Zhiyi Li

Dominic Masters, Josef Dean, Kerstin Klaser et al.

This technical report presents GPS++, the first-place solution to the Open Graph Benchmark Large-Scale Challenge (OGB-LSC 2022) for the PCQM4Mv2 molecular property prediction task. Our approach implements several key principles from the prior literature. At its core our GPS++ method is a hybrid MPNN/Transformer model that incorporates 3D atom positions and an auxiliary denoising task. The effectiveness of GPS++ is demonstrated by achieving 0.0719 mean absolute error on the independent test-challenge PCQM4Mv2 split. Thanks to Graphcore IPU acceleration, GPS++ scales to deep architectures (16 layers), training at 3 minutes per epoch, and large ensemble (112 models), completing the final predictions in 1 hour 32 minutes, well under the 4 hour inference budget allocated. Our implementation is publicly available at: https://github.com/graphcore/ogb-lsc-pcqm4mv2.

Dominic Masters, Josef Dean, Kerstin Klaser et al.

We present GPS++, a hybrid Message Passing Neural Network / Graph Transformer model for molecular property prediction. Our model integrates a well-tuned local message passing component and biased global attention with other key ideas from prior literature to achieve state-of-the-art results on large-scale molecular dataset PCQM4Mv2. Through a thorough ablation study we highlight the impact of individual components and find that nearly all of the model's performance can be maintained without any use of global self-attention, showing that message passing is still a competitive approach for 3D molecular property prediction despite the recent dominance of graph transformers. We also find that our approach is significantly more accurate than prior art when 3D positional information is not available.

Zhiyi Li, Douglas Orr, Valeriu Ohan et al.

Reducing the computational cost of running large scale neural networks using sparsity has attracted great attention in the deep learning community. While much success has been achieved in reducing FLOP and parameter counts while maintaining acceptable task performance, achieving actual speed improvements has typically been much more difficult, particularly on general purpose accelerators (GPAs) such as NVIDIA GPUs using low precision number formats. In this work we introduce PopSparse, a library that enables fast sparse operations on Graphcore IPUs by leveraging both the unique hardware characteristics of IPUs as well as any block structure defined in the data. We target two different types of sparsity: static, where the sparsity pattern is fixed at compile-time; and dynamic, where it can change each time the model is run. We present benchmark results for matrix multiplication for both of these modes on IPU with a range of block sizes, matrix sizes and densities. Results indicate that the PopSparse implementations are faster than dense matrix multiplications on IPU at a range of sparsity levels with large matrix size and block size. Furthermore, static sparsity in general outperforms dynamic sparsity. While previous work on GPAs has shown speedups only for very high sparsity (typically 99\% and above), the present work demonstrates that our static sparse implementation outperforms equivalent dense calculations in FP16 at lower sparsity (around 90%). IPU code is available to view and run at ipu.dev/sparsity-benchmarks, GPU code will be made available shortly.

Dominique Beaini, Shenyang Huang, Joao Alex Cunha et al.

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.

Mengyu Wang, Xiaoying Zhi, Zhiyi Li et al.

While the next-token prediction (NTP) paradigm enables large language models (LLMs) to express their intrinsic knowledge, its sequential nature constrains performance on specialized, non-generative tasks. We attribute this performance bottleneck to the LLMs' knowledge expression mechanism, rather than to deficiencies in knowledge acquisition. To address this, we propose Self-Knowledge Re-expression (SKR), a novel, task-agnostic adaptation method. SKR transforms the LLM's output from generic token generation to highly efficient, task-specific expression. SKR is a fully local method that uses only unannotated data, requiring neither human supervision nor model distillation. Experiments on a large financial document dataset demonstrate substantial improvements: over 40% in Recall@1 for information retrieval tasks, over 76% reduction in object detection latency, and over 33% increase in anomaly detection AUPRC. Our results on the MMDocRAG dataset surpass those of leading retrieval models by at least 12.6%.

Zhiyi Li, Lihe Ding, Tianfan Xue

Neural Radiance Fields (NeRFs) have demonstrated remarkable effectiveness in novel view synthesis within 3D environments. However, extracting a radiance field of one specific object from multi-view images encounters substantial challenges due to occlusion and background complexity, thereby presenting difficulties in downstream applications such as NeRF editing and 3D mesh extraction. To solve this problem, in this paper, we propose Obj-NeRF, a comprehensive pipeline that recovers the 3D geometry of a specific object from multi-view images using a single prompt. This method combines the 2D segmentation capabilities of the Segment Anything Model (SAM) in conjunction with the 3D reconstruction ability of NeRF. Specifically, we first obtain multi-view segmentation for the indicated object using SAM with a single prompt. Then, we use the segmentation images to supervise NeRF construction, integrating several effective techniques. Additionally, we construct a large object-level NeRF dataset containing diverse objects, which can be useful in various downstream tasks. To demonstrate the practicality of our method, we also apply Obj-NeRF to various applications, including object removal, rotation, replacement, and recoloring.

Mark Neumann, James Gin, Benjamin Rhodes et al.

We introduce Orb, a family of universal interatomic potentials for atomistic modelling of materials. Orb models are 3-6 times faster than existing universal potentials, stable under simulation for a range of out of distribution materials and, upon release, represented a 31% reduction in error over other methods on the Matbench Discovery benchmark. We explore several aspects of foundation model development for materials, with a focus on diffusion pretraining. We evaluate Orb as a model for geometry optimization, Monte Carlo and molecular dynamics simulations.

Pengcheng Hou, Tao Wang, Daniel Cerkoney et al.

Quantum field theory (QFT) for interacting many-electron systems is fundamental to condensed matter physics, yet achieving accurate solutions confronts computational challenges in managing the combinatorial complexity of Feynman diagrams, implementing systematic renormalization, and evaluating high-dimensional integrals. We present a unifying framework that integrates QFT computational workflows with an AI-powered technology stack. A cornerstone of this framework is representing Feynman diagrams as computational graphs, which structures the inherent mathematical complexity and facilitates the application of optimized algorithms developed for machine learning and high-performance computing. Consequently, automatic differentiation, native to these graph representations, delivers efficient, fully automated, high-order field-theoretic renormalization procedures. This graph-centric approach also enables sophisticated numerical integration; our neural-network-enhanced Monte Carlo method, accelerated via massively parallel GPU implementation, efficiently evaluates challenging high-dimensional diagrammatic integrals. Applying this framework to the uniform electron gas, we determine the quasiparticle effective mass to a precision significantly surpassing current state-of-the-art simulations. Our work demonstrates the transformative potential of integrating AI-driven computational advances with QFT, opening systematic pathways for solving complex quantum many-body problems across disciplines.

Yichen Li, Zhiyi Li, Brandon Feng et al.

Digital twin worlds with realistic interactive dynamics presents a new opportunity to develop generalist embodied agents in scannable environments with complex physical behaviors. To this end, we present GDGen (Generalized Representation for Generalized Dynamics Generation), a framework that takes a potential energy perspective to seamlessly integrate rigid body, articulated body, and soft body dynamics into a unified, geometry-agnostic system. GDGen operates from the governing principle that the potential energy for any stable physical system should be low. This fresh perspective allows us to treat the world as one holistic entity and infer underlying physical properties from simple motion observations. We extend classic elastodynamics by introducing directional stiffness to capture a broad spectrum of physical behaviors, covering soft elastic, articulated, and rigid body systems. We propose a specialized network to model the extended material property and employ a neural field to represent deformation in a geometry-agnostic manner. Extensive experiments demonstrate that GDGen robustly unifies diverse simulation paradigms, offering a versatile foundation for creating interactive virtual environments and training robotic agents in complex, dynamically rich scenarios.

Grace Yang, Zhiyi Li, Yadong Liu et al.

Named entity recognition (NER) is a crucial task that aims to identify structured information, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can facilitate the extraction and analysis of important information. However, NER for other than English is challenging due to limited data availability, as the high expertise, time, and expenses are required to annotate its data. In this paper, by using the limited data, we explore various factors including model structure, corpus annotation scheme and data augmentation techniques to improve the performance of a NER model for French. Our experiments demonstrate that these approaches can significantly improve the model's F1 score from original CRF score of 62.41 to 79.39. Our findings suggest that considering different extrinsic factors and combining these techniques is a promising approach for improving NER performance where the size of data is limited.

Zhiyi Li, Shengjie Zhang, Yujie Song et al.

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can facilitate the extraction and analysis of important biomedical information, which can be used to improve downstream applications including the healthcare system. However, NER in the biomedical domain is challenging due to limited data availability, as the high expertise, time, and expenses are required to annotate its data. In this paper, by using the limited data, we explore various extrinsic factors including the corpus annotation scheme, data augmentation techniques, semi-supervised learning and Brill transformation, to improve the performance of a NER model on a clinical text dataset (i2b2 2012, \citet{sun-rumshisky-uzuner:2013}). Our experiments demonstrate that these approaches can significantly improve the model's F1 score from original 73.74 to 77.55. Our findings suggest that considering different extrinsic factors and combining these techniques is a promising approach for improving NER performance in the biomedical domain where the size of data is limited.

Xuan Liu, Zhiyi Li, Zuyi Li

Power systems become more prone to cyber-attacks due to the high integration of information technologies. In this paper, we demonstrate that the outages of some lines can be masked by injecting false data into a set of measurements. The success of the topology attack can be guaranteed by making that: 1)the injected false data obeys KCL and KVL to avoid being detected by the bad data detection program in the state estimation; 2)the residual is increased such that the line outage cannot be detected by PMU data. A quadratic programming problem is set up to determine the optimal attack vector that can maximize the residual of the outaged line. The IEEE 39-bus system is used to demonstrate the masking scheme.