Speaking the Language of Science: Toward a General-Purpose Generative Foundation Model for the Natural Sciences

In this report, we present LOGOS (Language Of Generative Objects in Science), a scientific generative language model that unifies heterogeneous tasks across the natural sciences within a single autoregressive framework based on a shared scientific grammar. It encodes diverse scientific objects and their spatial interactions as token sequences over a common vocabulary. By representing spatial contact and constraint patterns as discrete tokens, the model captures complex structural interactions in a purely sequential manner, without relying on explicit coordinates or geometric neural networks. This unified representation enables a wide range of downstream tasks to be formulated consistently as next-token prediction in the same grammar space, creating strong alignment between continued multi-domain pre-training and downstream objectives. Across diverse tasks, LOGOS consistently matches or outperforms domain-specific baselines, providing preliminary evidence for the feasibility of "one model fits all" in the natural sciences. We train LOGOS models at different scales (1B, 3B, and 8B parameters) and find a consistent positive correlation between model size and performance. This suggests that the future of AI for Science (AI4S) may not lie in building an independent technical stack that is separated from large language models (LLMs). Instead, it may depend on deeply aligning scientific foundation models with LLMs through shared architectures, shared training paradigms, and shared inference infrastructure, so that LLMs can truly become a new entry point for AI4S. We release the model weights and associated resources to facilitate further research.

Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction

DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels. Accurately predicting regulatory activity from DNA sequences is valuable but challenging, as it requires understanding complex biological regulatory processes. Existing methods typically regress activity scores from sequences in a black-box manner, limiting both interpretability and regression performance. Meanwhile, large language models (LLMs) benefit from explicit reasoning processes, yet directly applying LLMs to raw DNA sequences performs poorly. In this paper, we bridge this gap by introducing R3LM, a framework that teaches LLMs reasoning-informed regression on regulatory DNA through structured biological knowledge. Specifically, we design a biologically grounded data format that structures DNA's regulatory information for improved LLM understanding, and construct CRE-ReasonBench, the first dataset that associates DNA sequences and activity scores with mechanistic reasoning traces. Through two-stage training that first teaches LLMs reasoning over structured biological information then performs regression, R3LM achieves state-of-the-art performance on enhancer prediction across three cell types, outperforming both LLMs with raw sequence input and specialized DNA models while providing interpretable mechanistic explanations. We expect R3LM as an interpretable reward model that can effectively assist biologists in CRE design. Code is available at https://github.com/DuanYi516/R3LM.

Pareto-Guided Optimal Transport for Multi-Reward Alignment

Text-to-image generation models have achieved remarkable progress in preference optimization, yet achieving robust alignment across diverse reward models remains a significant challenge. Existing multi-reward fusion approaches rely on weighted summation, which is costly to tune and insufficient for balancing conflicting objectives. More critically, optimization with reward models is highly susceptible to reward hacking, where reward scores increase while the perceived quality of generated images deteriorates. We demonstrate that optimizing against a unified global target under heterogeneous reward upper bounds can induce reward hacking, a risk further exacerbated by the inherent instability of weak reward models. To mitigate this, we propose a Pareto Frontier-Guided Optimal Transport (PG-OT) framework. Our method constructs a prompt-specific Pareto frontier and maps dominated samples toward it via distribution-aware optimal transport. Furthermore, we develop both online and offline optimization strategies tailored to diverse reward signal characteristics. To provide a more rigorous assessment, we introduce the Joint Domination Rate (JDR) and Joint Collapse Rate (JCR) as principled metrics to quantify multi-reward synergy and reward hacking. Experimental results show that our approach outperforms strong baselines with an 11% gain in JDR and achieves a near 80% win rate in human evaluations.

SciLT: Long-Tailed Classification in Scientific Image Domains

Long-tailed recognition has benefited from foundation models and fine-tuning paradigms, yet existing studies and benchmarks are mainly confined to natural image domains, where pre-training and fine-tuning data share similar distributions. In contrast, scientific images exhibit distinct visual characteristics and supervision signals, raising questions about the effectiveness of fine-tuning foundation models in such settings. In this work, we investigate scientific long-tailed recognition under a purely visual and parameter-efficient fine-tuning (PEFT) paradigm. Experiments on three scientific benchmarks show that fine-tuning foundation models yields limited gains, and reveal that penultimate-layer features play an important role, particularly for tail classes. Motivated by these findings, we propose SciLT, a framework that exploits multi-level representations through adaptive feature fusion and dual-supervision learning. By jointly leveraging penultimate- and final-layer features, SciLT achieves balanced performance across head and tail classes. Extensive experiments demonstrate that SciLT consistently outperforms existing methods, establishing a strong and practical baseline for scientific long-tailed recognition and providing valuable guidance for adapting foundation models to scientific data with substantial domain shifts.

One Model, Two Minds: Task-Conditioned Reasoning for Unified Image Quality and Aesthetic Assessment

Unifying Image Quality Assessment (IQA) and Image Aesthetic Assessment (IAA) in a single multimodal large language model is appealing, yet existing methods adopt a task-agnostic recipe that applies the same reasoning strategy and reward to both tasks. We show this is fundamentally misaligned: IQA relies on low-level, objective perceptual cues and benefits from concise distortion-focused reasoning, whereas IAA requires deliberative semantic judgment and is poorly served by point-wise score regression. We identify these as a reasoning mismatch and an optimization mismatch, and provide empirical evidence for both through controlled probes. Motivated by these findings, we propose TATAR (Task-Aware Thinking with Asymmetric Rewards), a unified framework that shares the visual-language backbone while conditioning post-training on each task's nature. TATAR combines three components: fast--slow task-specific reasoning construction that pairs IQA with concise perceptual rationales and IAA with deliberative aesthetic narratives; two-stage SFT+GRPO learning that establishes task-aware behavioral priors before reward-driven refinement; and asymmetric rewards that apply Gaussian score shaping for IQA and Thurstone-style completion ranking for IAA. Extensive experiments across eight benchmarks demonstrate that TATAR consistently outperforms prior unified baselines on both tasks under in-domain and cross-domain settings, remains competitive with task-specific specialized models, and yields more stable training dynamics for aesthetic assessment. Our results establish task-conditioned post-training as a principled paradigm for unified perceptual scoring. Our code is publicly available at https://github.com/yinwen2019/TATAR.

D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation

Early DNA foundation models adopted BERT-style training, achieving good performance on DNA understanding tasks but lacking generative capabilities. Recent autoregressive models enable DNA generation, but employ left-to-right causal modeling that is suboptimal for DNA where regulatory relationships are inherently bidirectional. We present D3LM (\textbf{D}iscrete \textbf{D}NA \textbf{D}iffusion \textbf{L}anguage \textbf{M}odel), which unifies bidirectional representation learning and DNA generation through masked diffusion. D3LM directly adopts the Nucleotide Transformer (NT) v2 architecture but reformulates the training objective as masked diffusion in discrete DNA space, enabling both bidirectional understanding and generation capabilities within a single model. Compared to NT v2 of the same size, D3LM achieves improved performance on understanding tasks. Notably, on regulatory element generation, D3LM achieves an SFID of 10.92, closely approaching real DNA sequences (7.85) and substantially outperforming the previous best result of 29.16 from autoregressive models. Our work suggests diffusion language models as a promising paradigm for unified DNA foundation models. We further present the first systematic study of masked diffusion models in the DNA domain, investigating practical design choices such as tokenization schemes and sampling strategies, thereby providing empirical insights and a solid foundation for future research. D3LM has been released at https://huggingface.co/collections/Hengchang-Liu/d3lm.

Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

Diffusion LMs Can Approximate Optimal Infilling Lengths Implicitly

Diffusion language models (DLMs) provide a bidirectional generation framework naturally suited for infilling, yet their performance is constrained by the pre-specified infilling length. In this paper, we reveal that DLMs possess an inherent ability to discover the correct infilling length. We identify two key statistical phenomena in the first-step denoising confidence: a local \textit{Oracle Peak} that emerges near the ground-truth length and a systematic \textit{Length Bias} that often obscures this signal. By leveraging this signal and calibrating the bias, our training-free method \textbf{CAL} (\textbf{C}alibrated \textbf{A}daptive \textbf{L}ength) enables DLMs to approximate the optimal length through an efficient search before formal decoding. Empirical evaluations demonstrate that CAL improves Pass@1 by up to 47.7\% over fixed-length baselines and 40.5\% over chat-based adaptive methods in code infilling, while boosting BLEU-2 and ROUGE-L by up to 8.5\% and 9.9\% in text infilling. These results demonstrate that CAL paves the way for robust DLM infilling without requiring any specialized training. Code is available at https://github.com/NiuHechang/Calibrated_Adaptive_Length.

Controlled LLM Training on Spectral Sphere

Scaling large models requires optimization strategies that ensure rapid convergence grounded in stability. Maximal Update Parametrization ($\boldsymbolμ$P) provides a theoretical safeguard for width-invariant $Θ(1)$ activation control, whereas emerging optimizers like Muon are only ``half-aligned'' with these constraints: they control updates but allow weights to drift. To address this limitation, we introduce the \textbf{Spectral Sphere Optimizer (SSO)}, which enforces strict module-wise spectral constraints on both weights and their updates. By deriving the steepest descent direction on the spectral sphere, SSO realizes a fully $\boldsymbolμ$P-aligned optimization process. To enable large-scale training, we implement SSO as an efficient parallel algorithm within Megatron. Through extensive pretraining on diverse architectures, including Dense 1.7B, MoE 8B-A1B, and 200-layer DeepNet models, SSO consistently outperforms AdamW and Muon. Furthermore, we observe significant practical stability benefits, including improved MoE router load balancing, suppressed outliers, and strictly bounded activations.

Enhancing Human Motion Prediction via Multi-range Decoupling Decoding with Gating-adjusting Aggregation

Expressive representation of pose sequences is crucial for accurate motion modeling in human motion prediction (HMP). While recent deep learning-based methods have shown promise in learning motion representations, these methods tend to overlook the varying relevance and dependencies between historical information and future moments, with a stronger correlation for short-term predictions and weaker for distant future predictions. This limits the learning of motion representation and then hampers prediction performance. In this paper, we propose a novel approach called multi-range decoupling decoding with gating-adjusting aggregation ($MD2GA$), which leverages the temporal correlations to refine motion representation learning. This approach employs a two-stage strategy for HMP. In the first stage, a multi-range decoupling decoding adeptly adjusts feature learning by decoding the shared features into distinct future lengths, where different decoders offer diverse insights into motion patterns. In the second stage, a gating-adjusting aggregation dynamically combines the diverse insights guided by input motion data. Extensive experiments demonstrate that the proposed method can be easily integrated into other motion prediction methods and enhance their prediction performance.