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Controlled generation with pre-trained Diffusion and Flow Matching models has vast applications. One strategy for guiding ODE-based generative models is through optimizing a target loss $R(x_1)$ while staying close to the prior distribution. Along this line, some recent work showed the effectiveness of guiding flow model by differentiating through its ODE sampling process. Despite the superior performance, the theoretical understanding of this line of methods is still preliminary, leaving space for algorithm improvement. Moreover, existing methods predominately focus on Euclidean data manifold, and there is a compelling need for guided flow methods on complex geometries such as SO(3), which prevails in high-stake scientific applications like protein design. We present OC-Flow, a general and theoretically grounded training-free framework for guided flow matching using optimal control. Building upon advances in optimal control theory, we develop effective and practical algorithms for solving optimal control in guided ODE-based generation and provide a systematic theoretical analysis of the convergence guarantee in both Euclidean and SO(3). We show that existing backprop-through-ODE methods can be interpreted as special cases of Euclidean OC-Flow. OC-Flow achieved superior performance in extensive experiments on text-guided image manipulation, conditional molecule generation, and all-atom peptide design.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which directly incorporates functional group information into the representations. This strategic reduction in tokenization granularity is intentionally aligned with key drivers of functional properties (i.e., functional groups), enhancing the model's understanding of chemical language. By expanding the chemical lexicon, FARM more effectively bridges SMILES and natural language, ultimately advancing the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research., Comment: Preprint

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce Neural P$^3$M, a versatile enhancer of geometric GNNs to expand the scope of their capabilities by incorporating mesh points alongside atoms and reimaging traditional mathematical operations in a trainable manner. Neural P$^3$M exhibits flexibility across a wide range of molecular systems and demonstrates remarkable accuracy in predicting energies and forces, outperforming on benchmarks such as the MD22 dataset. It also achieves an average improvement of 22% on the OE62 dataset while integrating with various architectures., Comment: Published as a conference paper at NeurIPS 2024

As scientific research proliferates, researchers face the daunting task of navigating and reading vast amounts of literature. Existing solutions, such as document QA, fail to provide personalized and up-to-date information efficiently. We present Paper Copilot, a self-evolving, efficient LLM system designed to assist researchers, based on thought-retrieval, user profile and high performance optimization. Specifically, Paper Copilot can offer personalized research services, maintaining a real-time updated database. Quantitative evaluation demonstrates that Paper Copilot saves 69.92\% of time after efficient deployment. This paper details the design and implementation of Paper Copilot, highlighting its contributions to personalized academic support and its potential to streamline the research process.

Learning from human feedback has been central to recent advances in artificial intelligence and machine learning. Since the collection of human feedback is costly, a natural question to ask is if the new feedback always needs to collected. Or could we evaluate a new model with the human feedback on responses of another model? This motivates us to study off-policy evaluation from logged human feedback. We formalize the problem, propose both model-based and model-free estimators for policy values, and show how to optimize them. We analyze unbiasedness of our estimators and evaluate them empirically. Our estimators can predict the absolute values of evaluated policies, rank them, and be optimized.

We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the results from information geometry. We demonstrate the effectiveness of our method on the discrete generation problem by instantiating SFM on the manifold of categorical distributions whose geometric properties remain unexplored in previous discrete generative models. Utilizing the Fisher information metric, we equip the manifold with a Riemannian structure whose intrinsic geometries are effectively leveraged by following the shortest paths of geodesics. We develop an efficient training and sampling algorithm that overcomes numerical stability issues with a diffeomorphism between manifolds. Our distinctive geometric perspective of statistical manifolds allows us to apply optimal transport during training and interpret SFM as following the steepest direction of the natural gradient. Unlike previous models that rely on variational bounds for likelihood estimation, SFM enjoys the exact likelihood calculation for arbitrary probability measures. We manifest that SFM can learn more complex patterns on the statistical manifold where existing models often fail due to strong prior assumptions. Comprehensive experiments on real-world generative tasks ranging from image, text to biological domains further demonstrate that SFM achieves higher sampling quality and likelihood than other discrete diffusion or flow-based models.

Learning of preference models from human feedback has been central to recent advances in artificial intelligence. Motivated by the cost of obtaining high-quality human annotations, we study the problem of data collection for learning preference models. The key idea in our work is to generalize the optimal design, a method for computing information gathering policies, to ranked lists. To show the generality of our ideas, we study both absolute and relative feedback on the lists. We design efficient algorithms for both settings and analyze them. We prove that our preference model estimators improve with more data and so does the ranking error under the estimators. Finally, we experiment with several synthetic and real-world datasets to show the statistical efficiency of our algorithms.

One emergent ability of large language models (LLMs) is that query-specific examples can be included in the prompt at inference time. In this work, we use active learning for adaptive prompt design and call it Active In-context Prompt Design (AIPD). We design the LLM prompt by adaptively choosing few-shot examples from a training set to optimize performance on a test set. The training examples are initially unlabeled and we obtain the label of the most informative ones, which maximally reduces uncertainty in the LLM prediction. We propose two algorithms, GO and SAL, which differ in how the few-shot examples are chosen. We analyze these algorithms in linear models: first GO and then use its equivalence with SAL. We experiment with many different tasks in small, medium-sized, and large language models; and show that GO and SAL outperform other methods for choosing few-shot examples in the LLM prompt at inference time.

Multi-objective optimization is a type of decision making problems where multiple conflicting objectives are optimized. We study offline optimization of multi-objective policies from data collected by an existing policy. We propose a pessimistic estimator for the multi-objective policy values that can be easily plugged into existing formulas for hypervolume computation and optimized. The estimator is based on inverse propensity scores (IPS), and improves upon a naive IPS estimator in both theory and experiments. Our analysis is general, and applies beyond our IPS estimators and methods for optimizing them. The pessimistic estimator can be optimized by policy gradients and performs well in all of our experiments.

We introduce the maximum $n$-times coverage problem that selects $k$ overlays to maximize the summed coverage of weighted elements, where each element must be covered at least $n$ times. We also define the min-cost $n$-times coverage problem where the objective is to select the minimum set of overlays such that the sum of the weights of elements that are covered at least $n$ times is at least $\tau$. Maximum $n$-times coverage is a generalization of the multi-set multi-cover problem, is NP-complete, and is not submodular. We introduce two new practical solutions for $n$-times coverage based on integer linear programming and sequential greedy optimization. We show that maximum $n$-times coverage is a natural way to frame peptide vaccine design, and find that it produces a pan-strain COVID-19 vaccine design that is superior to 29 other published designs in predicted population coverage and the expected number of peptides displayed by each individual's HLA molecules., Comment: ICLR 2022