Nevertheless, it remains elusive that whether the Transformer-based architecture can do molecular modeling as good as equivariant GNNs.

In recent years, transformer networks [V aswani et al., 2017] have been established as a fundamental neural architecture powering state-of-the-art results in many applications, including language

In recent years, transformer networks [V aswani et al., 2017] have been established as a fundamental neural architecture powering state-of-the-art results in many applications, including language

The in-context learning (ICL) capability of pre-trained models based on the transformer architecture has received growing interest in recent years. While theoretical understanding has been obtained for ICL in reinforcement learning (RL), the previous results are largely confined to the single-agent setting. This work proposes to further explore the in-context learning capabilities of pre-trained transformer models in competitive multi-agent games, i.e., in-context game-playing (ICGP). Focusing on the classical two-player zero-sum games, theoretical guarantees are provided to demonstrate that pre-trained transformers can provably learn to approximate Nash equilibrium in an in-context manner for both decentralized and centralized learning settings. As a key part of the proof, constructional results are established to demonstrate that the transformer architecture is sufficiently rich to realize celebrated multi-agent game-playing algorithms, in particular, decentralized V-learning and centralized VI-ULCB.

Planning is a crucial element of both human intelligence and contemporary large language models (LLMs). In this paper, we initiate a theoretical investigation into the emergence of planning capabilities in Transformer-based LLMs via their next-word prediction mechanisms. We model planning as a network path-finding task, where the objective is to generate a valid path from a specified source node to a designated target node. Our mathematical characterization shows that Transformer architectures can execute path-finding by embedding the adjacency and reachability matrices within their weights. Furthermore, our theoretical analysis of gradient-based learning dynamics reveals that LLMs can learn both the adjacency and a limited form of the reachability matrices. These theoretical insights are then validated through experiments, which demonstrate that Transformer architectures indeed learn the adjacency and an incomplete reachability matrices, consistent with our theoretical predictions. When applying our methodology to the real-world planning benchmark Blocksworld, our observations remain consistent. Additionally, our analyses uncover a fundamental limitation of current Transformer architectures in path-finding: these architectures cannot identify reachability relationships through transitivity, which leads to failures in generating paths when concatenation is required. These findings provide new insights into how the internal mechanisms of autoregressive learning facilitate intelligent planning and deepen our understanding of how future LLMs might achieve more advanced and general planning-and-reasoning capabilities across diverse applications.

We present a novel bi-directional Transformer architecture (BiXT) which scales linearly with input size in terms of computational cost and memory consumption, but does not suffer the drop in performance or limitation to only one input modality seen with other efficient Transformer-based approaches. BiXT is inspired by the Perceiver architectures but replaces iterative attention with an efficient bi-directional cross-attention module in which input tokens and latent variables attend to each other simultaneously, leveraging a naturally emerging attention-symmetry between the two. This approach unlocks a key bottleneck experienced by Perceiver-like architectures and enables the processing and interpretation of both semantics ('what') and location ('where') to develop alongside each other over multiple layers -- allowing its direct application to dense and instance-based tasks alike. By combining efficiency with the generality and performance of a full Transformer architecture, BiXT can process longer sequences like point clouds, text or images at higher feature resolutions and achieves competitive performance across a range of tasks like point cloud part segmentation, semantic image segmentation, image classification, hierarchical sequence modeling and document retrieval. Our experiments demonstrate that BiXT models outperform larger competitors by leveraging longer sequences more efficiently on vision tasks like classification and segmentation, and perform on par with full Transformer variants on sequence modeling and document retrieval -- but require 28\% fewer FLOPs and are up to $8.4\times$ faster.

Neural sequence models based on the transformer architecture have demonstrated remarkable \emph{in-context learning} (ICL) abilities, where they can perform new tasks when prompted with training and test examples, without any parameter update to the model. This work first provides a comprehensive statistical theory for transformers to perform ICL. Concretely, we show that transformers can implement a broad class of standard machine learning algorithms in context, such as least squares, ridge regression, Lasso, learning generalized linear models, and gradient descent on two-layer neural networks, with near-optimal predictive power on various in-context data distributions. Using an efficient implementation of in-context gradient descent as the underlying mechanism, our transformer constructions admit mild size bounds, and can be learned with polynomially many pretraining sequences. Building on these ``base'' ICL algorithms, intriguingly, we show that transformers can implement more complex ICL procedures involving \emph{in-context algorithm selection}, akin to what a statistician can do in real life---A \emph{single} transformer can adaptively select different base ICL algorithms---or even perform qualitatively different tasks---on different input sequences, without any explicit prompting of the right algorithm or task. We both establish this in theory by explicit constructions, and also observe this phenomenon experimentally. In theory, we construct two general mechanisms for algorithm selection with concrete examples: pre-ICL testing, and post-ICL validation. As an example, we use the post-ICL validation mechanism to construct a transformer that can perform nearly Bayes-optimal ICL on a challenging task---noisy linear models with mixed noise levels. Experimentally, we demonstrate the strong in-context algorithm selection capabilities of standard transformer architectures.

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.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.