GradPower: Powering Gradients for Faster Language Model Pre-Training

We propose GradPower, a lightweight gradient-transformation technique for accelerating language model pre-training. Given a gradient vector $g=(g_i)_i$, GradPower first applies the elementwise sign-power transformation: $\varphi_p(g)=({\rm sign}(g_i)|g_i|^p)_{i}$ for a fixed $p>0$, and then feeds the transformed gradient into a base optimizer. Notably, GradPower requires only a single-line code change and no modifications to the base optimizer's internal logic, including the hyperparameters. When applied to Adam (termed AdamPower), GradPower consistently achieves lower terminal loss across diverse architectures (LLaMA, Qwen2MoE), parameter scales (66M to 2B), datasets (C4, OpenWebText), and learning-rate schedules (cosine, warmup-stable-decay). The most pronounced gains are observed when training modern mixture-of-experts models with warmup-stable-decay schedules. GradPower also integrates seamlessly with other state-of-the-art optimizers, such as Muon, yielding further improvements. Finally, we provide theoretical analyses that reveal the underlying mechanism of GradPower and highlights the influence of gradient noise.

On the Expressive Power of Mixture-of-Experts for Structured Complex Tasks

Mixture-of-experts networks (MoEs) have demonstrated remarkable efficiency in modern deep learning. Despite their empirical success, the theoretical foundations underlying their ability to model complex tasks remain poorly understood. In this work, we conduct a systematic study of the expressive power of MoEs in modeling complex tasks with two common structural priors: low-dimensionality and sparsity. For shallow MoEs, we prove that they can efficiently approximate functions supported on low-dimensional manifolds, overcoming the curse of dimensionality. For deep MoEs, we show that $\cO(L)$-layer MoEs with $E$ experts per layer can approximate piecewise functions comprising $E^L$ pieces with compositional sparsity, i.e., they can exhibit an exponential number of structured tasks. Our analysis reveals the roles of critical architectural components and hyperparameters in MoEs, including the gating mechanism, expert networks, the number of experts, and the number of layers, and offers natural suggestions for MoE variants.

Scalable Complexity Control Facilitates Reasoning Ability of LLMs

The reasoning ability of large language models (LLMs) has been rapidly advancing in recent years, attracting interest in more fundamental approaches that can reliably enhance their generalizability. This work demonstrates that model complexity control, conveniently implementable by adjusting the initialization rate and weight decay coefficient, improves the scaling law of LLMs consistently over varying model sizes and data sizes. This gain is further illustrated by comparing the benchmark performance of 2.4B models pretrained on 1T tokens with different complexity hyperparameters. Instead of fixing the initialization std, we found that a constant initialization rate (the exponent of std) enables the scaling law to descend faster in both model and data sizes. These results indicate that complexity control is a promising direction for the continual advancement of LLMs.

RARE: Retrieval-Augmented Reasoning Modeling

Domain-specific intelligence demands specialized knowledge and sophisticated reasoning for problem-solving, posing significant challenges for large language models (LLMs) that struggle with knowledge hallucination and inadequate reasoning capabilities under constrained parameter budgets. Inspired by Bloom's Taxonomy in educational theory, we propose Retrieval-Augmented Reasoning Modeling (RARE), a novel paradigm that decouples knowledge storage from reasoning optimization. RARE externalizes domain knowledge to retrievable sources and internalizes domain-specific reasoning patterns during training. Specifically, by injecting retrieved knowledge into training prompts, RARE transforms learning objectives from rote memorization to contextualized reasoning application. It enables models to bypass parameter-intensive memorization and prioritize the development of higher-order cognitive processes. Our experiments demonstrate that lightweight RARE-trained models (e.g., Llama-3.1-8B) could achieve state-of-the-art performance, surpassing retrieval-augmented GPT-4 and Deepseek-R1 distilled counterparts. RARE establishes a paradigm shift where maintainable external knowledge bases synergize with compact, reasoning-optimized models, collectively driving more scalable domain-specific intelligence. Repo: https://github.com/Open-DataFlow/RARE

Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding (3D GU) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates 3D GU tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse 3D GU tasks within a single autoregressive framework. Extensive experiments across multiple microscopic 3D GU tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

The Sharpness Disparity Principle in Transformers for Accelerating Language Model Pre-Training

Transformers consist of diverse building blocks, such as embedding layers, normalization layers, self-attention mechanisms, and point-wise feedforward networks. Thus, understanding the differences and interactions among these blocks is important. In this paper, we uncover a clear Sharpness Disparity across these blocks, which emerges early in training and intriguingly persists throughout the training process. Motivated by this finding, we propose Blockwise Learning Rate (LR), a strategy that tailors the LR to each block's sharpness, accelerating large language model (LLM) pre-training. By integrating Blockwise LR into AdamW, we consistently achieve lower terminal loss and nearly $2\times$ speedup compared to vanilla AdamW. We demonstrate this acceleration across GPT-2 and LLaMA, with model sizes ranging from 0.12B to 1.1B and datasets of OpenWebText and MiniPile. Finally, we incorporate Blockwise LR into Adam-mini (Zhang et al., 2024), a recently proposed memory-efficient variant of Adam, achieving a combined $2\times$ speedup and $2\times$ memory saving. These results underscore the potential of exploiting the sharpness disparity to improve LLM training.

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

PaSa: An LLM Agent for Comprehensive Academic Paper Search

We introduce PaSa, an advanced Paper Search agent powered by large language models. PaSa can autonomously make a series of decisions, including invoking search tools, reading papers, and selecting relevant references, to ultimately obtain comprehensive and accurate results for complex scholarly queries. We optimize PaSa using reinforcement learning with a synthetic dataset, AutoScholarQuery, which includes 35k fine-grained academic queries and corresponding papers sourced from top-tier AI conference publications. Additionally, we develop RealScholarQuery, a benchmark collecting real-world academic queries to assess PaSa performance in more realistic scenarios. Despite being trained on synthetic data, PaSa significantly outperforms existing baselines on RealScholarQuery, including Google, Google Scholar, Google with GPT-4 for paraphrased queries, chatGPT (search-enabled GPT-4o), GPT-o1, and PaSa-GPT-4o (PaSa implemented by prompting GPT-4o). Notably, PaSa-7B surpasses the best Google-based baseline, Google with GPT-4o, by 37.78% in recall@20 and 39.90% in recall@50. It also exceeds PaSa-GPT-4o by 30.36% in recall and 4.25% in precision. Model, datasets, and code are available at https://github.com/bytedance/pasa.

Intelligent System for Automated Molecular Patent Infringement Assessment

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, a critical bottleneck persists in the inability of current automated frameworks to assess whether newly designed molecules infringe upon existing patents, posing significant legal and financial risks. We introduce PatentFinder, a novel tool-enhanced and multi-agent framework that accurately and comprehensively evaluates small molecules for patent infringement. It incorporates both heuristic and model-based tools tailored for decomposed subtasks, featuring: MarkushParser, which is capable of optical chemical structure recognition of molecular and Markush structures, and MarkushMatcher, which enhances large language models' ability to extract substituent groups from molecules accurately. On our benchmark dataset MolPatent-240, PatentFinder outperforms baseline approaches that rely solely on large language models, demonstrating a 13.8\% increase in F1-score and a 12\% rise in accuracy. Experimental results demonstrate that PatentFinder mitigates label bias to produce balanced predictions and autonomously generates detailed, interpretable patent infringement reports. This work not only addresses a pivotal challenge in automated drug discovery but also demonstrates the potential of decomposing complex scientific tasks into manageable subtasks for specialized, tool-augmented agents.

How Transformers Implement Induction Heads: Approximation and Optimization Analysis

Transformers have demonstrated exceptional in-context learning capabilities, yet the theoretical understanding of the underlying mechanisms remain limited. A recent work (Elhage et al., 2021) identified a "rich" in-context mechanism known as induction head, contrasting with "lazy" $n$-gram models that overlook long-range dependencies. In this work, we provide both approximation and optimization analyses of how transformers implement induction heads. In the approximation analysis, we formalize both standard and generalized induction head mechanisms, and examine how transformers can efficiently implement them, with an emphasis on the distinct role of each transformer submodule. For the optimization analysis, we study the training dynamics on a synthetic mixed target, composed of a 4-gram and an in-context 2-gram component. This setting enables us to precisely characterize the entire training process and uncover an {\em abrupt transition} from lazy (4-gram) to rich (induction head) mechanisms as training progresses.