Shuxin Zheng

Yu Shi, Shuxin Zheng, Guolin Ke et al. · microsoft-research, tsinghua

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. With these simple modifications, Graphormer could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on 2D and 3D molecular graph modeling tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Empirically, Graphormer could achieve much less MAE than the originally reported results on the PCQM4M quantum chemistry dataset used in KDD Cup 2021. In the meanwhile, it greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All codes could be found at https://github.com/Microsoft/Graphormer.

Shengjie Luo, Shanda Li, Shuxin Zheng et al.

Relative Positional Encoding (RPE), which encodes the relative distance between any pair of tokens, is one of the most successful modifications to the original Transformer. As far as we know, theoretical understanding of the RPE-based Transformers is largely unexplored. In this work, we mathematically analyze the power of RPE-based Transformers regarding whether the model is capable of approximating any continuous sequence-to-sequence functions. One may naturally assume the answer is in the affirmative -- RPE-based Transformers are universal function approximators. However, we present a negative result by showing there exist continuous sequence-to-sequence functions that RPE-based Transformers cannot approximate no matter how deep and wide the neural network is. One key reason lies in that most RPEs are placed in the softmax attention that always generates a right stochastic matrix. This restricts the network from capturing positional information in the RPEs and limits its capacity. To overcome the problem and make the model more powerful, we first present sufficient conditions for RPE-based Transformers to achieve universal function approximation. With the theoretical guidance, we develop a novel attention module, called Universal RPE-based (URPE) Attention, which satisfies the conditions. Therefore, the corresponding URPE-based Transformers become universal function approximators. Extensive experiments covering typical architectures and tasks demonstrate that our model is parameter-efficient and can achieve superior performance to strong baselines in a wide range of applications. The code will be made publicly available at https://github.com/lsj2408/URPE.

Yu Shi, Guolin Ke, Zhuoming Chen et al. · microsoft-research

Recent years have witnessed significant success in Gradient Boosting Decision Trees (GBDT) for a wide range of machine learning applications. Generally, a consensus about GBDT's training algorithms is gradients and statistics are computed based on high-precision floating points. In this paper, we investigate an essentially important question which has been largely ignored by the previous literature: how many bits are needed for representing gradients in training GBDT? To solve this mystery, we propose to quantize all the high-precision gradients in a very simple yet effective way in the GBDT's training algorithm. Surprisingly, both our theoretical analysis and empirical studies show that the necessary precisions of gradients without hurting any performance can be quite low, e.g., 2 or 3 bits. With low-precision gradients, most arithmetic operations in GBDT training can be replaced by integer operations of 8, 16, or 32 bits. Promisingly, these findings may pave the way for much more efficient training of GBDT from several aspects: (1) speeding up the computation of gradient statistics in histograms; (2) compressing the communication cost of high-precision statistical information during distributed training; (3) the inspiration of utilization and development of hardware architectures which well support low-precision computation for GBDT training. Benchmarked on CPUs, GPUs, and distributed clusters, we observe up to 2$\times$ speedup of our simple quantization strategy compared with SOTA GBDT systems on extensive datasets, demonstrating the effectiveness and potential of the low-precision training of GBDT. The code will be released to the official repository of LightGBM.

Mingqing Xiao, Shuxin Zheng, Chang Liu et al. · microsoft-research, tsinghua

Image rescaling is a commonly used bidirectional operation, which first downscales high-resolution images to fit various display screens or to be storage- and bandwidth-friendly, and afterward upscales the corresponding low-resolution images to recover the original resolution or the details in the zoom-in images. However, the non-injective downscaling mapping discards high-frequency contents, leading to the ill-posed problem for the inverse restoration task. This can be abstracted as a general image degradation-restoration problem with information loss. In this work, we propose a novel invertible framework to handle this general problem, which models the bidirectional degradation and restoration from a new perspective, i.e. invertible bijective transformation. The invertibility enables the framework to model the information loss of pre-degradation in the form of distribution, which could mitigate the ill-posed problem during post-restoration. To be specific, we develop invertible models to generate valid degraded images and meanwhile transform the distribution of lost contents to the fixed distribution of a latent variable during the forward degradation. Then restoration is made tractable by applying the inverse transformation on the generated degraded image together with a randomly-drawn latent variable. We start from image rescaling and instantiate the model as Invertible Rescaling Network (IRN), which can be easily extended to the similar decolorization-colorization task. We further propose to combine the invertible framework with existing degradation methods such as image compression for wider applications. Experimental results demonstrate the significant improvement of our model over existing methods in terms of both quantitative and qualitative evaluations of upscaling and colorizing reconstruction from downscaled and decolorized images, and rate-distortion of image compression.

Shengjie Luo, Tianlang Chen, Yixian Xu et al.

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D space. For molecular representation learning, most previous works designed neural networks only for a particular data format, making the learned models likely to fail for other data formats. We believe a general-purpose neural network model for chemistry should be able to handle molecular tasks across data modalities. To achieve this goal, in this work, we develop a novel Transformer-based Molecular model called Transformer-M, which can take molecular data of 2D or 3D formats as input and generate meaningful semantic representations. Using the standard Transformer as the backbone architecture, Transformer-M develops two separated channels to encode 2D and 3D structural information and incorporate them with the atom features in the network modules. When the input data is in a particular format, the corresponding channel will be activated, and the other will be disabled. By training on 2D and 3D molecular data with properly designed supervised signals, Transformer-M automatically learns to leverage knowledge from different data modalities and correctly capture the representations. We conducted extensive experiments for Transformer-M. All empirical results show that Transformer-M can simultaneously achieve strong performance on 2D and 3D tasks, suggesting its broad applicability. The code and models will be made publicly available at https://github.com/lsj2408/Transformer-M.

Shuxin Zheng, Jiyan He, Chang Liu et al. · microsoft-research

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science.

Quan Zheng, Yan Gao, Shaobin He et al.

LLM-agent simulation offers a flexible computational tool for studying population response trajectories that depend on scenario events, memory, demographics, and evolving social context. However, full multi-round simulation scales linearly with both population size and horizon, requiring every agent to query the LLM at every round. We propose Adaptive Prototype Simulation (APS), a framework that reframes scalable LLM-based simulation as a recurrent oracle-allocation problem. APS retains the designated LLM as the online transition oracle while querying adaptive core prototypes, selected singleton-tail agents, and shadow-audit agents. Prototype responses induce local response surfaces for nearby agents, reducing online LLM calls without replacing the underlying transition model. To control approximation bias, shadow-audit residual correction estimates propagation residuals for aggregate correction and future budget allocation, while tail-protected singleton routing directly queries selected isolated, heterogeneous, or high-curvature regions that are vulnerable to smoothing. Theoretically, we treat APS as an estimator for full-scale high-precision individual social simulation and decompose its errors into prototype-coverage error, shadow-audit residual-correction error, local-propagation bias, and temporal context mismatch. Under the reported protocols, APS gives lower reference-aligned distributional discrepancy than scale-oriented and same-budget baselines while reducing online LLM calls, with ablations and compact robustness checks diagnosing the main bias-control mechanisms. In a 10M-agent, multi-round public-opinion simulation, APS achieves a 381.1-fold reduction over full simulation, with reference-aligned final-round JSD of 0.094 against the corresponding full-LLM reference.

Zhenzhen Ren, Xinpeng Zhang, Zhenxing Qian et al. · microsoft-research

The integration of external tools is pivotal for empowering Large Language Model (LLM) agents with real-world capabilities. However, training these agents through direct, continuous interaction with diverse tools is often prohibitively expensive, slow, and introduces additional development and maintenance overhead. To address this challenge, we introduce the Generalist Tool Model (GTM), a 1.5-billion-parameter model that learns to act as a universal tool simulator. With only prompt-level configuration, GTM accesses tool functionalities along with input arguments and generates outputs that faithfully mimic real tool execution, providing a fast and cost-effective solution that eliminates development overhead. To build GTM, we propose the Context-Aware Response Generation (CARG) pipeline, which synthesizes comprehensive training data covering over 20,000 tools across 300 domains including physics, medicine, robotics, and finance. Through this pipeline, GTM learns to produce not only syntactically correct outputs but also logically coherent and contextually appropriate responses. Experiments demonstrate that GTM produces high-quality outputs with strong consistency and reliability. Besides when used in real reinforcement learning scenarios for agent training, GTM exhibits significantly faster simulation speed compared to real tools while maintaining comparable output quality, along with remarkable generalization and domain adaptability. Our results establish GTM as a foundational component for developing future AI agents, enabling efficient and scalable training of tool-augmented systems.

Yaosen Min, Ye Wei, Peizhuo Wang et al.

Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only take advantage of static crystal structures while the actual binding affinities are generally determined by the thermodynamic ensembles between proteins and ligands. One effective way to approximate such a thermodynamic ensemble is to use molecular dynamics (MD) simulation. Here, an MD dataset containing 3,218 different protein-ligand complexes is curated, and Dynaformer, a graph-based deep learning model is further developed to predict the binding affinities by learning the geometric characteristics of the protein-ligand interactions from the MD trajectories. In silico experiments demonstrated that the model exhibits state-of-the-art scoring and ranking power on the CASF-2016 benchmark dataset, outperforming the methods hitherto reported. Moreover, in a virtual screening on heat shock protein 90 (HSP90) using Dynaformer, 20 candidates are identified and their binding affinities are further experimentally validated. Dynaformer displayed promising results in virtual drug screening, revealing 12 hit compounds (two are in the submicromolar range), including several novel scaffolds. Overall, these results demonstrated that the approach offer a promising avenue for accelerating the early drug discovery process.

He Zhang, Siyuan Liu, Jiacheng You et al.

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research. However, its accuracy is limited by the kinetic energy density functional, which is notoriously hard to approximate for non-periodic molecular systems. Here we propose M-OFDFT, an OFDFT approach capable of solving molecular systems using a deep learning functional model. We build the essential non-locality into the model, which is made affordable by the concise density representation as expansion coefficients under an atomic basis. With techniques to address unconventional learning challenges therein, M-OFDFT achieves a comparable accuracy with Kohn-Sham DFT on a wide range of molecules untouched by OFDFT before. More attractively, M-OFDFT extrapolates well to molecules much larger than those seen in training, which unleashes the appealing scaling of OFDFT for studying large molecules including proteins, representing an advancement of the accuracy-efficiency trade-off frontier in quantum chemistry.

Zhixin Han, Yanzhi Zhang, Chuyang Wei et al.

Live future prediction refers to the task of making predictions about real-world events before they unfold. This task is increasingly studied using large language model-based agent systems, and it is important for building agents that can continually learn from real-world. Just as interactive environments have often driven progress in agents, advancing live future prediction naturally motivates viewing it as a learning environment. Prior works have explored future prediction from several different parts, but have generally not framed it as a unified learning environment. This task is appealing for learning because it can provide a large number of prediction questions grounded in diverse real-world events, while preventing answer leakage. To leverage the advantages of live future prediction, we present FutureWorld, a live agentic reinforcement learning environment that closes the training loop between prediction, outcome realization, and parameters update. In our environment, we take three open-source base models and train them for consecutive days. The results show that training is effective. Furthermore, we build a daily benchmark based on the environment and evaluate several frontier agents on it to establish performance baselines for current agent systems.

Chuyang Wei, Maohang Gao, Zhixin Han et al.

Many consequential decisions must be made before the relevant outcome is known. Such problems are commonly framed as future prediction, where an LLM agent must form a prediction for an unresolved question using only the public information available at the prediction time. The setting is difficult because public evidence evolves while useful supervision arrives only after the question is resolved, so most existing approaches still improve mainly from final outcomes. Yet final outcomes are too coarse to guide earlier factor tracking, evidence gathering and interpretation, or uncertainty handling. When the same unresolved question is revisited over time, temporal contrasts between earlier and later predictions can expose omissions in the earlier prediction process; we call this signal internal feedback. We introduce Milkyway, a self-evolving agent system that keeps the base model fixed and instead updates a persistent future prediction harness for factor tracking, evidence gathering and interpretation, and uncertainty handling. Across repeated predictions on the same unresolved question, Milkyway extracts internal feedback and writes reusable guidance back into the harness, so later predictions on that question can improve before the outcome is known. After the question is resolved, the final outcome provides a retrospective check before the updated harness is carried forward to subsequent questions. On FutureX and FutureWorld, Milkyway achieves the best overall score among the compared methods, improving FutureX from 44.07 to 60.90 and FutureWorld from 62.22 to 77.96.

Yanxi Wang, Zhiling Zhang, Wenbo Zhou et al.

GUI agents enable end-to-end automation through direct perception of and interaction with on-screen interfaces. However, these agents frequently access interfaces containing sensitive personal information, and screenshots are often transmitted to remote models, creating substantial privacy risks. These risks are particularly severe in GUI workflows: GUIs expose richer, more accessible private information, and privacy risks depend on interaction trajectories across sequential scenes. We propose GUIGuard, a three-stage framework for privacy-preserving GUI agents: (1) privacy recognition, (2) privacy protection, and (3) task execution under protection. We further construct GUIGuard-Bench, a cross-platform benchmark with 630 trajectories and 13,830 screenshots, annotated with region-level privacy grounding and fine-grained labels of risk level, privacy category, and task necessity. Evaluations reveal that existing agents exhibit limited privacy recognition, with state-of-the-art models achieving only 13.3% accuracy on Android and 1.4% on PC. Under privacy protection, task-planning semantics can still be maintained, with closed-source models showing stronger semantic consistency than open-source ones. Case studies on MobileWorld show that carefully designed protection strategies achieve higher task accuracy while preserving privacy. Our results highlight privacy recognition as a critical bottleneck for practical GUI agents. Project: https://futuresis.github.io/GUIGuard-page/

Tianlang Chen, Shengjie Luo, Di He et al.

Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the properties and simulate the behaviors of molecular systems. The molecular model is governed by physical laws, which impose geometric constraints such as invariance and equivariance to coordinate rotation and translation. While numerous deep learning approaches have been developed to learn molecular representations under these constraints, most of them are built upon heuristic and costly modules. We argue that there is a strong need for a general and flexible framework for learning both invariant and equivariant features. In this work, we introduce a novel Transformer-based molecular model called GeoMFormer to achieve this goal. Using the standard Transformer modules, two separate streams are developed to maintain and learn invariant and equivariant representations. Carefully designed cross-attention modules bridge the two streams, allowing information fusion and enhancing geometric modeling in each stream. As a general and flexible architecture, we show that many previous architectures can be viewed as special instantiations of GeoMFormer. Extensive experiments are conducted to demonstrate the power of GeoMFormer. All empirical results show that GeoMFormer achieves strong performance on both invariant and equivariant tasks of different types and scales. Code and models will be made publicly available at https://github.com/c-tl/GeoMFormer.

Yu Shi, Shuxin Zheng, Guolin Ke et al.

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. The "Graphormer-V2" could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on downstream tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Graphormer-V2 achieves much less MAE than the vanilla Graphormer on the PCQM4M quantum chemistry dataset used in KDD Cup 2021, where the latter one won the first place in this competition. In the meanwhile, Graphormer-V2 greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All models could be found at \url{https://github.com/Microsoft/Graphormer}.

Shengjie Luo, Kaiyuan Gao, Shuxin Zheng et al.

Transformer has demonstrated its great power to learn contextual word representations for multiple languages in a single model. To process multilingual sentences in the model, a learnable vector is usually assigned to each language, which is called "language embedding". The language embedding can be either added to the word embedding or attached at the beginning of the sentence. It serves as a language-specific signal for the Transformer to capture contextual representations across languages. In this paper, we revisit the use of language embedding and identify several problems in the existing formulations. By investigating the interaction between language embedding and word embedding in the self-attention module, we find that the current methods cannot reflect the language-specific word correlation well. Given these findings, we propose a new approach called Cross-lingual Language Projection (XLP) to replace language embedding. For a sentence, XLP projects the word embeddings into language-specific semantic space, and then the projected embeddings will be fed into the Transformer model to process with their language-specific meanings. In such a way, XLP achieves the purpose of appropriately encoding "language" in a multilingual Transformer model. Experimental results show that XLP can freely and significantly boost the model performance on extensive multilingual benchmark datasets. Codes and models will be released at https://github.com/lsj2408/XLP.

Zhuliang Yao, Yue Cao, Shuxin Zheng et al.

A well-known issue of Batch Normalization is its significantly reduced effectiveness in the case of small mini-batch sizes. When a mini-batch contains few examples, the statistics upon which the normalization is defined cannot be reliably estimated from it during a training iteration. To address this problem, we present Cross-Iteration Batch Normalization (CBN), in which examples from multiple recent iterations are jointly utilized to enhance estimation quality. A challenge of computing statistics over multiple iterations is that the network activations from different iterations are not comparable to each other due to changes in network weights. We thus compensate for the network weight changes via a proposed technique based on Taylor polynomials, so that the statistics can be accurately estimated and batch normalization can be effectively applied. On object detection and image classification with small mini-batch sizes, CBN is found to outperform the original batch normalization and a direct calculation of statistics over previous iterations without the proposed compensation technique. Code is available at https://github.com/Howal/Cross-iterationBatchNorm .

Yanzhi Zhang, Yitong Duan, Zhaoxi Zhang et al.

Test-time scaling has emerged as a promising direction for enhancing the reasoning capabilities of Large Language Models in last few years. In this work, we propose Population-Evolve, a training-free method inspired by Genetic Algorithms to optimize LLM reasoning. Our approach maintains a dynamic population of candidate solutions for each problem via parallel reasoning. By incorporating an evolve prompt, the LLM self-evolves its population in all iterations. Upon convergence, the final answer is derived via majority voting. Furthermore, we establish a unification framework that interprets existing test-time scaling strategies through the lens of genetic algorithms. Empirical results demonstrate that Population-Evolve achieves superior accuracy with low performance variance and computational efficiency. Our findings highlight the potential of evolutionary strategies to unlock the reasoning power of LLMs during inference.

Jiyan He, Weitao Feng, Yaosen Min et al. · microsoft-research

The expanding application of Artificial Intelligence (AI) in scientific fields presents unprecedented opportunities for discovery and innovation. However, this growth is not without risks. AI models in science, if misused, can amplify risks like creation of harmful substances, or circumvention of established regulations. In this study, we aim to raise awareness of the dangers of AI misuse in science, and call for responsible AI development and use in this domain. We first itemize the risks posed by AI in scientific contexts, then demonstrate the risks by highlighting real-world examples of misuse in chemical science. These instances underscore the need for effective risk management strategies. In response, we propose a system called SciGuard to control misuse risks for AI models in science. We also propose a red-teaming benchmark SciMT-Safety to assess the safety of different systems. Our proposed SciGuard shows the least harmful impact in the assessment without compromising performance in benign tests. Finally, we highlight the need for a multidisciplinary and collaborative effort to ensure the safe and ethical use of AI models in science. We hope that our study can spark productive discussions on using AI ethically in science among researchers, practitioners, policymakers, and the public, to maximize benefits and minimize the risks of misuse.

Yanzhi Zhang, Zhaoxi Zhang, Haoxiang Guan et al.

Reinforcement learning has emerged as a powerful paradigm for post-training large language models (LLMs) to improve reasoning. Approaches like Reinforcement Learning from Human Feedback (RLHF) and Reinforcement Learning with Verifiable Rewards (RLVR) have shown strong results, but they require extensive external supervision. We investigate an alternative class of methods, Reinforcement Learning from Internal Feedback (RLIF), which relies solely on intrinsic model-derived signals instead of external rewards. In particular, we leverage unsupervised reward proxies such as token-level entropy, trajectory-level entropy, and self-certainty. Our theoretical analysis shows these internal objectives are partially equivalent, and we empirically evaluate various RLIF strategies on challenging math reasoning benchmarks. Experimental results demonstrate that RLIF can boost the reasoning performance of base LLMs at the beginning phase of the training, matching or surpassing RLVR techniques on these tasks. However, when training progresses, performance degrades even below the model before training. Moreover, we find that RLIF yields little improvement for instruction-tuned models, indicating diminishing returns of intrinsic feedback once an LLM is already instruction-tuned. We further analyze this limitation by mixing model weights and explain the reason of RLIF's training behaviors, providing practical guidelines for integrating internal feedback signals into LLM training. We hope our analysis of internal feedback will inform more principled and effective strategies for LLM post-training.

Yingce Xia, Peiran Jin, Shufang Xie et al. · microsoft-research

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, RNA and even cells. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) top performance across different domains, matching or surpassing state-of-the-art specialist models. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Yiwen Zheng, Prakash Thakolkaran, Agni K. Biswal et al.

Vitrimer is a new, exciting class of sustainable polymers with the ability to heal due to their dynamic covalent adaptive network that can go through associative rearrangement reactions. However, a limited choice of constituent molecules restricts their property space, prohibiting full realization of their potential applications. To overcome this challenge, we couple molecular dynamics (MD) simulations and a novel graph variational autoencoder (VAE) machine learning model for inverse design of vitrimer chemistries with desired glass transition temperature (Tg) and synthesize a novel vitrimer polymer. We build the first vitrimer dataset of one million chemistries and calculate Tg on 8,424 of them by high-throughput MD simulations calibrated by a Gaussian process model. The proposed novel VAE employs dual graph encoders and a latent dimension overlapping scheme which allows for individual representation of multi-component vitrimers. By constructing a continuous latent space containing necessary information of vitrimers, we demonstrate high accuracy and efficiency of our framework in discovering novel vitrimers with desirable Tg beyond the training regime. To validate the effectiveness of our framework in experiments, we generate novel vitrimer chemistries with a target Tg = 323 K. By incorporating chemical intuition, we synthesize a vitrimer with Tg of 311-317 K, and experimentally demonstrate healability and flowability. The proposed framework offers an exciting tool for polymer chemists to design and synthesize novel, sustainable vitrimer polymers for a facet of applications.

Haoxiang Guan, Jiyan He, Shuxin Zheng et al. · microsoft-research

Large language models (LLMs) have demonstrated impressive performance on many tasks. However, to achieve optimal performance, specially designed prompting methods are still needed. These methods either rely on task-specific few-shot examples that require a certain level of domain knowledge, or are designed to be simple but only perform well on a few types of tasks. In this work, we attempt to introduce the concept of generalist prompting, which operates on the design principle of achieving optimal or near-optimal performance on a wide range of tasks while eliminating the need for manual selection and customization of prompts tailored to specific problems. Furthermore, we propose MeMo (Mental Models), an innovative prompting method that is simple-designed yet effectively fulfills the criteria of generalist prompting. MeMo distills the cores of various prompting methods into individual mental models and allows LLMs to autonomously select the most suitable mental models for the problem, achieving or being near to the state-of-the-art results on diverse tasks such as STEM, logical reasoning, and commonsense reasoning in zero-shot settings. We hope that the insights presented herein will stimulate further exploration of generalist prompting methods for LLMs.

Haoyu Dong, Pengkun Zhang, Yan Gao et al.

We introduce a finance & accounting benchmark (Finch) for evaluating AI agents on real-world, enterprise-grade professional workflows -- interleaving data entry, structuring, formatting, web search, cross-file retrieval, calculation, modeling, validation, translation, visualization, and reporting. Finch is sourced from authentic enterprise workspaces at Enron (15,000 spreadsheets and 500,000 emails from 150 employees) and other financial institutions, preserving in-the-wild messiness across multimodal artifacts (text, tables, formulas, charts, code, and images) and spanning diverse domains such as budgeting, trading, and asset management. We propose a workflow construction process that combines LLM-assisted discovery with expert annotation: (1) LLM-assisted, expert-verified derivation of workflows from real-world email threads and version histories of spreadsheet files, and (2) meticulous expert annotation for workflows, requiring over 700 hours of domain-expert effort. This yields 172 composite workflows with 384 tasks, involving 1,710 spreadsheets with 27 million cells, along with PDFs and other artifacts, capturing the intrinsically messy, long-horizon, knowledge-intensive, and collaborative nature of real-world enterprise work. We conduct both human and automated evaluations of frontier AI systems including GPT 5.1, Claude Sonnet 4.5, Gemini 3 Pro, Grok 4, and Qwen 3 Max, and GPT 5.1 Pro spends 16.8 minutes per workflow yet passes only 38.4% of workflows, while Claude Sonnet 4.5 passes just 25.0%. Comprehensive case studies further surface the challenges that real-world enterprise workflows pose for AI agents.

Shengjie Luo, Yixian Xu, Di He et al.

The accurate prediction of geometric state evolution in complex systems is critical for advancing scientific domains such as quantum chemistry and material modeling. Traditional experimental and computational methods face challenges in terms of environmental constraints and computational demands, while current deep learning approaches still fall short in terms of precision and generality. In this work, we introduce the Geometric Diffusion Bridge (GDB), a novel generative modeling framework that accurately bridges initial and target geometric states. GDB leverages a probabilistic approach to evolve geometric state distributions, employing an equivariant diffusion bridge derived by a modified version of Doob's $h$-transform for connecting geometric states. This tailored diffusion process is anchored by initial and target geometric states as fixed endpoints and governed by equivariant transition kernels. Moreover, trajectory data can be seamlessly leveraged in our GDB framework by using a chain of equivariant diffusion bridges, providing a more detailed and accurate characterization of evolution dynamics. Theoretically, we conduct a thorough examination to confirm our framework's ability to preserve joint distributions of geometric states and capability to completely model the underlying dynamics inducing trajectory distributions with negligible error. Experimental evaluations across various real-world scenarios show that GDB surpasses existing state-of-the-art approaches, opening up a new pathway for accurately bridging geometric states and tackling crucial scientific challenges with improved accuracy and applicability.

Shengjie Luo, Shanda Li, Tianle Cai et al.

The attention module, which is a crucial component in Transformer, cannot scale efficiently to long sequences due to its quadratic complexity. Many works focus on approximating the dot-then-exponentiate softmax function in the original attention, leading to sub-quadratic or even linear-complexity Transformer architectures. However, we show that these methods cannot be applied to more powerful attention modules that go beyond the dot-then-exponentiate style, e.g., Transformers with relative positional encoding (RPE). Since in many state-of-the-art models, relative positional encoding is used as default, designing efficient Transformers that can incorporate RPE is appealing. In this paper, we propose a novel way to accelerate attention calculation for Transformers with RPE on top of the kernelized attention. Based upon the observation that relative positional encoding forms a Toeplitz matrix, we mathematically show that kernelized attention with RPE can be calculated efficiently using Fast Fourier Transform (FFT). With FFT, our method achieves $\mathcal{O}(n\log n)$ time complexity. Interestingly, we further demonstrate that properly using relative positional encoding can mitigate the training instability problem of vanilla kernelized attention. On a wide range of tasks, we empirically show that our models can be trained from scratch without any optimization issues. The learned model performs better than many efficient Transformer variants and is faster than standard Transformer in the long-sequence regime.

Chengxuan Ying, Mingqi Yang, Shuxin Zheng et al.

In this technical report, we present our solution of KDD Cup 2021 OGB Large-Scale Challenge - PCQM4M-LSC Track. We adopt Graphormer and ExpC as our basic models. We train each model by 8-fold cross-validation, and additionally train two Graphormer models on the union of training and validation sets with different random seeds. For final submission, we use a naive ensemble for these 18 models by taking average of their outputs. Using our method, our team MachineLearning achieved 0.1200 MAE on test set, which won the first place in KDD Cup graph prediction track.

Chengxuan Ying, Tianle Cai, Shengjie Luo et al.

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.

Dinglan Peng, Shuxin Zheng, Yatao Li et al.

Semantic understanding of programs is a fundamental problem for programming language processing (PLP). Recent works that learn representations of code based on pre-training techniques in NLP have pushed the frontiers in this direction. However, the semantics of PL and NL have essential differences. These being ignored, we believe it is difficult to build a model to better understand programs, by either directly applying off-the-shelf NLP pre-training techniques to the source code, or adding features to the model by the heuristic. In fact, the semantics of a program can be rigorously defined by formal semantics in PL theory. For example, the operational semantics, describes the meaning of a valid program as updating the environment (i.e., the memory address-value function) through fundamental operations, such as memory I/O and conditional branching. Inspired by this, we propose a novel program semantics learning paradigm, that the model should learn from information composed of (1) the representations which align well with the fundamental operations in operational semantics, and (2) the information of environment transition, which is indispensable for program understanding. To validate our proposal, we present a hierarchical Transformer-based pre-training model called OSCAR to better facilitate the understanding of programs. OSCAR learns from intermediate representation (IR) and an encoded representation derived from static analysis, which are used for representing the fundamental operations and approximating the environment transitions respectively. OSCAR empirically shows the outstanding capability of program semantics understanding on many practical software engineering tasks.

Yaolong Wang, Mingqing Xiao, Chang Liu et al.

Lossy image compression is one of the most commonly used operators for digital images. Most recently proposed deep-learning-based image compression methods leverage the auto-encoder structure, and reach a series of promising results in this field. The images are encoded into low dimensional latent features first, and entropy coded subsequently by exploiting the statistical redundancy. However, the information lost during encoding is unfortunately inevitable, which poses a significant challenge to the decoder to reconstruct the original images. In this work, we propose a novel invertible framework called Invertible Lossy Compression (ILC) to largely mitigate the information loss problem. Specifically, ILC introduces an invertible encoding module to replace the encoder-decoder structure to produce the low dimensional informative latent representation, meanwhile, transform the lost information into an auxiliary latent variable that won't be further coded or stored. The latent representation is quantized and encoded into bit-stream, and the latent variable is forced to follow a specified distribution, i.e. isotropic Gaussian distribution. In this way, recovering the original image is made tractable by easily drawing a surrogate latent variable and applying the inverse pass of the module with the sampled variable and decoded latent features. Experimental results demonstrate that with a new component replacing the auto-encoder in image compression methods, ILC can significantly outperform the baseline method on extensive benchmark datasets by combining with the existing compression algorithms.

Zhenhui Xu, Linyuan Gong, Guolin Ke et al.

Pre-trained contextual representations (e.g., BERT) have become the foundation to achieve state-of-the-art results on many NLP tasks. However, large-scale pre-training is computationally expensive. ELECTRA, an early attempt to accelerate pre-training, trains a discriminative model that predicts whether each input token was replaced by a generator. Our studies reveal that ELECTRA's success is mainly due to its reduced complexity of the pre-training task: the binary classification (replaced token detection) is more efficient to learn than the generation task (masked language modeling). However, such a simplified task is less semantically informative. To achieve better efficiency and effectiveness, we propose a novel meta-learning framework, MC-BERT. The pre-training task is a multi-choice cloze test with a reject option, where a meta controller network provides training input and candidates. Results over GLUE natural language understanding benchmark demonstrate that our proposed method is both efficient and effective: it outperforms baselines on GLUE semantic tasks given the same computational budget.

Mingqing Xiao, Shuxin Zheng, Chang Liu et al.

High-resolution digital images are usually downscaled to fit various display screens or save the cost of storage and bandwidth, meanwhile the post-upscaling is adpoted to recover the original resolutions or the details in the zoom-in images. However, typical image downscaling is a non-injective mapping due to the loss of high-frequency information, which leads to the ill-posed problem of the inverse upscaling procedure and poses great challenges for recovering details from the downscaled low-resolution images. Simply upscaling with image super-resolution methods results in unsatisfactory recovering performance. In this work, we propose to solve this problem by modeling the downscaling and upscaling processes from a new perspective, i.e. an invertible bijective transformation, which can largely mitigate the ill-posed nature of image upscaling. We develop an Invertible Rescaling Net (IRN) with deliberately designed framework and objectives to produce visually-pleasing low-resolution images and meanwhile capture the distribution of the lost information using a latent variable following a specified distribution in the downscaling process. In this way, upscaling is made tractable by inversely passing a randomly-drawn latent variable with the low-resolution image through the network. Experimental results demonstrate the significant improvement of our model over existing methods in terms of both quantitative and qualitative evaluations of image upscaling reconstruction from downscaled images.

Ruibin Xiong, Yunchang Yang, Di He et al.

The Transformer is widely used in natural language processing tasks. To train a Transformer however, one usually needs a carefully designed learning rate warm-up stage, which is shown to be crucial to the final performance but will slow down the optimization and bring more hyper-parameter tunings. In this paper, we first study theoretically why the learning rate warm-up stage is essential and show that the location of layer normalization matters. Specifically, we prove with mean field theory that at initialization, for the original-designed Post-LN Transformer, which places the layer normalization between the residual blocks, the expected gradients of the parameters near the output layer are large. Therefore, using a large learning rate on those gradients makes the training unstable. The warm-up stage is practically helpful for avoiding this problem. On the other hand, our theory also shows that if the layer normalization is put inside the residual blocks (recently proposed as Pre-LN Transformer), the gradients are well-behaved at initialization. This motivates us to remove the warm-up stage for the training of Pre-LN Transformers. We show in our experiments that Pre-LN Transformers without the warm-up stage can reach comparable results with baselines while requiring significantly less training time and hyper-parameter tuning on a wide range of applications.

Shuxin Zheng, Qi Meng, Huishuai Zhang et al.

Recently, path norm was proposed as a new capacity measure for neural networks with Rectified Linear Unit (ReLU) activation function, which takes the rescaling-invariant property of ReLU into account. It has been shown that the generalization error bound in terms of the path norm explains the empirical generalization behaviors of the ReLU neural networks better than that of other capacity measures. Moreover, optimization algorithms which take path norm as the regularization term to the loss function, like Path-SGD, have been shown to achieve better generalization performance. However, the path norm counts the values of all paths, and hence the capacity measure based on path norm could be improperly influenced by the dependency among different paths. It is also known that each path of a ReLU network can be represented by a small group of linearly independent basis paths with multiplication and division operation, which indicates that the generalization behavior of the network only depends on only a few basis paths. Motivated by this, we propose a new norm \emph{Basis-path Norm} based on a group of linearly independent paths to measure the capacity of neural networks more accurately. We establish a generalization error bound based on this basis path norm, and show it explains the generalization behaviors of ReLU networks more accurately than previous capacity measures via extensive experiments. In addition, we develop optimization algorithms which minimize the empirical risk regularized by the basis-path norm. Our experiments on benchmark datasets demonstrate that the proposed regularization method achieves clearly better performance on the test set than the previous regularization approaches.

Qi Meng, Shuxin Zheng, Huishuai Zhang et al.

It is well known that neural networks with rectified linear units (ReLU) activation functions are positively scale-invariant. Conventional algorithms like stochastic gradient descent optimize the neural networks in the vector space of weights, which is, however, not positively scale-invariant. This mismatch may lead to problems during the optimization process. Then, a natural question is: \emph{can we construct a new vector space that is positively scale-invariant and sufficient to represent ReLU neural networks so as to better facilitate the optimization process }? In this paper, we provide our positive answer to this question. First, we conduct a formal study on the positive scaling operators which forms a transformation group, denoted as $\mathcal{G}$. We show that the value of a path (i.e. the product of the weights along the path) in the neural network is invariant to positive scaling and prove that the value vector of all the paths is sufficient to represent the neural networks under mild conditions. Second, we show that one can identify some basis paths out of all the paths and prove that the linear span of their value vectors (denoted as $\mathcal{G}$-space) is an invariant space with lower dimension under the positive scaling group. Finally, we design stochastic gradient descent algorithm in $\mathcal{G}$-space (abbreviated as $\mathcal{G}$-SGD) to optimize the value vector of the basis paths of neural networks with little extra cost by leveraging back-propagation. Our experiments show that $\mathcal{G}$-SGD significantly outperforms the conventional SGD algorithm in optimizing ReLU networks on benchmark datasets.

Shuxin Zheng, Qi Meng, Taifeng Wang et al.

With the fast development of deep learning, it has become common to learn big neural networks using massive training data. Asynchronous Stochastic Gradient Descent (ASGD) is widely adopted to fulfill this task for its efficiency, which is, however, known to suffer from the problem of delayed gradients. That is, when a local worker adds its gradient to the global model, the global model may have been updated by other workers and this gradient becomes "delayed". We propose a novel technology to compensate this delay, so as to make the optimization behavior of ASGD closer to that of sequential SGD. This is achieved by leveraging Taylor expansion of the gradient function and efficient approximation to the Hessian matrix of the loss function. We call the new algorithm Delay Compensated ASGD (DC-ASGD). We evaluated the proposed algorithm on CIFAR-10 and ImageNet datasets, and the experimental results demonstrate that DC-ASGD outperforms both synchronous SGD and asynchronous SGD, and nearly approaches the performance of sequential SGD.