Efficient and provably convergent end-to-end training of deep neural networks with linear constraints

Training a deep neural network with the outputs of selected layers satisfying linear constraints is required in many contemporary data-driven applications. While this can be achieved by incorporating projection layers into the neural network, its end-to-end training remains challenging due to the lack of rigorous theory and efficient algorithms for backpropagation. A key difficulty in developing the theory and efficient algorithms for backpropagation arose from the nonsmoothness of the solution mapping of the projection layer. To address this bottleneck, we introduce an efficiently computable HS-Jacobian to the projection layer. Importantly, we prove that the HS-Jacobian is a conservative mapping for the projection operator onto the polyhedral set, enabling its seamless integration into the nonsmooth automatic differentiation framework for backpropagation. Therefore, many efficient algorithms, such as Adam, can be applied for end-to-end training of deep neural networks with linear constraints. Particularly, we establish convergence guarantees of the HS-Jacobian based Adam algorithm for training linearly constrained deep neural networks. Extensive experiment results on several important applications, including finance, computer vision, and network architecture design, demonstrate the superior performance of our method compared to other existing popular methods.

SciIntegrity-Bench: A Benchmark for Evaluating Academic Integrity in AI Scientist Systems

AI scientist systems are increasingly deployed for autonomous research, yet their academic integrity has never been systematically evaluated. We introduce SCIINTEGRITY-BENCH, the first benchmark designed around a dilemmatic evaluation paradigm: each of its 33 scenarios across 11 trap categories is constructed so that honest acknowledgment of failure is the only correct response, while task completion requires misconduct. Across 231 evaluation runs spanning 7 state-of-the-art LLMs, the overall integrity problem rate reaches 34.2%, and no model achieves zero failures. Most strikingly, across missing-data scenarios, all seven models generate synthetic data rather than acknowledging infeasibility, differing only in whether they disclose the substitution. A further prompt ablation study separates two drivers: removing explicit completion pressure sharply reduces undisclosed fabrication from 20.6% to 3.2%, while the underlying synthesis rate remains unchanged, revealing an intrinsic completion bias that persists independent of prompt-level instructions. These findings point to the absence of honest refusal as a trained disposition as the primary driver of observed failures. We release SCIINTEGRITY-BENCH at https://github.com/liuxingtong/Sci-Integrity-Bench.

PolyReal: A Benchmark for Real-World Polymer Science Workflows

Multimodal Large Language Models (MLLMs) excel in general domains but struggle with complex, real-world science. We posit that polymer science, an interdisciplinary field spanning chemistry, physics, biology, and engineering, is an ideal high-stakes testbed due to its diverse multimodal data. Yet, existing benchmarks related to polymer science largely overlook real-world workflows, limiting their practical utility and failing to systematically evaluate MLLMs across the full, practice-grounded lifecycle of experimentation. We introduce PolyReal, a novel multimodal benchmark grounded in real-world scientific practices to evaluate MLLMs on the full lifecycle of polymer experimentation. It covers five critical capabilities: (1) foundational knowledge application; (2) lab safety analysis; (3) experiment mechanism reasoning; (4) raw data extraction; and (5) performance & application exploration. Our evaluation of leading MLLMs on PolyReal reveals a capability imbalance. While models perform well on knowledge-intensive reasoning (e.g., Experiment Mechanism Reasoning), they drop sharply on practice-based tasks (e.g., Lab Safety Analysis and Raw Data Extraction). This exposes a severe gap between abstract scientific knowledge and its practical, context-dependent application, showing that these real-world tasks remain challenging for MLLMs. Thus, PolyReal helps address this evaluation gap and provides a practical benchmark for assessing AI systems in real-world scientific workflows.

From 50% to Mastery in 3 Days: A Low-Resource SOP for Localizing Graduate-Level AI Tutors via Shadow-RAG

Deploying high-fidelity AI tutors in schools is often blocked by the Resource Curse -- the need for expensive cloud GPUs and massive data engineering. In this practitioner report, we present a replicable Standard Operating Procedure that breaks this barrier. Using a Vision-Language Model data cleaning strategy and a novel Shadow-RAG architecture, we localized a graduate-level Applied Mathematics tutor using only 3 person-days of non-expert labor and open-weights 32B models deployable on a single consumer-grade GPU. Our pilot study on a full graduate-level final exam reveals a striking emergence phenomenon: while both zero-shot baselines and standard retrieval stagnate around 50-60% accuracy across model generations, the Shadow Agent, which provides structured reasoning guidance, triggers a massive capability surge in newer 32B models, boosting performance from 74% (Naive RAG) to mastery level (90%). In contrast, older models see only modest gains (~10%). This suggests that such guidance is the key to unlocking the latent power of modern small language models. This work offers a cost-effective, scientifically grounded blueprint for ubiquitous AI education.

MOOSE-Star: Unlocking Tractable Training for Scientific Discovery by Breaking the Complexity Barrier

While large language models (LLMs) show promise in scientific discovery, existing research focuses on inference or feedback-driven training, leaving the direct modeling of the generative reasoning process, $P(\text{hypothesis}|\text{background})$ ($P(h|b)$), unexplored. We demonstrate that directly training $P(h|b)$ is mathematically intractable due to the combinatorial complexity ($O(N^k)$) inherent in retrieving and composing inspirations from a vast knowledge base. To break this barrier, we introduce MOOSE-Star, a unified framework enabling tractable training and scalable inference. In the best case, MOOSE-Star reduces complexity from exponential to logarithmic ($O(\log N)$) by (1) training on decomposed subtasks derived from the probabilistic equation of discovery, (2) employing motivation-guided hierarchical search to enable logarithmic retrieval and prune irrelevant subspaces, and (3) utilizing bounded composition for robustness against retrieval noise. To facilitate this, we release TOMATO-Star, a dataset of 108,717 decomposed papers (38,400 GPU hours) for training. Furthermore, we show that while brute-force sampling hits a ''complexity wall,'' MOOSE-Star exhibits continuous test-time scaling.

A unified foundational framework for knowledge injection and evaluation of Large Language Models in Combustion Science

To advance foundation Large Language Models (LLMs) for combustion science, this study presents the first end-to-end framework for developing domain-specialized models for the combustion community. The framework comprises an AI-ready multimodal knowledge base at the 3.5 billion-token scale, extracted from over 200,000 peer-reviewed articles, 8,000 theses and dissertations, and approximately 400,000 lines of combustion CFD code; a rigorous and largely automated evaluation benchmark (CombustionQA, 436 questions across eight subfields); and a three-stage knowledge-injection pathway that progresses from lightweight retrieval-augmented generation (RAG) to knowledge-graph-enhanced retrieval and continued pretraining. We first quantitatively validate Stage 1 (naive RAG) and find a hard ceiling: standard RAG accuracy peaks at 60%, far surpassing zero-shot performance (23%) yet well below the theoretical upper bound (87%). We further demonstrate that this stage's performance is severely constrained by context contamination. Consequently, building a domain foundation model requires structured knowledge graphs and continued pretraining (Stages 2 and 3).

Accelerating RLHF Training with Reward Variance Increase

Reinforcement learning from human feedback (RLHF) is an essential technique for ensuring that large language models (LLMs) are aligned with human values and preferences during the post-training phase. As an effective RLHF approach, group relative policy optimization (GRPO) has demonstrated success in many LLM-based applications. However, efficient GRPO-based RLHF training remains a challenge. Recent studies reveal that a higher reward variance of the initial policy model leads to faster RLHF training. Inspired by this finding, we propose a practical reward adjustment model to accelerate RLHF training by provably increasing the reward variance and preserving the relative preferences and reward expectation. Our reward adjustment method inherently poses a nonconvex optimization problem, which is NP-hard to solve in general. To overcome the computational challenges, we design a novel $O(n \log n)$ algorithm to find a global solution of the nonconvex reward adjustment model by explicitly characterizing the extreme points of the feasible set. As an important application, we naturally integrate this reward adjustment model into the GRPO algorithm, leading to a more efficient GRPO with reward variance increase (GRPOVI) algorithm for RLHF training. As an interesting byproduct, we provide an indirect explanation for the empirical effectiveness of GRPO with rule-based reward for RLHF training, as demonstrated in DeepSeek-R1. Experiment results demonstrate that the GRPOVI algorithm can significantly improve the RLHF training efficiency compared to the original GRPO algorithm.

MOOSE-Chem2: Exploring LLM Limits in Fine-Grained Scientific Hypothesis Discovery via Hierarchical Search

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the novel task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent chemistry literature show that our method consistently outperforms strong baselines.

MOOSE-Chem3: Toward Experiment-Guided Hypothesis Ranking via Simulated Experimental Feedback

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

ResearchBench: Benchmarking LLMs in Scientific Discovery via Inspiration-Based Task Decomposition

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.