$f$-PO: Generalizing Preference Optimization with $f$-divergence Minimization

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.

TabDiff: a Multi-Modal Diffusion Model for Tabular Data Generation

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. In this paper, we introduce TabDiff, a joint diffusion framework that models all multi-modal distributions of tabular data in one model. 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. TabDiff is parameterized by a transformer handling different input types, and the entire framework can be efficiently optimized in an end-to-end fashion. 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. Comprehensive experiments on seven datasets demonstrate that TabDiff achieves superior average performance over existing competitive baselines across all eight metrics, with up to $22.5\%$ improvement over the state-of-the-art model on pair-wise column correlation estimations. Code is available at https://github.com/MinkaiXu/TabDiff.

Energy-Based Diffusion Language Models for Text Generation

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.

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

The cell is arguably the smallest unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of AI-powered Virtual Cells, where robust representations of cells and cellular systems under different conditions are directly learned from growing biological data across measurements and scales. We discuss desired capabilities of AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using Virtual Instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions is within reach.

LLMs generate structurally realistic social networks but overestimate political homophily

Generating social networks is essential for many applications, such as epidemic modeling and social simulations. Prior approaches either involve deep learning models, which require many observed networks for training, or stylized models, which are limited in their realism and flexibility. In contrast, LLMs offer the potential for zero-shot and flexible network generation. However, two key questions are: (1) are LLM's generated networks realistic, and (2) what are risks of bias, given the importance of demographics in forming social ties? To answer these questions, we develop three prompting methods for network generation and compare the generated networks to real social networks. We find that more realistic networks are generated with "local" methods, where the LLM constructs relations for one persona at a time, compared to "global" methods that construct the entire network at once. We also find that the generated networks match real networks on many characteristics, including density, clustering, community structure, and degree. However, we find that LLMs emphasize political homophily over all other types of homophily and overestimate political homophily relative to real-world measures.

RelBench: A Benchmark for Deep Learning on Relational Databases

We present RelBench, a public benchmark for solving predictive tasks over relational databases with graph neural networks. RelBench provides databases and tasks spanning diverse domains and scales, and is intended to be a foundational infrastructure for future research. We use RelBench to conduct the first comprehensive study of Relational Deep Learning (RDL) (Fey et al., 2024), which combines graph neural network predictive models with (deep) tabular models that extract initial entity-level representations from raw tables. End-to-end learned RDL models fully exploit the predictive signal encoded in primary-foreign key links, marking a significant shift away from the dominant paradigm of manual feature engineering combined with tabular models. To thoroughly evaluate RDL against this prior gold-standard, we conduct an in-depth user study where an experienced data scientist manually engineers features for each task. In this study, RDL learns better models whilst reducing human work needed by more than an order of magnitude. This demonstrates the power of deep learning for solving predictive tasks over relational databases, opening up many new research opportunities enabled by RelBench.

Learning production functions for supply chains with graph neural networks

The global economy relies on the flow of goods over supply chain networks, with nodes as firms and edges as transactions between firms. While we may observe these external transactions, they are governed by unseen production functions, which determine how firms internally transform the input products they receive into output products that they sell. In this setting, it can be extremely valuable to infer these production functions, to better understand and improve supply chains, and to forecast future transactions more accurately. However, existing graph neural networks (GNNs) cannot capture these hidden relationships between nodes' inputs and outputs. Here, we introduce a new class of models for this setting, by combining temporal GNNs with a novel inventory module, which learns production functions via attention weights and a special loss function. We evaluate our models extensively on real supply chains data, along with data generated from our new open-source simulator, SupplySim. Our models successfully infer production functions, with a 6-50% improvement over baselines, and forecast future transactions on real and synthetic data, outperforming baselines by 11-62%.

Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization

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.

AvaTaR: Optimizing LLM Agents for Tool-Assisted Knowledge Retrieval

Large language model (LLM) agents have demonstrated impressive capability in utilizing external tools and knowledge to boost accuracy and reduce hallucinations. However, developing the prompting techniques that make LLM agents able to effectively use external tools and knowledge is a heuristic and laborious task. Here, we introduce AvaTaR, a novel and automatic framework that optimizes an LLM agent to effectively use the provided tools and improve its performance on a given task/domain. During optimization, we design a comparator module to iteratively provide insightful and holistic prompts to the LLM agent via reasoning between positive and negative examples sampled from training data. We demonstrate AvaTaR on four complex multimodal retrieval datasets featuring textual, visual, and relational information. We find AvaTaR consistently outperforms state-of-the-art approaches across all four challenging tasks and exhibits strong generalization ability when applied to novel cases, achieving an average relative improvement of 14% on the Hit@1 metric. Code and dataset are available at https://github.com/zou-group/avatar.

Reverse Image Retrieval Cues Parametric Memory in Multimodal LLMs

Despite impressive advances in recent multimodal large language models (MLLMs), state-of-the-art models such as from the GPT-4 suite still struggle with knowledge-intensive tasks. To address this, we consider Reverse Image Retrieval (RIR) augmented generation, a simple yet effective strategy to augment MLLMs with web-scale reverse image search results. RIR robustly improves knowledge-intensive visual question answering (VQA) of GPT-4V by 37-43%, GPT-4 Turbo by 25-27%, and GPT-4o by 18-20% in terms of open-ended VQA evaluation metrics. To our surprise, we discover that RIR helps the model to better access its own world knowledge. Concretely, our experiments suggest that RIR augmentation helps by providing further visual and textual cues without necessarily containing the direct answer to a query. In addition, we elucidate cases in which RIR can hurt performance and conduct a human evaluation. Finally, we find that the overall advantage of using RIR makes it difficult for an agent that can choose to use RIR to perform better than an approach where RIR is the default setting.