Wanjia Zhao

Haixin Wang, Yadi Cao, Zijie Huang et al. · stanford

This paper explores the recent advancements in enhancing Computational Fluid Dynamics (CFD) tasks through Machine Learning (ML) techniques. We begin by introducing fundamental concepts, traditional methods, and benchmark datasets, then examine the various roles ML plays in improving CFD. The literature systematically reviews papers in recent five years and introduces a novel classification for forward modeling: Data-driven Surrogates, Physics-Informed Surrogates, and ML-assisted Numerical Solutions. Furthermore, we also review the latest ML methods in inverse design and control, offering a novel classification and providing an in-depth discussion. Then we highlight real-world applications of ML for CFD in critical scientific and engineering disciplines, including aerodynamics, combustion, atmosphere & ocean science, biology fluid, plasma, symbolic regression, and reduced order modeling. Besides, we identify key challenges and advocate for future research directions to address these challenges, such as multi-scale representation, physical knowledge encoding, scientific foundation model and automatic scientific discovery. This review serves as a guide for the rapidly expanding ML for CFD community, aiming to inspire insights for future advancements. We draw the conclusion that ML is poised to significantly transform CFD research by enhancing simulation accuracy, reducing computational time, and enabling more complex analyses of fluid dynamics. The paper resources can be viewed at https://github.com/WillDreamer/Awesome-AI4CFD.

Huajian Xin, Z. Z. Ren, Junxiao Song et al. · pku, stanford

We introduce DeepSeek-Prover-V1.5, an open-source language model designed for theorem proving in Lean 4, which enhances DeepSeek-Prover-V1 by optimizing both training and inference processes. Pre-trained on DeepSeekMath-Base with specialization in formal mathematical languages, the model undergoes supervised fine-tuning using an enhanced formal theorem proving dataset derived from DeepSeek-Prover-V1. Further refinement is achieved through reinforcement learning from proof assistant feedback (RLPAF). Beyond the single-pass whole-proof generation approach of DeepSeek-Prover-V1, we propose RMaxTS, a variant of Monte-Carlo tree search that employs an intrinsic-reward-driven exploration strategy to generate diverse proof paths. DeepSeek-Prover-V1.5 demonstrates significant improvements over DeepSeek-Prover-V1, achieving new state-of-the-art results on the test set of the high school level miniF2F benchmark ($63.5\%$) and the undergraduate level ProofNet benchmark ($25.3\%$).

Zijie Huang, Wanjia Zhao, Jingdong Gao et al. · stanford

Learning complex multi-agent system dynamics from data is crucial across many domains, such as in physical simulations and material modeling. Extended from purely data-driven approaches, existing physics-informed approaches such as Hamiltonian Neural Network strictly follow energy conservation law to introduce inductive bias, making their learning more sample efficiently. However, many real-world systems do not strictly conserve energy, such as spring systems with frictions. Recognizing this, we turn our attention to a broader physical principle: Time-Reversal Symmetry, which depicts that the dynamics of a system shall remain invariant when traversed back over time. It still helps to preserve energies for conservative systems and in the meanwhile, serves as a strong inductive bias for non-conservative, reversible systems. To inject such inductive bias, in this paper, we propose a simple-yet-effective self-supervised regularization term as a soft constraint that aligns the forward and backward trajectories predicted by a continuous graph neural network-based ordinary differential equation (GraphODE). It effectively imposes time-reversal symmetry to enable more accurate model predictions across a wider range of dynamical systems under classical mechanics. In addition, we further provide theoretical analysis to show that our regularization essentially minimizes higher-order Taylor expansion terms during the ODE integration steps, which enables our model to be more noise-tolerant and even applicable to irreversible systems. Experimental results on a variety of physical systems demonstrate the effectiveness of our proposed method. Particularly, it achieves an MSE improvement of 11.5 % on a challenging chaotic triple-pendulum systems.

Wanjia Zhao, Ludwig Schmidt, James Zou et al. · cmu

Tool-augmented large language models (LLMs) must tightly couple multi-step reasoning with external actions, yet existing benchmarks often confound this interplay with complex environment dynamics, memorized knowledge or dataset contamination. In this paper, we introduce ZebraArena, a procedurally generated diagnostic environment for studying reasoning-action coupling in tool-augmented LLMs, with controllable difficulty and a knowledge-minimal design, which limits gains from memorization or dataset contamination. Each task in ZebraArena requires a set of critical information which is available only through targeted tool use, yielding an interpretable interface between external information acquisition and deductive reasoning. This design provides deterministic evaluation via unique solutions, and a theoretical optimal query count for measuring efficient tool use. We show that ZebraArena requires a combination of in-depth reasoning and accurate external tool calling, which remains a challenge as frontier reasoning models such as GPT-5 and Gemini 2.5 Pro only achieves 60% accuracy on the hard instances. We also observe a persistent gaps between theoretical optimality and practical tool usage. For example, GPT-5 uses 70-270% more tool calls than the theoretical optimum. We highlight the key findings in our evaluation, and hope ZebraArena stimulates further research on the interplay between internal reasoning and external action.

Dachuan Shi, Hanlin Zhu, Xiangchi Yuan et al.

Chain-of-thought (CoT) is a standard approach for eliciting reasoning capabilities from large language models (LLMs). However, the common CoT paradigm treats thinking as a prerequisite for answering, which can delay access to plausible answers and incur unnecessary token costs even when the model is able to identify an answer before extended thinking, a behavior known as performative reasoning. In this paper, we introduce CopT, a reformulated reasoning pipeline that reverses the usual order of thinking and answering. Instead of thinking before answering, CopT first elicits a draft answer and then invokes subsequent on-policy thinking conditioned on its own draft answer for reflection and correction. To assess whether the draft answer should be trusted, CopT recasts continuous embeddings as inference-time contrastive verifiers. Specifically, it contrasts the model's support for the same generated tokens under discrete-token inputs and continuous-embedding inputs, yielding a sequence-level reverse KL estimator for answer reliability. Our analysis shows that under certain assumptions, the expected estimate equals the mutual information between the unresolved latent state and the emitted answer token, explaining why it captures answer-relevant uncertainty rather than arbitrary uncertainty in the latent state. When the answer is deemed insufficiently reliable, CopT performs further on-policy thinking, where a second KL estimator dynamically controls draft-answer visibility, preserving useful partial information while reducing the risk of being misled by unreliable content. Across mathematics, coding, and agentic reasoning tasks, CopT improves peak accuracy by up to 23% and reduces token usage by up to 57% at comparable or higher accuracy, without any additional training. The code is available at https://github.com/sdc17/CopT.

DeepSeek-AI, Daya Guo, Dejian Yang et al. · stanford, tsinghua

We introduce our first-generation reasoning models, DeepSeek-R1-Zero and DeepSeek-R1. DeepSeek-R1-Zero, a model trained via large-scale reinforcement learning (RL) without supervised fine-tuning (SFT) as a preliminary step, demonstrates remarkable reasoning capabilities. Through RL, DeepSeek-R1-Zero naturally emerges with numerous powerful and intriguing reasoning behaviors. However, it encounters challenges such as poor readability, and language mixing. To address these issues and further enhance reasoning performance, we introduce DeepSeek-R1, which incorporates multi-stage training and cold-start data before RL. DeepSeek-R1 achieves performance comparable to OpenAI-o1-1217 on reasoning tasks. To support the research community, we open-source DeepSeek-R1-Zero, DeepSeek-R1, and six dense models (1.5B, 7B, 8B, 14B, 32B, 70B) distilled from DeepSeek-R1 based on Qwen and Llama.

Z. Z. Ren, Zhihong Shao, Junxiao Song et al. · stanford, tsinghua

We introduce DeepSeek-Prover-V2, an open-source large language model designed for formal theorem proving in Lean 4, with initialization data collected through a recursive theorem proving pipeline powered by DeepSeek-V3. The cold-start training procedure begins by prompting DeepSeek-V3 to decompose complex problems into a series of subgoals. The proofs of resolved subgoals are synthesized into a chain-of-thought process, combined with DeepSeek-V3's step-by-step reasoning, to create an initial cold start for reinforcement learning. This process enables us to integrate both informal and formal mathematical reasoning into a unified model. The resulting model, DeepSeek-Prover-V2-671B, achieves state-of-the-art performance in neural theorem proving, reaching 88.9% pass ratio on the MiniF2F-test and solving 49 out of 658 problems from PutnamBench. In addition to standard benchmarks, we introduce ProverBench, a collection of 325 formalized problems, to enrich our evaluation, including 15 selected problems from the recent AIME competitions (years 24-25). Further evaluation on these 15 AIME problems shows that the model successfully solves 6 of them. In comparison, DeepSeek-V3 solves 8 of these problems using majority voting, highlighting that the gap between formal and informal mathematical reasoning in large language models is substantially narrowing.

Etash Guha, Ryan Marten, Sedrick Keh et al. · cmu

Reasoning models have made rapid progress on many benchmarks involving math, code, and science. Yet, there are still many open questions about the best training recipes for reasoning since state-of-the-art models often rely on proprietary datasets with little to no public information available. To address this, the goal of the OpenThoughts project is to create open-source datasets for training reasoning models. After initial explorations, our OpenThoughts2-1M dataset led to OpenThinker2-32B, the first model trained on public reasoning data to match DeepSeek-R1-Distill-32B on standard reasoning benchmarks such as AIME and LiveCodeBench. We then improve our dataset further by systematically investigating each step of our data generation pipeline with 1,000+ controlled experiments, which led to OpenThoughts3. Scaling the pipeline to 1.2M examples and using QwQ-32B as teacher yields our OpenThoughts3-7B model, which achieves state-of-the-art results: 53% on AIME 2025, 51% on LiveCodeBench 06/24-01/25, and 54% on GPQA Diamond - improvements of 15.3, 17.2, and 20.5 percentage points compared to the DeepSeek-R1-Distill-Qwen-7B. All of our datasets and models are available on https://openthoughts.ai.

Yijia Xiao, Wanjia Zhao, Junkai Zhang et al.

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

DeepSeek-AI, Aixin Liu, Bei Feng et al. · stanford, tsinghua

We present DeepSeek-V3, a strong Mixture-of-Experts (MoE) language model with 671B total parameters with 37B activated for each token. To achieve efficient inference and cost-effective training, DeepSeek-V3 adopts Multi-head Latent Attention (MLA) and DeepSeekMoE architectures, which were thoroughly validated in DeepSeek-V2. Furthermore, DeepSeek-V3 pioneers an auxiliary-loss-free strategy for load balancing and sets a multi-token prediction training objective for stronger performance. We pre-train DeepSeek-V3 on 14.8 trillion diverse and high-quality tokens, followed by Supervised Fine-Tuning and Reinforcement Learning stages to fully harness its capabilities. Comprehensive evaluations reveal that DeepSeek-V3 outperforms other open-source models and achieves performance comparable to leading closed-source models. Despite its excellent performance, DeepSeek-V3 requires only 2.788M H800 GPU hours for its full training. In addition, its training process is remarkably stable. Throughout the entire training process, we did not experience any irrecoverable loss spikes or perform any rollbacks. The model checkpoints are available at https://github.com/deepseek-ai/DeepSeek-V3.

Wanjia Zhao, Mert Yuksekgonul, Shirley Wu et al. · stanford

Multi-agent AI systems powered by large language models (LLMs) are increasingly applied to solve complex tasks. However, these systems often rely on fragile, manually designed prompts and heuristics, making optimization difficult. A key challenge in optimizing multi-agent systems is acquiring suitable training data for specialized agents. We introduce SiriuS, a self-improving, reasoning-driven optimization framework for multi-agent systems. Central to our approach is the construction of an experience library: a repository of high-quality reasoning trajectories. The library is built by retaining reasoning steps that lead to successful outcomes, providing a robust training set for optimizing multi-agent system. Additionally, we introduce a library augmentation procedure that refines unsuccessful trajectories, further enriching the library. SiriuS boosts performance by 2.86\% to 21.88\% on reasoning and biomedical QA and enhances agent negotiation in competitive settings. Our results show that SiriuS enhances multi-agent performance while generating reusable data for self-correction and self-play enhancement in the future.

Wanjia Zhao, Qinwei Ma, Jingzhe Shi et al.

Benchmarks for competition-style reasoning have advanced evaluation in mathematics and programming, yet physics remains comparatively explored. Most existing physics benchmarks evaluate only final answers, which fail to capture reasoning processes, while recent stepwise methods rely on heuristic LLM-as-judge scoring or restrictive linear assumptions, limiting reliability and diagnostic validity. We introduce PRISM-Physics, a process-level evaluation framework and benchmark for complex physics reasoning problems. Solutions are represented as directed acyclic graphs (DAGs) of formulas, explicitly encoding causal dependencies among intermediate steps to enable fine-grained, interpretable, and theoretically grounded scoring. We prove the optimality of the DAG representation and the corresponding scoring policy. Combining with a fully rule-based method for symbolic formula equivalence matching that we developed, we ensure consistent validation across diverse formulations without heuristic judgments. Results show that our evaluation framework is more aligned with human experts' scoring. Experiments on state-of-the-art LLMs reveal persistent reasoning failures in physics, while step-level scoring offers both diagnostic insight and rich signals for later training. By combining structural rigor, theoretical guarantees, and symbolic validation, PRISM-Physics provides a principled foundation for advancing process-level evaluation and guiding the development of models with deeper scientific reasoning capabilities.

Wanjia Zhao, Jiaqi Han, Siyi Gu et al.

Geometric diffusion models have shown remarkable success in molecular dynamics and structure generation. However, efficiently fine-tuning them for downstream tasks with varying geometric controls remains underexplored. In this work, we propose an SE(3)-equivariant adapter framework ( GeoAda) that enables flexible and parameter-efficient fine-tuning for controlled generative tasks without modifying the original model architecture. GeoAda introduces a structured adapter design: control signals are first encoded through coupling operators, then processed by a trainable copy of selected pretrained model layers, and finally projected back via decoupling operators followed by an equivariant zero-initialized convolution. By fine-tuning only these lightweight adapter modules, GeoAda preserves the model's geometric consistency while mitigating overfitting and catastrophic forgetting. We theoretically prove that the proposed adapters maintain SE(3)-equivariance, ensuring that the geometric inductive biases of the pretrained diffusion model remain intact during adaptation. We demonstrate the wide applicability of GeoAda across diverse geometric control types, including frame control, global control, subgraph control, and a broad range of application domains such as particle dynamics, molecular dynamics, human motion prediction, and molecule generation. Empirical results show that GeoAda achieves state-of-the-art fine-tuning performance while preserving original task accuracy, whereas other baselines experience significant performance degradation due to overfitting and catastrophic forgetting.