Molecular relational learning (MRL) focuses on understanding the interaction dynamics between molecules and has gained significant attention from researchers thanks to its diverse applications [20]. For instance, understanding how a medication dissolves in different solvents (medication-solvent interaction) is vital in pharmacy [30, 26, 3], while predicting the optical and photophysical properties of chromophores in various solvents (chromophore-solvent interaction) is essential for material discovery [16]. Because of the expensive time and financial costs associated with conducting wet lab experiments to test the interaction behavior of all possible molecular pairs [31], machine learning methods have been quickly embraced for MRL. Despite recent advancements in MRL, previous works tend to ignore molecules' 3D geometric information and instead focus solely on their 2D topological structures. However, in molecular science, the 3D geometric information of molecules (Figure 1 (a)) is crucial for understanding and predicting molecular behavior across various contexts, ranging from physical properties [1] to biological functions [10, 46]. This is particularly important in MRL, as geometric information plays a key role in molecular interactions by determining how molecules recognize, interact, and bind with one another in their interaction environment [34]. In traditional molecular dynamics simulations, explicit solvent models, which directly consider the detailed environment of molecular interaction, have demonstrated superior performance compared to implicit solvent models, which simplify the solvent as a continuous medium, highlighting the significance of explicitly modeling the complex geometries of interaction environments [47]. However, acquiring stereochemical structures of molecules is often very costly, resulting in limited availability of such 3D geometric information for downstream tasks [23].

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

Synthesizing high-quality tabular data is an important topic in many data science tasks, ranging from dataset augmentation to privacy protection. However, developing expressive generative models for tabular data is challenging due to its inherent heterogeneous data types, complex inter-correlations, and intricate column-wise distributions. Our key innovation is the development of a joint continuous-time diffusion process for numerical and categorical data, where we propose feature-wise learnable diffusion processes to counter the high disparity of different feature distributions. We further introduce a multi-modal stochastic sampler to automatically correct the accumulated decoding error during sampling, and propose classifier-free guidance for conditional missing column value imputation. Code is available at https://github.com/MinkaiXu/TabDiff. Tabular data is ubiquitous in various databases, and developing effective generative models for it is a fundamental problem in many data processing and analysis tasks, ranging from training data augmentation (Fonseca & Bacao, 2023), data privacy protection (Assefa et al., 2021; Hernandez et al., 2022), to missing value imputation (You et al., 2020; Zheng & Charoenphakdee, 2022). With versatile synthetic tabular data that share the same format and statistical properties as the existing dataset, we are able to completely replace real data in a workflow or supplement the data to enhance its utility, which makes it easier to share and use. The capability of anonymizing data and enlarging sample size without compromising the overall data quality enables it to revolutionize the field of data science.

Despite remarkable progress in autoregressive language models, alternative generative paradigms beyond left-to-right generation are still being actively explored. Discrete diffusion models, with the capacity for parallel generation, have recently emerged as a promising alternative. Unfortunately, these models still underperform the autoregressive counterparts, with the performance gap increasing when reducing the number of sampling steps. Our analysis reveals that this degradation is a consequence of an imperfect approximation used by diffusion models. In this work, we propose Energy-based Diffusion Language Model (EDLM), an energy-based model operating at the full sequence level for each diffusion step, introduced to improve the underlying approximation used by diffusion models. More specifically, we introduce an EBM in a residual form, and show that its parameters can be obtained by leveraging a pretrained autoregressive model or by finetuning a bidirectional transformer via noise contrastive estimation. We also propose an efficient generation algorithm via parallel important sampling. Comprehensive experiments on language modeling benchmarks show that our model can consistently outperform state-of-the-art diffusion models by a significant margin, and approaches autoregressive models' perplexity. We further show that, without any generation performance drop, our framework offers a 1.3$\times$ sampling speedup over existing diffusion models.

Preference optimization has made significant progress recently, with numerous methods developed to align language models with human preferences. This paper introduces $f$-divergence Preference Optimization ($f$-PO), a novel framework that generalizes and extends existing approaches. $f$-PO minimizes $f$-divergences between the optimized policy and the optimal policy, encompassing a broad family of alignment methods using various divergences. Our approach unifies previous algorithms like DPO and EXO, while offering new variants through different choices of $f$-divergences. We provide theoretical analysis of $f$-PO's properties and conduct extensive experiments on state-of-the-art language models using benchmark datasets. Results demonstrate $f$-PO's effectiveness across various tasks, achieving superior performance compared to existing methods on popular benchmarks such as AlpacaEval 2, Arena-Hard, and MT-Bench. Additionally, we present ablation studies exploring the impact of different $f$-divergences, offering insights into the trade-offs between regularization and performance in offline preference optimization. Our work contributes both practical algorithms and theoretical understanding to the field of language model alignment. Code is available at https://github.com/MinkaiXu/fPO.

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static structures, neglecting the fact that physical systems are always dynamic in nature. In this work, we propose geometric trajectory diffusion models (GeoTDM), the first diffusion model for modeling the temporal distribution of 3D geometric trajectories. Modeling such distribution is challenging as it requires capturing both the complex spatial interactions with physical symmetries and temporal correspondence encapsulated in the dynamics. We theoretically justify that diffusion models with equivariant temporal kernels can lead to density with desired symmetry, and develop a novel transition kernel leveraging SE(3)-equivariant spatial convolution and temporal attention. Furthermore, to induce an expressive trajectory distribution for conditional generation, we introduce a generalized learnable geometric prior into the forward diffusion process to enhance temporal conditioning. We conduct extensive experiments on both unconditional and conditional generation in various scenarios, including physical simulation, molecular dynamics, and pedestrian motion. Empirical results on a wide suite of metrics demonstrate that GeoTDM can generate realistic geometric trajectories with significantly higher quality.

Large language models (LLMs) like GPT-4, PaLM, and LLaMA have shown significant improvements in various reasoning tasks. However, smaller models such as Llama-3-8B and DeepSeekMath-Base still struggle with complex mathematical reasoning because they fail to effectively identify and correct reasoning errors. Recent reflection-based methods aim to address these issues by enabling self-reflection and self-correction, but they still face challenges in independently detecting errors in their reasoning steps. To overcome these limitations, we propose SuperCorrect, a novel two-stage framework that uses a large teacher model to supervise and correct both the reasoning and reflection processes of a smaller student model. In the first stage, we extract hierarchical high-level and detailed thought templates from the teacher model to guide the student model in eliciting more fine-grained reasoning thoughts. In the second stage, we introduce cross-model collaborative direct preference optimization (DPO) to enhance the self-correction abilities of the student model by following the teacher's correction traces during training. This cross-model DPO approach teaches the student model to effectively locate and resolve erroneous thoughts with error-driven insights from the teacher model, breaking the bottleneck of its thoughts and acquiring new skills and knowledge to tackle challenging problems. Extensive experiments consistently demonstrate our superiority over previous methods. Notably, our SuperCorrect-7B model significantly surpasses powerful DeepSeekMath-7B by 7.8%/5.3% and Qwen2.5-Math-7B by 15.1%/6.3% on MATH/GSM8K benchmarks, achieving new SOTA performance among all 7B models. Code: https://github.com/YangLing0818/SuperCorrect-llm

Homophily principle, \ie{} nodes with the same labels or similar attributes are more likely to be connected, has been commonly believed to be the main reason for the superiority of Graph Neural Networks (GNNs) over traditional Neural Networks (NNs) on graph-structured data, especially on node-level tasks. However, recent work has identified a non-trivial set of datasets where GNN's performance compared to the NN's is not satisfactory. Heterophily, i.e. low homophily, has been considered the main cause of this empirical observation. People have begun to revisit and re-evaluate most existing graph models, including graph transformer and its variants, in the heterophily scenario across various kinds of graphs, e.g. heterogeneous graphs, temporal graphs and hypergraphs. Moreover, numerous graph-related applications are found to be closely related to the heterophily problem. In the past few years, considerable effort has been devoted to studying and addressing the heterophily issue. In this survey, we provide a comprehensive review of the latest progress on heterophilic graph learning, including an extensive summary of benchmark datasets and evaluation of homophily metrics on synthetic graphs, meticulous classification of the most updated supervised and unsupervised learning methods, thorough digestion of the theoretical analysis on homophily/heterophily, and broad exploration of the heterophily-related applications. Notably, through detailed experiments, we are the first to categorize benchmark heterophilic datasets into three sub-categories: malignant, benign and ambiguous heterophily. Malignant and ambiguous datasets are identified as the real challenging datasets to test the effectiveness of new models on the heterophily challenge. Finally, we propose several challenges and future directions for heterophilic graph representation learning.

Generating ligand molecules for specific protein targets, known as structure-based drug design, is a fundamental problem in therapeutics development and biological discovery. Recently, target-aware generative models, especially diffusion models, have shown great promise in modeling protein-ligand interactions and generating candidate drugs. However, existing models primarily focus on learning the chemical distribution of all drug candidates, which lacks effective steerability on the chemical quality of model generations. In this paper, we propose a novel and general alignment framework to align pretrained target diffusion models with preferred functional properties, named AliDiff. AliDiff shifts the target-conditioned chemical distribution towards regions with higher binding affinity and structural rationality, specified by user-defined reward functions, via the preference optimization approach. To avoid the overfitting problem in common preference optimization objectives, we further develop an improved Exact Energy Preference Optimization method to yield an exact and efficient alignment of the diffusion models, and provide the closed-form expression for the converged distribution. Empirical studies on the CrossDocked2020 benchmark show that AliDiff can generate molecules with state-of-the-art binding energies with up to -7.07 Avg. Vina Score, while maintaining strong molecular properties.

We introduce Buffer of Thoughts (BoT), a novel and versatile thought-augmented reasoning approach for enhancing accuracy, efficiency and robustness of large language models (LLMs). Specifically, we propose meta-buffer to store a series of informative high-level thoughts, namely thought-template, distilled from the problem-solving processes across various tasks. Then for each problem, we retrieve a relevant thought-template and adaptively instantiate it with specific reasoning structures to conduct efficient reasoning. To guarantee the scalability and stability, we further propose buffer-manager to dynamically update the meta-buffer, thus enhancing the capacity of meta-buffer as more tasks are solved. We conduct extensive experiments on 10 challenging reasoning-intensive tasks, and achieve significant performance improvements over previous SOTA methods: 11% on Game of 24, 20% on Geometric Shapes and 51% on Checkmate-in-One. Further analysis demonstrate the superior generalization ability and model robustness of our BoT, while requiring only 12% of the cost of multi-query prompting methods (e.g., tree/graph of thoughts) on average. Notably, we find that our Llama3-8B + BoT has the potential to surpass Llama3-70B model.