacking disorder. The lack of synthetic single crystals has limited research on the magnetism in brochantite to powders and natural mineral crystals. We grew crystals which we find to be a new polytype with a tendency toward ABAC stacking and some anion disorder, alongside the expected stacking disorder. Comparison to previous results on natural mineral specimens suggests that cation disorder is more deleterious to the magnetism than anion and stacking disorder. Our specific heat data suggest a double transition on cooling into the magnetically ordered state.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

In this paper we study the out-of-equilibrium phase diagram of the quantum version of Derrida's Random Energy Model, which is the simplest model of mean-field spin glasses. We interpret its corresponding quantum dynamics in Fock space as a one-particle problem in very high dimension to which we apply different theoretical methods tailored for high-dimensional lattices: the Forward-Scattering Approximation, a mapping to the Rosenzweig-Porter model, and the cavity method. Our results indicate the existence of two transition lines and three distinct dynamical phases: a completely many-body localized phase at low energy, a fully ergodic phase at high energy, and a multifractal "bad metal" phase at intermediate energy. In the latter, eigenfunctions occupy a diverging volume, yet an exponentially vanishing fraction of the total Hilbert space. We discuss the limitations of our approximations and the relationship with previous studies.

Humans can learn a variety of concepts and skills incrementally over the course of their lives while exhibiting many desirable properties, such as continual learning without forgetting, forward transfer and backward transfer of knowledge, and learning a new concept or task with only a few examples. Several lines of machine learning research, such as lifelong machine learning, few-shot learning, and transfer learning attempt to capture these properties. However, most previous approaches can only demonstrate subsets of these properties, often by different complex mechanisms. In this work, we propose a simple yet powerful unified deep learning framework that supports almost all of these properties and approaches through one central mechanism. Experiments on toy examples support our claims. We also draw connections between many peculiarities of human learning (such as memory loss and "rain man") and our framework. As academics, we often lack resources required to build and train, deep neural networks with billions of parameters on hundreds of TPUs. Thus, while our framework is still conceptual, and our experiment results are surely not SOTA, we hope that this unified lifelong learning framework inspires new work towards large-scale experiments and understanding human learning in general. This paper is summarized in two short YouTube videos: https://youtu.be/gCuUyGETbTU (part 1) and https://youtu.be/XsaGI01b-1o (part 2).

Understanding how semantic meaning is encoded in the representation spaces of large language models is a fundamental problem in interpretability. In this paper, we study the two foundational questions in this area. First, how are categorical concepts, such as {'mammal', 'bird', 'reptile', 'fish'}, represented? Second, how are hierarchical relations between concepts encoded? For example, how is the fact that 'dog' is a kind of 'mammal' encoded? We show how to extend the linear representation hypothesis to answer these questions. We find a remarkably simple structure: simple categorical concepts are represented as simplices, hierarchically related concepts are orthogonal in a sense we make precise, and (in consequence) complex concepts are represented as polytopes constructed from direct sums of simplices, reflecting the hierarchical structure. We validate these theoretical results on the Gemma large language model, estimating representations for 957 hierarchically related concepts using data from WordNet.

We consider concept generalization at a large scale in the diverse and natural visual spectrum. Established computational modes (i.e., rule-based or similarity-based) are primarily studied isolated and focus on confined and abstract problem spaces. In this work, we study these two modes when the problem space scales up, and the complexity of concepts becomes diverse. Specifically, at the representational level, we seek to answer how the complexity varies when a visual concept is mapped to the representation space. Prior psychology literature has shown that two types of complexities (i.e., subjective complexity and visual complexity) (Griffiths and Tenenbaum, 2003) build an inverted-U relation (Donderi, 2006; Sun and Firestone, 2021). Leveraging Representativeness of Attribute (RoA), we computationally confirm the following observation: Models use attributes with high RoA to describe visual concepts, and the description length falls in an inverted-U relation with the increment in visual complexity. At the computational level, we aim to answer how the complexity of representation affects the shift between the rule- and similarity-based generalization. We hypothesize that category-conditioned visual modeling estimates the co-occurrence frequency between visual and categorical attributes, thus potentially serving as the prior for the natural visual world. Experimental results show that representations with relatively high subjective complexity outperform those with relatively low subjective complexity in the rule-based generalization, while the trend is the opposite in the similarity-based generalization.

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

Wentzel, Kramers, Brillouin (WKB) approximation for fractional systems is investigated in this paper using the fractional calculus. In the fractional case the wave function is constructed such that the phase factor is the same as the Hamilton's principle function "S". To demonstrate our proposed approach two examples are investigated in details.

We discuss why AI is hard and why physics is simple. We discuss how physical intuition and the approach of theoretical physics can be brought to bear on the field of artificial intelligence and specifically machine learning. We suggest that the underlying project of machine learning and the underlying project of physics are strongly coupled through the principle of sparsity, and we call upon theoretical physicists to work on AI as physicists. As a first step in that direction, we discuss an upcoming book on the principles of deep learning theory that attempts to realize this approach.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Computational complexity has often been ignored in philosophy of mind, in philosophical artificial intelligence studies. The purpose of this paper is threefold. First and foremost, to show the importance of complexity rather than computability in philosophical and AI problems. Second, to rephrase the notion of computability in terms of solvability, i.e. treating computability as non-sufficient for establishing intelligence. The Church-Turing thesis is therefore revisited and rephrased in order to capture the ontological background of spatial and temporal complexity. Third, to emphasize ontological differences between different time complexities, which seem to provide a solid base towards better understanding of artificial intelligence in general.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

One might think that, once we know something is computable, how efficiently it can be computed is a practical question with little further philosophical importance. In this essay, I offer a detailed case that one would be wrong. In particular, I argue that computational complexity theory -- the field that studies the resources (such as time, space, and randomness) needed to solve computational problems -- leads to new perspectives on the nature of mathematical knowledge, the strong AI debate, computationalism, the problem of logical omniscience, Hume's problem of induction, Goodman's grue riddle, the foundations of quantum mechanics, economic rationality, closed timelike curves, and several other topics of philosophical interest. I end by discussing aspects of complexity theory itself that could benefit from philosophical analysis.

In October 2007, a Research Proposal for the University of Sydney, Australia, the author suggested that biovie-physical phenomenon as `electrodynamic dependant biological vision', is governed by relativistic quantum laws and biovision. The phenomenon on the basis of `biovielectroluminescence', satisfies man/microbio/megabio/computer vision (MMMCV), as a robust candidate for physical and visual sciences. The general aim of this addendum is to present a refined text of Sections 1-3 of that proposal and highlighting the contents of its Appendix in form of a `Mechanisms' Section. We then briefly remind in an article aimed for December 2007, by appending two more equations into Section 3, a theoretical II-time scenario as a time model well-proposed for the phenomenon. The time model within the core of the proposal, plays a significant role in emphasizing the principle points on Objectives no. 1-8, Sub-hypothesis 3.1.2, mentioned in Article [arXiv:0710.0410]. It also expresses the time concept in terms of causing quantized energy f(|E|) of time |t|, emit in regard to shortening the probability of particle loci as predictable patterns of particle's un-occurred motion, a solution to Heisenberg's uncertainty principle (HUP) into a simplistic manner. We conclude that, practical frames via a time algorithm to this model, fixates such predictable patterns of motion of scenery bodies onto recordable observation points of a MMMCV system. It even suppresses/predicts superposition phenomena coming from a human subject and/or other bio-subjects for any decision making event, e.g., brainwave quantum patterns based on vision. Maintaining the existential probability of Riemann surfaces of II-time scenarios in the context of biovielectroluminescence, makes motion-prediction a possibility.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Nearly 30 years ago, two-photon interference was observed, marking the beginning of a new quantum era. Indeed, two-photon interference has no classical analogue, giving it a distinct advantage for a range of applications. The peculiarities of quantum physics may now be used to our advantage to outperform classical computations, securely communicate information, simulate highly complex physical systems and increase the sensitivity of precise measurements. This separation from classical to quantum physics has motivated physicists to study two-particle interference for both fermionic and bosonic quantum objects. So far, two-particle interference has been observed with massive particles, among others, such as electrons and atoms, in addition to plasmons, demonstrating the extent of this effect to larger and more complex quantum systems. A wide array of novel applications to this quantum effect is to be expected in the future. This review will thus cover the progress and applications of two-photon (two-particle) interference over the last three decades.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website https://alchemy.tencent.com. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

We report on the trapping of single rubidium atoms in large arrays of optical tweezers comprising up to 2088 sites in a cryogenic environment at 6 K. Our approach relies on the use of microscope objectives that are in-vacuum but at room temperature, in combination with windowless thermal shields into which the objectives are protruding to ensure a cryogenic environment for the trapped atoms. To achieve enough optical power for efficient trapping, we combine two lasers at slightly different wavelengths. We discuss the performance and limitations of our design. Finally, we demonstrate atom-by-atom rearrangement of an 828-atom target array using moving optical tweezers controlled by a field-programmable gate array.

A characteristic feature of human semantic cognition is its ability to not only store and retrieve the properties of concepts observed through experience, but to also facilitate the inheritance of properties (can breathe) from superordinate concepts (animal) to their subordinates (dog) -- i.e. demonstrate property inheritance. In this paper, we present COMPS, a collection of minimal pair sentences that jointly tests pre-trained language models (PLMs) on their ability to attribute properties to concepts and their ability to demonstrate property inheritance behavior. Analyses of 22 different PLMs on COMPS reveal that they can easily distinguish between concepts on the basis of a property when they are trivially different, but find it relatively difficult when concepts are related on the basis of nuanced knowledge representations. Furthermore, we find that PLMs can demonstrate behavior consistent with property inheritance to a great extent, but fail in the presence of distracting information, which decreases the performance of many models, sometimes even below chance. This lack of robustness in demonstrating simple reasoning raises important questions about PLMs' capacity to make correct inferences even when they appear to possess the prerequisite knowledge.

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Scientific discovery is a complex cognitive process that has driven human knowledge and technological progress for centuries. While artificial intelligence (AI) has made significant advances in automating aspects of scientific reasoning, simulation, and experimentation, we still lack integrated AI systems capable of performing autonomous long-term scientific research and discovery. This paper examines the current state of AI for scientific discovery, highlighting recent progress in large language models and other AI techniques applied to scientific tasks. We then outline key challenges and promising research directions toward developing more comprehensive AI systems for scientific discovery, including the need for science-focused AI agents, improved benchmarks and evaluation metrics, multimodal scientific representations, and unified frameworks combining reasoning, theorem proving, and data-driven modeling. Addressing these challenges could lead to transformative AI tools to accelerate progress across disciplines towards scientific discovery.

Generative artificial intelligence (AI) systems based on large-scale pretrained foundation models (PFMs) such as vision-language models, large language models (LLMs), diffusion models and vision-language-action (VLA) models have demonstrated the ability to solve complex and truly non-trivial AI problems in a wide variety of domains and contexts. Multimodal large language models (MLLMs), in particular, learn from vast and diverse data sources, allowing rich and nuanced representations of the world and, thereby, providing extensive capabilities, including the ability to reason, engage in meaningful dialog; collaborate with humans and other agents to jointly solve complex problems; and understand social and emotional aspects of humans. Despite this impressive feat, the cognitive abilities of state-of-the-art LLMs trained on large-scale datasets are still superficial and brittle. Consequently, generic LLMs are severely limited in their generalist capabilities. A number of foundational problems -- embodiment, symbol grounding, causality and memory -- are required to be addressed for LLMs to attain human-level general intelligence. These concepts are more aligned with human cognition and provide LLMs with inherent human-like cognitive properties that support the realization of physically-plausible, semantically meaningful, flexible and more generalizable knowledge and intelligence. In this work, we discuss the aforementioned foundational issues and survey state-of-the art approaches for implementing these concepts in LLMs. Specifically, we discuss how the principles of embodiment, symbol grounding, causality and memory can be leveraged toward the attainment of artificial general intelligence (AGI) in an organic manner.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Many challenging reasoning tasks require not just rapid, intuitive responses, but a more deliberate, multi-step approach. Recent progress in large language models (LLMs) highlights an important shift from the "System 1" way of quick reactions to the "System 2" style of reflection-and-correction problem solving. However, current benchmarks heavily rely on the final-answer accuracy, leaving much of a model's intermediate reasoning steps unexamined. This fails to assess the model's ability to reflect and rectify mistakes within the reasoning process. To bridge this gap, we introduce FINEREASON, a logic-puzzle benchmark for fine-grained evaluation of LLMs' reasoning capabilities. Each puzzle can be decomposed into atomic steps, making it ideal for rigorous validation of intermediate correctness. Building on this, we introduce two tasks: state checking, and state transition, for a comprehensive evaluation of how models assess the current situation and plan the next move. To support broader research, we also provide a puzzle training set aimed at enhancing performance on general mathematical tasks. We show that models trained on our state checking and transition data demonstrate gains in math reasoning by up to 5.1% on GSM8K.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Crystalline materials are a fundamental component in next-generation technologies, yet modeling their distribution presents unique computational challenges. Of the plausible arrangements of atoms in a periodic lattice only a vanishingly small percentage are thermodynamically stable, which is a key indicator of the materials that can be experimentally realized. Two fundamental tasks in this area are to (a) predict the stable crystal structure of a known composition of elements and (b) propose novel compositions along with their stable structures. We present FlowMM, a pair of generative models that achieve state-of-the-art performance on both tasks while being more efficient and more flexible than competing methods. We generalize Riemannian Flow Matching to suit the symmetries inherent to crystals: translation, rotation, permutation, and periodic boundary conditions. Our framework enables the freedom to choose the flow base distributions, drastically simplifying the problem of learning crystal structures compared with diffusion models. In addition to standard benchmarks, we validate FlowMM's generated structures with quantum chemistry calculations, demonstrating that it is about 3x more efficient, in terms of integration steps, at finding stable materials compared to previous open methods.

The study of high-speed rotating matter is a crucial research topic in physics due to the emergence of novel phenomena. In this paper, we combined cranking covariant density functional theory (CDFT) with a similar renormalization group approach to decompose the Hamiltonian from the cranking CDFT into different Hermit components, including the non-relativistic term, the dynamical term, the spin-orbit coupling, and the Darwin term. Especially, we obtained the rotational term, the term relating to Zeeman effect-like, and the spin-rotation coupling due to consideration of rotation and spatial component of vector potential. By exploring these operators, we aim to identify novel phenomena that may occur in rotating nuclei. Signature splitting, Zeeman effect-like, spin-rotation coupling, and spin current are among the potential novelties that may arise in rotating nuclei. Additionally, we investigated the observability of these phenomena and their dependence on various factors such as nuclear deformation, rotational angular velocity, and strength of magnetic field.

This article provides an introduction to surface code quantum computing. We first estimate the size and speed of a surface code quantum computer. We then introduce the concept of the stabilizer, using two qubits, and extend this concept to stabilizers acting on a two-dimensional array of physical qubits, on which we implement the surface code. We next describe how logical qubits are formed in the surface code array and give numerical estimates of their fault-tolerance. We outline how logical qubits are physically moved on the array, how qubit braid transformations are constructed, and how a braid between two logical qubits is equivalent to a controlled-NOT. We then describe the single-qubit Hadamard, S and T operators, completing the set of required gates for a universal quantum computer. We conclude by briefly discussing physical implementations of the surface code. We include a number of appendices in which we provide supplementary information to the main text.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

We provide conceptual and mathematical foundations for near-term quantum natural language processing (QNLP), and do so in quantum computer scientist friendly terms. We opted for an expository presentation style, and provide references for supporting empirical evidence and formal statements concerning mathematical generality. We recall how the quantum model for natural language that we employ canonically combines linguistic meanings with rich linguistic structure, most notably grammar. In particular, the fact that it takes a quantum-like model to combine meaning and structure, establishes QNLP as quantum-native, on par with simulation of quantum systems. Moreover, the now leading Noisy Intermediate-Scale Quantum (NISQ) paradigm for encoding classical data on quantum hardware, variational quantum circuits, makes NISQ exceptionally QNLP-friendly: linguistic structure can be encoded as a free lunch, in contrast to the apparently exponentially expensive classical encoding of grammar. Quantum speed-up for QNLP tasks has already been established in previous work with Will Zeng. Here we provide a broader range of tasks which all enjoy the same advantage. Diagrammatic reasoning is at the heart of QNLP. Firstly, the quantum model interprets language as quantum processes via the diagrammatic formalism of categorical quantum mechanics. Secondly, these diagrams are via ZX-calculus translated into quantum circuits. Parameterisations of meanings then become the circuit variables to be learned. Our encoding of linguistic structure within quantum circuits also embodies a novel approach for establishing word-meanings that goes beyond the current standards in mainstream AI, by placing linguistic structure at the heart of Wittgenstein's meaning-is-context.

This paper addresses the problem of formalizing and quantifying the concept of "intensional inheritance" between two concepts. We begin by conceiving the intensional inheritance of W from F as the amount of information the proposition "x is F " provides about the proposition "x is W. To flesh this out, we consider concepts F and W defined by sets of properties left{F_{1}, F_{2}, ldots, F_{n}right} and left{W_{1}, W_{2}, ldots, W_{m}right} with associated degrees left{d_{1}, d_{2}, ldots, d_{n}right} and left{e_{1}, e_{2}, ldots, e_{m}right}, respectively, where the properties may overlap. We then derive formulas for the intensional inheritance using both Shannon information theory and algorithmic information theory, incorporating interaction information among properties. We examine a special case where all properties are mutually exclusive and calculate the intensional inheritance in this case in both frameworks. We also derive expressions for P(W mid F) based on the mutual information formula. Finally we consider the relationship between intensional inheritance and conventional set-theoretic "extensional" inheritance, concluding that in our information-theoretic framework, extensional inheritance emerges as a special case of intensional inheritance.

Ultracold gases of highly magnetic lanthanide atoms have enabled the realisation of dipolar quantum droplets and supersolids. However, future studies could be limited by the achievable atom numbers and hindered by high three-body loss rates. Here we study density-dependent atom loss in an ultracold gas of {}^{166}Er for magnetic fields below 4 G, identifying six previously unknown features which display both a strong temperature dependence and also sensitivity to the polarisation and intensity of the light used to optically trap the atoms. This detailed knowledge of the loss landscape allows us to optimise the production of dipolar BECs with more than 2 times 10^5 atoms and points towards optimal strategies for the study of large-atom-number dipolar gases in the droplet and supersolid regimes.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Commonsense knowledge (CSK) about concepts and their properties is useful for AI applications such as robust chatbots. Prior works like ConceptNet, TupleKB and others compiled large CSK collections, but are restricted in their expressiveness to subject-predicate-object (SPO) triples with simple concepts for S and monolithic strings for P and O. Also, these projects have either prioritized precision or recall, but hardly reconcile these complementary goals. This paper presents a methodology, called Ascent, to automatically build a large-scale knowledge base (KB) of CSK assertions, with advanced expressiveness and both better precision and recall than prior works. Ascent goes beyond triples by capturing composite concepts with subgroups and aspects, and by refining assertions with semantic facets. The latter are important to express temporal and spatial validity of assertions and further qualifiers. Ascent combines open information extraction with judicious cleaning using language models. Intrinsic evaluation shows the superior size and quality of the Ascent KB, and an extrinsic evaluation for QA-support tasks underlines the benefits of Ascent. A web interface, data and code can be found at https://ascent.mpi-inf.mpg.de/.

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

We present a new knowledge-base of hasPart relationships, extracted from a large corpus of generic statements. Complementary to other resources available, it is the first which is all three of: accurate (90% precision), salient (covers relationships a person may mention), and has high coverage of common terms (approximated as within a 10 year old's vocabulary), as well as having several times more hasPart entries than in the popular ontologies ConceptNet and WordNet. In addition, it contains information about quantifiers, argument modifiers, and links the entities to appropriate concepts in Wikipedia and WordNet. The knowledge base is available at https://allenai.org/data/haspartkb

In an ongoing effort to understand planet formation the link between the chemistry of the protoplanetary disk and the properties of resulting planets have long been a subject of interest. These connections have generally been made between mature planets and young protoplanetary disks through the carbon-to-oxygen (C/O) ratio. In a rare number of systems, young protoplanets have been found within their natal protoplanetary disks. These systems offer a unique opportunity to directly study the delivery of gas from the protoplanetary disk to the planet. In this work we post-process 3D numerical simulations of an embedded Jupiter-massed planet in its protoplanetary disk to explore the chemical evolution of gas as it flows from the disk to the planet. The relevant dust to this chemical evolution is assumed to be small, co-moving grains with a reduced dust-to-gas ratio indicative of the upper atmosphere of a protoplanetary disk. We find that as the gas enters deep into the planet's gravitational well, it warms significantly (up to sim 800 K), releasing all of the volatile content from the ice phase. This change in phase can influence our understanding of the delivery of volatile species to the atmospheres of giant planets. The primary carbon, oxygen, and sulfur carrying ices: CO_2, H_2O, and H_2S are released into the gas phase and along with the warm gas temperatures near the embedded planets lead to the production of unique species like CS, SO, and SO_2 compared to the protoplanetary disk. We compute the column densities of SO, SO_2, CS, and H_2CS in our model and find that their values are consistent with previous observational studies.

We identify five selected open problems in the theory of quantum information, which are rather simple to formulate, were well-studied in the literature, but are technically not easy. As these problems enjoy diverse mathematical connections, they offer a huge breakthrough potential. The first four concern existence of certain objects relevant for quantum information, namely a family of symmetric informationally complete generalized measurements in an infinite sequence of dimensions, mutually unbiased bases in dimension six, absolutely maximally entangled states for four subsystems with six levels each and bound entangled states with negative partial transpose. The fifth problem requires checking whether a certain state of a two-ququart system is 2-copy distillable. An award for solving each of them is announced.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

Existing methods, such as concept bottleneck models (CBMs), have been successful in providing concept-based interpretations for black-box deep learning models. They typically work by predicting concepts given the input and then predicting the final class label given the predicted concepts. However, (1) they often fail to capture the high-order, nonlinear interaction between concepts, e.g., correcting a predicted concept (e.g., "yellow breast") does not help correct highly correlated concepts (e.g., "yellow belly"), leading to suboptimal final accuracy; (2) they cannot naturally quantify the complex conditional dependencies between different concepts and class labels (e.g., for an image with the class label "Kentucky Warbler" and a concept "black bill", what is the probability that the model correctly predicts another concept "black crown"), therefore failing to provide deeper insight into how a black-box model works. In response to these limitations, we propose Energy-based Concept Bottleneck Models (ECBMs). Our ECBMs use a set of neural networks to define the joint energy of candidate (input, concept, class) tuples. With such a unified interface, prediction, concept correction, and conditional dependency quantification are then represented as conditional probabilities, which are generated by composing different energy functions. Our ECBMs address both limitations of existing CBMs, providing higher accuracy and richer concept interpretations. Empirical results show that our approach outperforms the state-of-the-art on real-world datasets.

This position paper argues that, in order to understand AI, we cannot rely on our existing vocabulary of human words. Instead, we should strive to develop neologisms: new words that represent precise human concepts that we want to teach machines, or machine concepts that we need to learn. We start from the premise that humans and machines have differing concepts. This means interpretability can be framed as a communication problem: humans must be able to reference and control machine concepts, and communicate human concepts to machines. Creating a shared human-machine language through developing neologisms, we believe, could solve this communication problem. Successful neologisms achieve a useful amount of abstraction: not too detailed, so they're reusable in many contexts, and not too high-level, so they convey precise information. As a proof of concept, we demonstrate how a "length neologism" enables controlling LLM response length, while a "diversity neologism" allows sampling more variable responses. Taken together, we argue that we cannot understand AI using our existing vocabulary, and expanding it through neologisms creates opportunities for both controlling and understanding machines better.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Isotopic substitution in molecular systems can affect fundamental molecular properties including the energy position and spacing of electronic, vibrational and rotational levels, thus modifying the dynamics associated to their coherent superposition. In extreme ultraviolet spectroscopy, the photoelectron leaving the molecule after the absorption of a single photon can trigger an ultrafast nuclear motion in the cation, which can lead, eventually, to molecular fragmentation. This dynamics depends on the mass of the constituents of the cation, thus showing, in general, a significant isotopic dependence. In time-resolved attosecond photoelectron interferometry, the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional quantum of energy (typically in the infrared spectral range) with the photoelectron-photoion system, offering the opportunity to investigate in time the influence of isotopic substitution on the characteristics of the photoionisation dynamics. Here we show that attosecond photoelectron interferometry is sensitive to isotopic substitution by investigating the two-color photoionisation spectra measured in a mixture of methane (CH_4) and deuteromethane (CD_4). The isotopic dependence manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks generated in the two-color field with the two isotopologues. The observed effects are interpreted considering the differences in the time evolution of the nuclear autocorrelation functions in the two molecules.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.

AI video generation is undergoing a revolution, with quality and realism advancing rapidly. These advances have led to a passionate scientific debate: Do video models learn ``world models'' that discover laws of physics -- or, alternatively, are they merely sophisticated pixel predictors that achieve visual realism without understanding the physical principles of reality? We address this question by developing Physics-IQ, a comprehensive benchmark dataset that can only be solved by acquiring a deep understanding of various physical principles, like fluid dynamics, optics, solid mechanics, magnetism and thermodynamics. We find that across a range of current models (Sora, Runway, Pika, Lumiere, Stable Video Diffusion, and VideoPoet), physical understanding is severely limited, and unrelated to visual realism. At the same time, some test cases can already be successfully solved. This indicates that acquiring certain physical principles from observation alone may be possible, but significant challenges remain. While we expect rapid advances ahead, our work demonstrates that visual realism does not imply physical understanding. Our project page is at https://physics-iq.github.io; code at https://github.com/google-deepmind/physics-IQ-benchmark.

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

Formulas involving fundamental mathematical constants had a great impact on various fields of science and mathematics, for example aiding in proofs of irrationality of constants. However, the discovery of such formulas has historically remained scarce, often perceived as an act of mathematical genius by great mathematicians such as Ramanujan, Euler, and Gauss. Recent efforts to automate the discovery of formulas for mathematical constants, such as the Ramanujan Machine project, relied on exhaustive search. Despite several successful discoveries, exhaustive search remains limited by the space of options that can be covered and by the need for vast amounts of computational resources. Here we propose a fundamentally different method to search for conjectures on mathematical constants: through analysis of integer sequences. We introduce the Enumerated Signed-continued-fraction Massey Approve (ESMA) algorithm, which builds on the Berlekamp-Massey algorithm to identify patterns in integer sequences that represent mathematical constants. The ESMA algorithm found various known formulas for e, e^2, tan(1), and ratios of values of Bessel functions. The algorithm further discovered a large number of new conjectures for these constants, some providing simpler representations and some providing faster numerical convergence than the corresponding simple continued fractions. Along with the algorithm, we present mathematical tools for manipulating continued fractions. These connections enable us to characterize what space of constants can be found by ESMA and quantify its algorithmic advantage in certain scenarios. Altogether, this work continues in the development of augmenting mathematical intuition by computer algorithms, to help reveal mathematical structures and accelerate mathematical research.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

There is vast evidence from observations of multiple stellar populations (MPs) in globular clusters (GCs). To explore the issue theoretically, this work considers two subsolar metallicities, two ages, and two initial abundance patterns: a first population of standard alpha-enhanced metal mixture stars and a second stellar population displaying C-N and Na-O anticorrelations chemical abundance patterns, along with an enhanced helium fraction. Analysing the predictions for these extreme compositions, we provide insights into the observability of not-resolved MPs into individual stars of GCs. We use colours and spectrophotometric indices measurable with modern facilities (e.g. Euclid, LSST, DES, JWST).

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

With the development in cognitive science and Large Language Models (LLMs), increasing connections have come to light between these two distinct fields. Building upon these connections, we propose a conjecture suggesting the existence of a duality between LLMs and Tulving's theory of memory. We identify a potential correspondence between Tulving's synergistic ecphory model (SEM) of retrieval and the emergent abilities observed in LLMs, serving as supporting evidence for our conjecture. Furthermore, we speculate that consciousness may be considered a form of emergent ability based on this duality. We also discuss how other theories of consciousness intersect with our research.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and the neural network potential is optimized to match the corresponding equilibrium potential at every intermediate time-step. Once the interpolating potentials and samples are well-aligned, the free-energy difference can be estimated using (neural) thermodynamic integration. To target molecular systems, we simultaneously couple Lennard-Jones and electrostatic interactions and model the rigid-body rotation of molecules. We report accurate results for several benchmark systems: a Lennard-Jones particle in a Lennard-Jones fluid, as well as the insertion of both water and methane solutes in a water solvent at atomistic resolution using a simple three-body neural-network potential.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

In this paper I apply newly-proposed information-theoretic principles to thermodynamic work extraction. I show that if it is possible to extract work deterministically from a physical system prepared in any one of a set of states, then those states must be distinguishable from one another. This result is formulated independently of scale and of particular dynamical laws; it also provides a novel connection between thermodynamics and information theory, established via the law of conservation of energy (rather than the second law of thermodynamics). Albeit compatible with these conclusions, existing thermodynamics approaches cannot provide a result of such generality, because they are scale-dependent (relying on ensembles or coarse-graining) or tied to particular dynamical laws. This paper thus provides a broader foundation for thermodynamics, with implications for the theory of von Neumann's universal constructor

Exotic hadrons are a new class of hadronic states whose properties do not allow them to be classified as conventional quark-antiquark mesons or three quark baryons. Finding new and understanding established exotic states is the most important topic in today's hadron spectroscopy and a promising avenue to advance our knowledge on Quantum Chromodynamics in the non-perturbative regime. While several high-quality reviews on the topic exist, they are all at an advanced level. The present article aims to address new-comers to the field with a simple introduction to exotic hadrons with an emphasis on the experimental studies.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

We explain how the so-called Einstein locality is to be understood in the Schr\"odinger picture of quantum mechanics. This notion is perfectly compatible with the Bell non-locality exhibited by entangled states. Contrary to some beliefs that quantum mechanics is incomplete, it is, in fact, its overcompleteness as exemplified by different pictures of quantum physics, that points to the same underlying reality.

We analyse perception and memory, using mathematical models for knowledge graphs and tensors, to gain insights into the corresponding functionalities of the human mind. Our discussion is based on the concept of propositional sentences consisting of subject-predicate-object (SPO) triples for expressing elementary facts. SPO sentences are the basis for most natural languages but might also be important for explicit perception and declarative memories, as well as intra-brain communication and the ability to argue and reason. A set of SPO sentences can be described as a knowledge graph, which can be transformed into an adjacency tensor. We introduce tensor models, where concepts have dual representations as indices and associated embeddings, two constructs we believe are essential for the understanding of implicit and explicit perception and memory in the brain. We argue that a biological realization of perception and memory imposes constraints on information processing. In particular, we propose that explicit perception and declarative memories require a semantic decoder, which, in a simple realization, is based on four layers: First, a sensory memory layer, as a buffer for sensory input, second, an index layer representing concepts, third, a memoryless representation layer for the broadcasting of information ---the "blackboard", or the "canvas" of the brain--- and fourth, a working memory layer as a processing center and data buffer. We discuss the operations of the four layers and relate them to the global workspace theory. In a Bayesian brain interpretation, semantic memory defines the prior for observable triple statements. We propose that ---in evolution and during development--- semantic memory, episodic memory, and natural language evolved as emergent properties in agents' process to gain a deeper understanding of sensory information.

Informally, the 'linear representation hypothesis' is the idea that high-level concepts are represented linearly as directions in some representation space. In this paper, we address two closely related questions: What does "linear representation" actually mean? And, how do we make sense of geometric notions (e.g., cosine similarity or projection) in the representation space? To answer these, we use the language of counterfactuals to give two formalizations of "linear representation", one in the output (word) representation space, and one in the input (sentence) space. We then prove these connect to linear probing and model steering, respectively. To make sense of geometric notions, we use the formalization to identify a particular (non-Euclidean) inner product that respects language structure in a sense we make precise. Using this causal inner product, we show how to unify all notions of linear representation. In particular, this allows the construction of probes and steering vectors using counterfactual pairs. Experiments with LLaMA-2 demonstrate the existence of linear representations of concepts, the connection to interpretation and control, and the fundamental role of the choice of inner product.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.

Concept-based interpretability methods offer a lens into the internals of foundation models by decomposing their embeddings into high-level concepts. These concept representations are most useful when they are compositional, meaning that the individual concepts compose to explain the full sample. We show that existing unsupervised concept extraction methods find concepts which are not compositional. To automatically discover compositional concept representations, we identify two salient properties of such representations, and propose Compositional Concept Extraction (CCE) for finding concepts which obey these properties. We evaluate CCE on five different datasets over image and text data. Our evaluation shows that CCE finds more compositional concept representations than baselines and yields better accuracy on four downstream classification tasks. Code and data are available at https://github.com/adaminsky/compositional_concepts .

Interior models of gas giants in the Solar System traditionally assume a fully convective molecular hydrogen envelope. However, recent observations from the Juno mission suggest a possible depletion of alkali metals in Jupiter's molecular hydrogen envelope, indicating that a stable radiative layer could exist at the kilobar level. Recent studies propose that deep stable layers help reconcile various Jupiter observations, including its atmospheric water and CO abundances and the depth of its zonal winds. However, opacity tables used to infer stable layers are often outdated and incomplete, leaving the precise molecular hydrogen envelope composition required for a deep radiative zone uncertain. In this paper, we determine atmospheric compositions that can lead to the formation of a radiative zone at the kilobar level in Jupiter and Saturn today. We computed radiative opacity tables covering pressures up to 10^5 bar, including the most abundant molecules present in the gas giants of the Solar System, as well as contributions from free electrons, metal hydrides, oxides, and atomic species, using the most up-to-date line lists published in the literature. These tables were used to calculate Rosseland-mean opacities for the molecular hydrogen envelopes of Jupiter and Saturn, which were then compared to the critical mean opacity required to maintain convection. We find that the presence of a radiative zone is controlled by the existence of K, Na, and NaH in the atmosphere of Jupiter and Saturn. For Jupiter, the elemental abundance of K and Na must be less than sim 10^{-3} times solar to form a radiative zone. In contrast, for Saturn, the required abundance for K and Na is below sim 10^{-4} times solar.