The widespread adoption of Transformer architectures in various data modalities has opened new avenues for the applications in molecular modeling. Nevertheless, it remains elusive that whether the Transformer-based architecture can do molecular modeling as good as equivariant GNNs. In this paper, by designing Interatomic Positional Encoding (IPE) thatparameterizes atomic environments as Transformer's positional encodings,we propose Geoformer, a novel geometric Transformer to effectively model molecular structures for various molecular property prediction. We evaluate Geoformer on several benchmarks, including the QM9 dataset and the recently proposed Molecule3D dataset.

We introduce a new paradigm for building large causal models (LCMs) that exploits the enormous potential latent in today's large language models (LLMs). We describe our ongoing experiments with an implemented system called DEMOCRITUS (Decentralized Extraction of Manifold Ontologies of Causal Relations Integrating Topos Universal Slices) aimed at building, organizing, and visualizing LCMs that span disparate domains extracted from carefully targeted textual queries to LLMs. DEMOCRITUS is methodologically distinct from traditional narrow domain and hypothesis centered causal inference that builds causal models from experiments that produce numerical data. A high-quality LLM is used to propose topics, generate causal questions, and extract plausible causal statements from a diverse range of domains. The technical challenge is then to take these isolated, fragmented, potentially ambiguous and possibly conflicting causal claims, and weave them into a coherent whole, converting them into relational causal triples and embedding them into a LCM. Addressing this technical challenge required inventing new categorical machine learning methods, which we can only briefly summarize in this paper, as it is focused more on the systems side of building DEMOCRITUS. We describe the implementation pipeline for DEMOCRITUS comprising of six modules, examine its computational cost profile to determine where the current bottlenecks in scaling the system to larger models. We describe the results of using DEMOCRITUS over a wide range of domains, spanning archaeology, biology, climate change, economics, medicine and technology. We discuss the limitations of the current DEMOCRITUS system, and outline directions for extending its capabilities.

The widespread adoption of Transformer architectures in various data modalities has opened new avenues for the applications in molecular modeling. Nevertheless, it remains elusive that whether the Transformer-based architecture can do molecular modeling as good as equivariant GNNs. In this paper, by designing Interatomic Positional Encoding (IPE) thatparameterizes atomic environments as Transformer's positional encodings,we propose Geoformer, a novel geometric Transformer to effectively model molecular structures for various molecular property prediction. We evaluate Geoformer on several benchmarks, including the QM9 dataset and the recently proposed Molecule3D dataset.

Several problems in stochastic analysis are defined through their geometry, and preserving that geometric structure is essential to generating meaningful predictions. Nevertheless, how to design principled deep learning (DL) models capable of encoding these geometric structures remains largely unknown. We address this open problem by introducing a universal causal geometric DL framework in which the user specifies a suitable pair of metric spaces $\mathscr{X}$ and $\mathscr{Y}$ and our framework returns a DL model capable of causally approximating any ``regular'' map sending time series in $\mathscr{X}^{\mathbb{Z}}$ to time series in $\mathscr{Y}^{\mathbb{Z}}$ while respecting their forward flow of information throughout time. Suitable geometries on $\mathscr{Y}$ include various (adapted) Wasserstein spaces arising in optimal stopping problems, a variety of statistical manifolds describing the conditional distribution of continuous-time finite state Markov chains, and all Fr\'{e}chet spaces admitting a Schauder basis, e.g. as in classical finance. Suitable spaces $\mathscr{X}$ are compact subsets of any Euclidean space. Our results all quantitatively express the number of parameters needed for our DL model to achieve a given approximation error as a function of the target map's regularity and the geometric structure both of $\mathscr{X}$ and of $\mathscr{Y}$. Even when omitting any temporal structure, our universal approximation theorems are the first guarantees that H\"{o}lder functions, defined between such $\mathscr{X}$ and $\mathscr{Y}$ can be approximated by DL models.