Investigating Data Pruning for Pretraining Biological Foundation Models at Scale

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility, particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). We empirically validate our method on two representative BioFMs, RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.

Coherence Mechanisms for Provable Self-Improvement

Self-improvement is a critical capability for large language models and other intelligent systems, enabling them to refine their behavior and internal consistency without external supervision. Despite its importance, prior approaches largely rely on empirical heuristics and lack formal guarantees. In this paper, we propose a principled framework for self-improvement based on the concept of \emph{coherence}, which requires that a model's outputs remain consistent under task-preserving transformations of the input. We formalize this concept using projection-based mechanisms that update a baseline model to be coherent while remaining as close as possible to its original behavior. We provide rigorous theoretical guarantees that these mechanisms achieve \emph{monotonic improvement}, measured by a reduction in expected Bregman divergence. Our analysis is comprehensive, covering both \emph{direct} and \emph{two-step} projection methods, and robustly extends these guarantees to non-realizable settings, empirical (finite-sample) distributions, and relaxed coherence constraints. Furthermore, we establish a general \emph{characterization theorem}, showing that any mechanism with similar provable improvement guarantees must inherently conform to a coherence-based structure. This culminates in rigidity results under the demand for universal improvement, establishing coherence as a fundamental and, in a formal sense, necessary principle for provable self-improvement.

Scaling Agent Learning via Experience Synthesis

While reinforcement learning (RL) can empower autonomous agents by enabling self-improvement through interaction, its practical adoption remains challenging due to costly rollouts, limited task diversity, unreliable reward signals, and infrastructure complexity, all of which obstruct the collection of scalable experience data. To address these challenges, we introduce DreamGym, the first unified framework designed to synthesize diverse experiences with scalability in mind to enable effective online RL training for autonomous agents. Rather than relying on expensive real-environment rollouts, DreamGym distills environment dynamics into a reasoning-based experience model that derives consistent state transitions and feedback signals through step-by-step reasoning, enabling scalable agent rollout collection for RL. To improve the stability and quality of transitions, DreamGym leverages an experience replay buffer initialized with offline real-world data and continuously enriched with fresh interactions to actively support agent training. To improve knowledge acquisition, DreamGym adaptively generates new tasks that challenge the current agent policy, enabling more effective online curriculum learning. Experiments across diverse environments and agent backbones demonstrate that DreamGym substantially improves RL training, both in fully synthetic settings and in sim-to-real transfer scenarios. On non-RL-ready tasks like WebArena, DreamGym outperforms all baselines by over 30%. And in RL-ready but costly settings, it matches GRPO and PPO performance using only synthetic interactions. When transferring a policy trained purely on synthetic experiences to real-environment RL, DreamGym yields significant additional performance gains while requiring far fewer real-world interactions, providing a scalable warm-start strategy for general-purpose RL.

VisJudge-Bench: Aesthetics and Quality Assessment of Visualizations

Visualization, a domain-specific yet widely used form of imagery, is an effective way to turn complex datasets into intuitive insights, and its value depends on whether data are faithfully represented, clearly communicated, and aesthetically designed. However, evaluating visualization quality is challenging: unlike natural images, it requires simultaneous judgment across data encoding accuracy, information expressiveness, and visual aesthetics. Although multimodal large language models (MLLMs) have shown promising performance in aesthetic assessment of natural images, no systematic benchmark exists for measuring their capabilities in evaluating visualizations. To address this, we propose VisJudge-Bench, the first comprehensive benchmark for evaluating MLLMs' performance in assessing visualization aesthetics and quality. It contains 3,090 expert-annotated samples from real-world scenarios, covering single visualizations, multiple visualizations, and dashboards across 32 chart types. Systematic testing on this benchmark reveals that even the most advanced MLLMs (such as GPT-5) still exhibit significant gaps compared to human experts in judgment, with a Mean Absolute Error (MAE) of 0.551 and a correlation with human ratings of only 0.429. To address this issue, we propose VisJudge, a model specifically designed for visualization aesthetics and quality assessment. Experimental results demonstrate that VisJudge significantly narrows the gap with human judgment, reducing the MAE to 0.442 (a 19.8% reduction) and increasing the consistency with human experts to 0.681 (a 58.7% improvement) compared to GPT-5. The benchmark is available at https://github.com/HKUSTDial/VisJudgeBench.

Criticality-Based Dynamic Topology Optimization for Enhancing Aerial-Marine Swarm Resilience

Heterogeneous marine-aerial swarm networks encounter substantial difficulties due to targeted communication disruptions and structural weaknesses in adversarial environments. This paper proposes a two-step framework to strengthen the network's resilience. Specifically, our framework combines the node prioritization based on criticality with multi-objective topology optimization. First, we design a three-layer architecture to represent structural, communication, and task dependencies of the swarm networks. Then, we introduce the SurBi-Ranking method, which utilizes graph convolutional networks, to dynamically evaluate and rank the criticality of nodes and edges in real time. Next, we apply the NSGA-III algorithm to optimize the network topology, aiming to balance communication efficiency, global connectivity, and mission success rate. Experiments demonstrate that compared to traditional methods like K-Shell, our SurBi-Ranking method identifies critical nodes and edges with greater accuracy, as deliberate attacks on these components cause more significant connectivity degradation. Furthermore, our optimization approach, when prioritizing SurBi-Ranked critical components under attack, reduces the natural connectivity degradation by around 30%, achieves higher mission success rates, and incurs lower communication reconfiguration costs, ensuring sustained connectivity and mission effectiveness across multi-phase operations.

ChartMark: A Structured Grammar for Chart Annotation

Chart annotations enhance visualization accessibility but suffer from fragmented, non-standardized representations that limit cross-platform reuse. We propose ChartMark, a structured grammar that separates annotation semantics from visualization implementations. ChartMark features a hierarchical framework mapping onto annotation dimensions (e.g., task, chart context), supporting both abstract intents and precise visual details. Our toolkit demonstrates converting ChartMark specifications into Vega-Lite visualizations, highlighting its flexibility, expressiveness, and practical applicability.

Filter-And-Refine: A MLLM Based Cascade System for Industrial-Scale Video Content Moderation

Effective content moderation is essential for video platforms to safeguard user experience and uphold community standards. While traditional video classification models effectively handle well-defined moderation tasks, they struggle with complicated scenarios such as implicit harmful content and contextual ambiguity. Multimodal large language models (MLLMs) offer a promising solution to these limitations with their superior cross-modal reasoning and contextual understanding. However, two key challenges hinder their industrial adoption. First, the high computational cost of MLLMs makes full-scale deployment impractical. Second, adapting generative models for discriminative classification remains an open research problem. In this paper, we first introduce an efficient method to transform a generative MLLM into a multimodal classifier using minimal discriminative training data. To enable industry-scale deployment, we then propose a router-ranking cascade system that integrates MLLMs with a lightweight router model. Offline experiments demonstrate that our MLLM-based approach improves F1 score by 66.50% over traditional classifiers while requiring only 2% of the fine-tuning data. Online evaluations show that our system increases automatic content moderation volume by 41%, while the cascading deployment reduces computational cost to only 1.5% of direct full-scale deployment.

Aligned Textual Scoring Rules

Scoring rules elicit probabilistic predictions from a strategic agent by scoring the prediction against a ground truth state. A scoring rule is proper if, from the agent's perspective, reporting the true belief maximizes the expected score. With the development of language models, Wu and Hartline (2024) proposes a reduction from textual information elicitation to the numerical (i.e. probabilistic) information elicitation problem, which achieves provable properness for textual elicitation. However, not all proper scoring rules are well aligned with human preference over text. Our paper designs the Aligned Scoring rule (ASR) for text by optimizing and minimizing the mean squared error between a proper scoring rule and a reference score (e.g. human score). Our experiments show that our ASR outperforms previous methods in aligning with human preference while maintaining properness.

TransXSSM: A Hybrid Transformer State Space Model with Unified Rotary Position Embedding

Transformers exhibit proficiency in capturing long-range dependencies, whereas State Space Models (SSMs) facilitate linear-time sequence modeling. Notwithstanding their synergistic potential, the integration of these architectures presents a significant challenge, primarily attributable to a fundamental incongruity in their respective positional encoding mechanisms: Transformers rely on explicit Rotary Position Embeddings (RoPE), while SSMs leverage implicit positional representations via convolutions. This divergence often precipitates discontinuities and suboptimal performance. To address this impediment, we propose a unified rotary position embedding (Unified RoPE) methodology, thereby establishing a consistent positional encoding framework for both self-attention and state-space components. Using this Unified RoPE, we introduce TransXSSM, a hybrid architecture that coherently integrates the Transformer and SSM layers under this unified positional encoding scheme. At a 4K sequence length, TransXSSM exhibits training and inference speeds that are 42.3\% and 29.5\% faster, respectively, relative to standard Transformer models. It also delivers higher accuracy: under comparable settings, it surpasses a Transformer baseline by over 4\% on language modeling benchmarks.TransXSSM furthermore scales more effectively: TransXSSM-1.3B gains 7.22\% in average accuracy over its 320M version (versus about 6\% gains for equivalent Transformers or SSMs). Our results show that unified positional encoding resolves positional incompatibility in hybrid models, enabling efficient, high-performance long-context modeling.

Concise Reasoning, Big Gains: Pruning Long Reasoning Trace with Difficulty-Aware Prompting

Existing chain-of-thought (CoT) distillation methods can effectively transfer reasoning abilities to base models but suffer from two major limitations: excessive verbosity of reasoning traces and inadequate adaptability to problem difficulty. Long reasoning traces significantly increase inference costs, and uniform-length solutions prevent base models from learning adaptive reasoning strategies. To address these issues, we propose a difficulty-aware prompting (DAP) method to dynamically shorten reasoning traces without performance loss. In our approach, a large teacher model first judges each problem's difficulty and then rewrites its reasoning traces to an appropriate shorter length, yielding concise yet complete reasoning traces. Leveraging the DAP pipeline, we curate a distilled dataset called LiteCoT consisting of 100K concise reasoning examples, with solutions averaging only 720 tokens (an order of magnitude shorter than typical CoTs). Using LiteCoT, we distilled a new family of reasoning models called Liter (1.5B, 7B, and 32B) based on the Qwen2.5 architecture. Experiments show that a student model fine-tuned on just 100K of these difficulty-pruned CoT samples outperforms a model distilled on 800K original Long CoT samples, while significantly reducing training and inference costs. Our method also generalizes well: across 11 diverse benchmarks, the shorter difficulty-aware CoTs achieve equal or better accuracy than Long chains, using far fewer tokens. For example, on the challenging AIME24 exam, our approach reaches $74.2\%$ Pass@1 using only about 5K inference tokens, surpassing other methods that consume many more tokens. Our code and data are available at https://github.com/Evanwu1125/LiteCoT.