Middo: Model-Informed Dynamic Data Optimization for Enhanced LLM Fine-Tuning via Closed-Loop Learning

Supervised Fine-Tuning (SFT) Large Language Models (LLM) fundamentally rely on high-quality training data. While data selection and data synthesis are two common strategies to improve data quality, existing approaches often face limitations in static dataset curation that fail to adapt to evolving model capabilities. In this paper, we introduce Middo, a self-evolving Model-informed dynamic data optimization framework that uses model-aware data selection and context-preserving data refinement. Unlike conventional one-off filtering/synthesis methods, our framework establishes a closed-loop optimization system: (1) A self-referential diagnostic module proactively identifies suboptimal samples through tri-axial model signals - loss patterns (complexity), embedding cluster dynamics (diversity), and self-alignment scores (quality); (2) An adaptive optimization engine then transforms suboptimal samples into pedagogically valuable training points while preserving semantic integrity; (3) This optimization process continuously evolves with model capability through dynamic learning principles. Experiments on multiple benchmarks demonstrate that our \method consistently enhances the quality of seed data and boosts LLM's performance with improving accuracy by 7.15% on average while maintaining the original dataset scale. This work establishes a new paradigm for sustainable LLM training through dynamic human-AI co-evolution of data and models. Our datasets, models, and code are coming soon.

IDEAL: Data Equilibrium Adaptation for Multi-Capability Language Model Alignment

Large Language Models (LLMs) have achieved impressive performance through Supervised Fine-tuning (SFT) on diverse instructional datasets. When training on multiple capabilities simultaneously, the mixture training dataset, governed by volumes of data from different domains, is a critical factor that directly impacts the final model's performance. Unlike many studies that focus on enhancing the quality of training datasets through data selection methods, few works explore the intricate relationship between the compositional quantity of mixture training datasets and the emergent capabilities of LLMs. Given the availability of a high-quality multi-domain training dataset, understanding the impact of data from each domain on the model's overall capabilities is crucial for preparing SFT data and training a well-balanced model that performs effectively across diverse domains. In this work, we introduce IDEAL, an innovative data equilibrium adaptation framework designed to effectively optimize volumes of data from different domains within mixture SFT datasets, thereby enhancing the model's alignment and performance across multiple capabilities. IDEAL employs a gradient-based approach to iteratively refine the training data distribution, dynamically adjusting the volumes of domain-specific data based on their impact on downstream task performance. By leveraging this adaptive mechanism, IDEAL ensures a balanced dataset composition, enabling the model to achieve robust generalization and consistent proficiency across diverse tasks. Experiments across different capabilities demonstrate that IDEAL outperforms conventional uniform data allocation strategies, achieving a comprehensive improvement of approximately 7% in multi-task evaluation scores.

CipherBank: Exploring the Boundary of LLM Reasoning Capabilities through Cryptography Challenges

Large language models (LLMs) have demonstrated remarkable capabilities, especially the recent advancements in reasoning, such as o1 and o3, pushing the boundaries of AI. Despite these impressive achievements in mathematics and coding, the reasoning abilities of LLMs in domains requiring cryptographic expertise remain underexplored. In this paper, we introduce CipherBank, a comprehensive benchmark designed to evaluate the reasoning capabilities of LLMs in cryptographic decryption tasks. CipherBank comprises 2,358 meticulously crafted problems, covering 262 unique plaintexts across 5 domains and 14 subdomains, with a focus on privacy-sensitive and real-world scenarios that necessitate encryption. From a cryptographic perspective, CipherBank incorporates 3 major categories of encryption methods, spanning 9 distinct algorithms, ranging from classical ciphers to custom cryptographic techniques. We evaluate state-of-the-art LLMs on CipherBank, e.g., GPT-4o, DeepSeek-V3, and cutting-edge reasoning-focused models such as o1 and DeepSeek-R1. Our results reveal significant gaps in reasoning abilities not only between general-purpose chat LLMs and reasoning-focused LLMs but also in the performance of current reasoning-focused models when applied to classical cryptographic decryption tasks, highlighting the challenges these models face in understanding and manipulating encrypted data. Through detailed analysis and error investigations, we provide several key observations that shed light on the limitations and potential improvement areas for LLMs in cryptographic reasoning. These findings underscore the need for continuous advancements in LLM reasoning capabilities.

MathFusion: Enhancing Mathematic Problem-solving of LLM through Instruction Fusion

Large Language Models (LLMs) have shown impressive progress in mathematical reasoning. While data augmentation is promising to enhance mathematical problem-solving ability, current approaches are predominantly limited to instance-level modifications-such as rephrasing or generating syntactic variations-which fail to capture and leverage the intrinsic relational structures inherent in mathematical knowledge. Inspired by human learning processes, where mathematical proficiency develops through systematic exposure to interconnected concepts, we introduce MathFusion, a novel framework that enhances mathematical reasoning through cross-problem instruction synthesis. MathFusion implements this through three fusion strategies: (1) sequential fusion, which chains related problems to model solution dependencies; (2) parallel fusion, which combines analogous problems to reinforce conceptual understanding; and (3) conditional fusion, which creates context-aware selective problems to enhance reasoning flexibility. By applying these strategies, we generate a new dataset, \textbf{MathFusionQA}, followed by fine-tuning models (DeepSeekMath-7B, Mistral-7B, Llama3-8B) on it. Experimental results demonstrate that MathFusion achieves substantial improvements in mathematical reasoning while maintaining high data efficiency, boosting performance by 18.0 points in accuracy across diverse benchmarks while requiring only 45K additional synthetic instructions, representing a substantial improvement over traditional single-instruction approaches. Our datasets, models, and code are publicly available at https://github.com/QizhiPei/mathfusion.

MetaLadder: Ascending Mathematical Solution Quality via Analogical-Problem Reasoning Transfer

Large Language Models (LLMs) have demonstrated promising capabilities in solving mathematical reasoning tasks, leveraging Chain-of-Thought (CoT) data as a vital component in guiding answer generation. Current paradigms typically generate CoT and answers directly for a given problem, diverging from human problem-solving strategies to some extent. Humans often solve problems by recalling analogous cases and leveraging their solutions to reason about the current task. Inspired by this cognitive process, we propose \textbf{MetaLadder}, a novel framework that explicitly prompts LLMs to recall and reflect on meta-problems, those structurally or semantically analogous problems, alongside their CoT solutions before addressing the target problem. Additionally, we introduce a problem-restating mechanism to enhance the model's comprehension of the target problem by regenerating the original question, which further improves reasoning accuracy. Therefore, the model can achieve reasoning transfer from analogical problems, mimicking human-like "learning from examples" and generalization abilities. Extensive experiments on mathematical benchmarks demonstrate that our MetaLadder significantly boosts LLMs' problem-solving accuracy, largely outperforming standard CoT-based methods (\textbf{10.3\%} accuracy gain) and other methods. Our code and data has been released at https://github.com/LHL3341/MetaLadder.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors

Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are often slow and costly. The advent of deep learning-based approaches has shown significant promise, offering increases in both accuracy and efficiency. Building upon the foundational work of FABind, a model designed with a focus on speed and accuracy, we present FABind+, an enhanced iteration that largely boosts the performance of its predecessor. We identify pocket prediction as a critical bottleneck in molecular docking and propose a novel methodology that significantly refines pocket prediction, thereby streamlining the docking process. Furthermore, we introduce modifications to the docking module to enhance its pose generation capabilities. In an effort to bridge the gap with conventional sampling/generative methods, we incorporate a simple yet effective sampling technique coupled with a confidence model, requiring only minor adjustments to the regression framework of FABind. Experimental results and analysis reveal that FABind+ remarkably outperforms the original FABind, achieves competitive state-of-the-art performance, and delivers insightful modeling strategies. This demonstrates FABind+ represents a substantial step forward in molecular docking and drug discovery. Our code is in https://github.com/QizhiPei/FABind.