NeurIPS 2025 论文列表

Conference on Neural Information Processing Systems

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MLR-Bench: Evaluating AI Agents on Open-Ended Machine Learning Research

Hui Chen, Miao Xiong, Yujie Lu, Wei Han, Ailin Deng, Yufei He, Jiaying Wu, Yibo Li, Yue Liu, Bryan Hooi

展开摘要

Recent advancements in AI agents have demonstrated their growing potential to drive and support scientific discovery. In this work, we introduce MLR-Bench, a comprehensive benchmark for evaluating AI agents on open-ended machine learning research. MLR-Bench includes three key components: (1) 201 research tasks sourced from NeurIPS, ICLR, and ICML workshops covering diverse ML topics; (2) MLR-Judge, an automated evaluation framework combining LLM-based reviewers with carefully designed review rubrics to assess research quality; and (3) MLR-Agent, a modular agent scaffold capable of completing research tasks through four stages: idea generation, proposal formulation, experimentation, and paper writing. Our framework supports both stepwise assessment across these distinct research stages, and end-to-end evaluation of the final research paper. We then use MLR-Bench to evaluate six frontier LLMs and an advanced coding agent, finding that while LLMs are effective at generating coherent ideas and well-structured papers, current coding agents frequently (e.g., in 80\% of the cases) produce fabricated or invalidated experimental results—posing a major barrier to scientific reliability. We validate MLR-Judge through human evaluation, showing high agreement with expert reviewers, supporting its potential as a scalable tool for research evaluation. We open-source MLR-Bench to help the community benchmark, diagnose, and improve AI research agents toward trustworthy and transparent scientific discovery.

Poster
Harnessing Feature Resonance under Arbitrary Target Alignment for Out-of-Distribution Node Detection

Shenzhi Yang, Junbo Zhao, Sharon Li, Shouqing Yang, Dingyu Yang, Xiaofang Zhang, Haobo Wang

展开摘要

Out-of-distribution (OOD) node detection in graphs is a critical yet challenging task. Most existing approaches rely heavily on fine-grained labeled data to obtain a pre-trained supervised classifier, inherently assuming the existence of a well-defined pretext classification task. However, when such a task is ill-defined or absent, their applicability becomes severely limited. To overcome this limitation, there is an urgent need to propose a more scalable OOD detection method that is independent of both pretext tasks and label supervision. We harness a new phenomenon called **Feature Resonance**, focusing on the feature space rather than the label space. We observe that, ideally, during the optimization of known ID samples, unknown ID samples undergo more significant representation changes than OOD samples, even when the model is trained to align arbitrary targets. The rationale behind it is that even without gold labels, the local manifold may still exhibit smooth resonance. Based on this, we further develop a novel graph OOD framework, dubbed **R**esonance-based **S**eparation and **L**earning (**RSL**), which comprises two core modules: (i)-a more practical micro-level proxy of feature resonance that measures the movement of feature vectors in one training step. (ii)-integrate with a synthetic OOD node strategy to train an effective OOD classifier. Theoretically, we derive an error bound showing the superior separability of OOD nodes during the resonance period. Extensive experiments on a total of thirteen real-world graph datasets empirically demonstrate that RSL achieves state-of-the-art performance.

Poster
PANORAMA: A Dataset and Benchmarks Capturing Decision Trails and Rationales in Patent Examination

Hyunseung Lim, Sooyohn Nam, Sungmin Na, Ji Yong Cho, June Yong Yang, Hyungyu Shin, Yoonjoo Lee, Juho Kim, Moontae Lee, Hwajung Hong

展开摘要

Patent examination remains an ongoing challenge in the NLP literature even after the advent of large language models (LLMs), as it requires an extensive yet nuanced human judgment on whether a submitted $\textit{claim}$ meets the statutory standards of $\textit{novelty}$ and $\textit{non-obviousness}$ against previously granted claims—$\textit{prior art}$—in expert domains. Previous NLP studies have approached this challenge as a prediction task (e.g., forecasting grant outcomes) with high-level proxies such as similarity metrics or classifiers trained on historical labels. However, this approach often overlooks the step-by-step evaluations that examiners must make with profound information, including rationales for the decisions provided in $\textit{office actions}$ documents, which also makes it harder to measure the current state of techniques in patent review processes. To fill this gap, we construct PANORAMA, a dataset of 8,143 U.S. patent examination records that preserves the full decision trails, including original applications, all cited references, $\textit{Non-Final Rejections}$, and $\textit{Notices of Allowance}$. Also, PANORAMA decomposes the trails into sequential benchmarks that emulate patent professionals' patent review processes and allow researchers to examine large language models' capabilities at each step of them. Our findings indicate that, although LLMs are relatively effective at retrieving relevant prior art and pinpointing the pertinent paragraphs, they struggle to assess the novelty and non-obviousness of patent claims. We discuss these results and argue that advancing NLP, including LLMs, in the patent domain requires a deeper understanding of real-world patent examination. Our dataset is openly available at https://huggingface.co/datasets/LG-AI-Research/PANORAMA.

Poster
Cost-Efficient LLM Training with Lifetime-Aware Tensor Offloading via GPUDirect Storage

Ziqi Yuan, Haoyang Zhang, Yirui Eric Zhou, Apoorve Mohan, I-Hsin Chung, Seetharami Seelam, Jian Huang

展开摘要

We present the design and implementation of a new lifetime-aware tensor offloading framework for GPU memory expansion using low-cost PCIe-based solid-state drives (SSDs). Our framework, TERAIO, is developed explicitly for large language model (LLM) training with multiple GPUs and multiple SSDs. Its design is driven by our observation that the active tensors take only a small fraction (1.7% on average) of allocated GPU memory in each LLM training iteration, the inactive tensors are usually large and will not be used for a long period of time, creating ample opportunities for offloading/prefetching tensors to/from slow SSDs without stalling the GPU training process. TERAIO accurately estimates the lifetime (active period of time in GPU memory) of each tensor with the profiling of the first few iterations in the training process. With the tensor lifetime analysis, TERAIO will generate an optimized tensor offloading/prefetching plan and integrate it into the compiled LLM program via PyTorch. TERAIO has a runtime tensor migration engine to execute the offloading/prefetching plan via GPUDirect storage, which allows direct tensor migration between GPUs and SSDs for alleviating the CPU bottleneck and maximizing the SSD bandwidth utilization. In comparison with state-of-the-art studies such as ZeRO-Offload and ZeRO-Infinity, we show that TERAIO improves the training performance of various LLMs by 1.47× on average, and achieves 80.7% of the ideal performance assuming unlimited GPU memory.

Poster
PUO-Bench: A Panel Understanding and Operation Benchmark with A Privacy-Preserving Framework

Wei Lin, Yiwei Zhou, Junkai Zhang, Rui Shao, Zhiyuan Zhao, Junyu Gao, Antoni B. Chan, Xuelong Li

展开摘要

Recent advancements in Vision-Language Models (VLMs) have enabled GUI agents to leverage visual features for interface understanding and operation in the digital world. However, limited research has addressed the interpretation and interaction with control panels in real-world settings. To bridge this gap, we propose the Panel Understanding and Operation (PUO) benchmark, comprising annotated panel images from appliances and associated vision-language instruction pairs. Experimental results on the benchmark demonstrate significant performance disparities between zero-shot and fine-tuned VLMs, revealing the lack of PUO-specific capabilities in existing language models. Furthermore, we introduce a Privacy-Preserving Framework (PPF) to address privacy concerns in cloud-based panel parsing and reasoning. PPF employs a dual-stage architecture, performing panel understanding on edge devices while delegating complex reasoning to cloud-based LLMs. Although this design introduces a performance trade-off due to edge model limitations, it eliminates the transmission of raw visual data, thereby mitigating privacy risks. Overall, this work provides foundational resources and methodologies for advancing interactive human-machine systems and robotic field in panel-centric applications.

Poster
Constrained Best Arm Identification

Tyron Darnell Lardy, Christina Katsimerou, Wouter M Koolen

展开摘要

In real-world decision-making problems, one needs to pick among multiple policies the one that performs best while respecting economic constraints. This motivates the problem of constrained best-arm identification for bandit problems where every arm is a joint distribution of reward and cost. We investigate the general case where reward and cost are dependent. The goal is to accurately identify the arm with the highest mean reward among all arms whose mean cost is below a given threshold. We prove information-theoretic lower bounds on the sample complexity for three models: Gaussian with fixed covariance, Gaussian with unknown covariance, and non-parametric distributions of rectangular support. We propose a combination of a sampling and a stopping rule that correctly identifies the constrained best arm and matches the optimal sample complexities for each of the three models. Simulations demonstrate the performance of our algorithms.

Poster
Generalizable Hand-Object Modeling from Monocular RGB Images via 3D Gaussians

Xingyu Liu, Pengfei Ren, Qi Qi, Haifeng Sun, Zirui Zhuang, Jing Wang, Jianxin Liao, Jingyu Wang

展开摘要

Recent advances in hand-object interaction modeling have employed implicit representations, such as Signed Distance Functions (SDF) and Neural Radiance Fields (NeRF) to reconstruct hands and objects with arbitrary topology and photo-realistic detail. However, these methods often rely on dense 3D surface annotations, or are tailored to short clips constrained in motion trajectories and scene contexts, limiting their generalization to diverse environments and movement patterns. In this work, we present HOGS, an adaptively perceptive 3D Gaussian Splatting (3DGS) framework for generalizable hand-object modeling from unconstrained monocular RGB images. By integrating photometric cues from the visual modality with the physically grounded structure of 3D Gaussians, HOGS disentangles inherent geometry from transient lighting and motion-induced appearance changes. This endows hand-object assets with the ability to generalize to unseen environments and dynamic motion patterns. Experiments on two challenging datasets demonstrate that HOGS outperforms state-of-the-art methods in monocular hand-object reconstruction and photo-realistic rendering.

Poster
FerretNet: Efficient Synthetic Image Detection via Local Pixel Dependencies

Shuqiao Liang, Jian Liu, Chen Renzhang, Quanlong Guan

展开摘要

The increasing realism of synthetic images generated by advanced models such as VAEs, GANs, and LDMs poses significant challenges for synthetic image detection. To address this issue, we explore two artifact types introduced during the generation process: (1) latent distribution deviations and (2) decoding-induced smoothing effects, which manifest as inconsistencies in local textures, edges, and color transitions. Leveraging local pixel dependencies (LPD) properties rooted in Markov Random Fields, we reconstruct synthetic images using neighboring pixel information to expose disruptions in texture continuity and edge coherence. Building upon LPD, we propose FerretNet, a lightweight neural network with only 1.1M parameters that delivers efficient and robust synthetic image detection. Extensive experiments demonstrate that FerretNet—trained exclusively on the 4-class ProGAN dataset—achieves an average accuracy of 97.1% on an open-world benchmark comprising 22 generative models. Our code and datasets are publicly available at https://github.com/xigua7105/FerretNet.

Poster
Towards Multiscale Graph-based Protein Learning with Geometric Secondary Structural Motifs

Shih-Hsin Wang, Yuhao Huang, Taos Transue, Justin M. Baker, Jonathan Forstater, Thomas Strohmer, Bao Wang

展开摘要

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale representations and modeling long-range dependencies efficiently. In this work, we propose an efficient multiscale graph-based learning framework tailored to proteins. Our proposed framework contains two crucial components: (1) It constructs a hierarchical graph representation comprising a collection of fine-grained subgraphs, each corresponding to a secondary structure motif (e.g., $\alpha$-helices, $\beta$-strands, loops), and a single coarse-grained graph that connects these motifs based on their spatial arrangement and relative orientation. (2) It employs two GNNs for feature learning: the first operates within individual secondary motifs to capture local interactions, and the second models higher-level structural relationships across motifs. Our modular framework allows a flexible choice of GNN in each stage. Theoretically, we show that our hierarchical framework preserves the desired maximal expressiveness, ensuring no loss of critical structural information. Empirically, we demonstrate that integrating baseline GNNs into our multiscale framework remarkably improves prediction accuracy and reduces computational cost across various benchmarks.

Poster
FracFace: Breaking The Visual Clues—Fractal-Based Privacy-Preserving Face Recognition

Wanying Dai, Beibei Li, Naipeng Dong, Guangdong Bai, Jin Song Dong

展开摘要

Face recognition is essential for identity authentication, but the rich visual clues in facial images pose significant privacy risks, highlighting the critical importance of privacy-preserving solutions. For instance, numerous studies have shown that generative models are capable of effectively performing reconstruction attacks that result in the restoration of original visual clues. To mitigate this threat, we introduce FracFace, a fractal-based privacy-preserving face recognition framework. This approach effectively weakens the visual clues that can be exploited by reconstruction attacks by disrupting the spatial structure in frequency domain features, while retaining the vital visual clues required for identity recognition. To achieve this, we craft a Frequency Channels Refining module that reduces sparsity in the frequency domain. It suppresses visual clues that could be exploited by reconstruction attacks, while preserving features indispensable for recognition, thus making these attacks more challenging. More significantly, we design a Frequency Fractal Mapping module that obfuscates deep representations by remapping refined frequency channels into a fractal-based privacy structure. By leveraging the self-similarity of fractals, this module preserves identity relevant features while enhancing defense capabilities, thereby improving the overall robustness of the protection scheme. Experiments conducted on multiple public face recognition benchmarks demonstrate that the proposed FracFace significantly reduces the visual recoverability of facial features, while maintaining high recognition accuracy, as well as the superiorities over state-of-the-art privacy protection approaches.

Poster
GRAPE: Optimize Data Mixture for Group Robust Multi-target Adaptive Pretraining

Simin Fan, Maria Ios Glarou, Martin Jaggi

展开摘要

The performance of large language models (LLMs) across diverse downstream applications is fundamentally governed by the quality and composition of their pretraining corpora. Existing domain reweighting algorithms primarily optimize data mixtures for a single target task, thereby resulting in models that overfit to specialized objectives while exhibiting substantial performance degradation on other benchmarks. This paper introduces $\textbf{G}$roup $\textbf{R}$obust Multi-target $\textbf{A}$daptive $\textbf{P}$r$\textbf{E}$training (GRAPE), a novel multi-source-multi-target domain reweighting framework designed to calibrate pretraining data mixtures for robust performance across multiple target tasks simultaneously. GRAPE dynamically adjusts sampling weights across source domains ($\textit{domain weights}$) while concurrently modulating $\textit{task weights}$ that quantify the relative importance of each individual target task. This adaptive process prioritizes tasks based on their learning difficulty throughout training. We formulate this interleaved reweighting mechanism as a minimax optimization problem: The inner maximization adjusts task weights leveraging group distributed-robust-optimization (DRO), where those tasks demonstrating the least improvement under the current data mixture are prioritized with higher weights; The outer minimization then optimizes domain weights to maximize loss reduction on the prioritized tasks. Experiments on $\texttt{ClimbLab}$ and $\texttt{SlimPajama}$ datasets demonstrate that GRAPE consistently outperforms baseline methods in terms of reasoning accuracies across 6 benchmarks. Furthermore, when applied to multilingual targets, GRAPE effectively identifies optimal training mixtures from mainstream languages, achieving superior language modeling capabilities across 8 low-resource target languages.

Poster
RL Tango: Reinforcing Generator and Verifier Together for Language Reasoning

Kaiwen Zha, Zhengqi Gao, Maohao Shen, Zhang-Wei Hong, Duane S Boning, Dina Katabi

展开摘要

Reinforcement learning (RL) has recently emerged as a compelling approach for enhancing the reasoning capabilities of large language models (LLMs), where an LLM generator serves as a policy guided by a verifier (reward model). However, current RL post-training methods for LLMs typically use verifiers that are fixed (rule-based or frozen pretrained) or trained discriminatively via supervised fine-tuning (SFT). Such designs are susceptible to reward hacking and generalize poorly beyond their training distributions. To overcome these limitations, we propose Tango, a novel framework that uses RL to concurrently train both an LLM generator and a verifier in an interleaved manner. A central innovation of Tango is its generative, process-level LLM verifier, which is trained via RL and co-evolves with the generator. Importantly, the verifier is trained solely based on outcome-level verification correctness rewards without requiring explicit process-level annotations. This generative RL-trained verifier exhibits improved robustness and superior generalization compared to deterministic or SFT-trained verifiers, fostering effective mutual reinforcement with the generator. Extensive experiments demonstrate that both components of Tango achieve state-of-the-art results among 7B/8B-scale models: the generator attains best-in-class performance across five competition-level math benchmarks and four challenging out-of-domain reasoning tasks, while the verifier leads on the ProcessBench dataset. Remarkably, both components exhibit particularly substantial improvements on the most difficult mathematical reasoning problems.

Poster
Face-Human-Bench: A Comprehensive Benchmark of Face and Human Understanding for Multi-modal Assistants

lixiong Qin, Shilong Ou, Miaoxuan Zhang, Jiangning Wei, Yuhang Zhang, Xiaoshuai Song, Yuchen Liu, Mei Wang, Weiran Xu

展开摘要

Faces and humans are crucial elements in social interaction and are widely included in everyday photos and videos. Therefore, a deep understanding of faces and humans will enable multi-modal assistants to achieve improved response quality and broadened application scope. Currently, the multi-modal assistant community lacks a comprehensive and scientific evaluation of face and human understanding abilities. In this paper, we first propose a hierarchical ability taxonomy that includes three levels of abilities. Then, based on this taxonomy, we collect images and annotations from publicly available datasets in the face and human community and build a semi-automatic data pipeline to produce problems for the new benchmark. Finally, the obtained Face-Human-Bench includes a development set and a test set, each with 1800 problems, supporting both English and Chinese. We conduct evaluations over 25 mainstream multi-modal large language models (MLLMs) with our Face-Human-Bench, focusing on the correlation between abilities, the impact of the relative position of targets on performance, and the impact of Chain of Thought (CoT) prompting on performance. We also explore which abilities of MLLMs need to be supplemented by specialist models. The dataset and evaluation code have been made publicly available at https://face-human-bench.github.io.

Poster
Stab-SGD: Noise-Adaptivity in Smooth Optimization with Stability Ratios

David A. R. Robin, Killian Bakong, Kevin Scaman

展开摘要

In the context of smooth stochastic optimization with first order methods, we introduce the stability ratio of gradient estimates, as a measure of local relative noise level, from zero for pure noise to one for negligible noise. We show that a schedule-free variant (Stab-SGD) of stochastic gradient descent obtained by just shrinking the learning rate by the stability ratio achieves real adaptivity to noise levels (i.e. without tuning hyperparameters to the gradient's variance), with all key properties of a good schedule-free algorithm: neither plateau nor explosion at intialization, and no saturation of the loss. We believe this theoretical development reveals the importance of estimating the local stability ratio in the construction of well-behaved (last-iterate) schedule-free algorithms, particularly when hyperparameter-tuning budgets are a small fraction of the total budget since noise-adaptivity and cheaper horizon-free tuning are most crucial in this regime.

Poster
What Really is a Member? Discrediting Membership Inference via Poisoning

Neal Mangaokar, Ashish Hooda, Zhuohang Li, Bradley A. Malin, Kassem Fawaz, Somesh Jha, Atul Prakash, Amrita Roy Chowdhury

展开摘要

Membership inference tests aim to determine whether a particular data point was included in a language model's training set. However, recent works have shown that such tests often fail under the strict definition of membership based on exact matching, and have suggested relaxing this definition to include semantic neighbors as members as well. In this work, we show that membership inference tests are still *unreliable* under this relaxation - it is possible to poison the training dataset in a way that causes the test to produce incorrect predictions for a target point. We theoretically reveal a trade-off between a test’s accuracy and its robustness to poisoning. We also present a concrete instantiation of this poisoning attack and empirically validate its effectiveness. Our results show that it can degrade the performance of existing tests to well below random.

Poster
Brain-Informed Fine-Tuning for Improved Multilingual Understanding in Language Models

Anuja Negi, SUBBA REDDY OOTA, Anwar O Nunez-Elizalde, Manish Gupta, Fatma Deniz

展开摘要

Recent studies have demonstrated that fine-tuning language models with brain data can improve their semantic understanding, although these findings have so far been limited to English. Interestingly, similar to the shared multilingual embedding space of pretrained multilingual language models, human studies provide strong evidence for a shared semantic system in bilingual individuals. Here, we investigate whether fine-tuning language models with bilingual brain data changes model representations in a way that improves them across multiple languages. To test this, we fine-tune monolingual and multilingual language models using brain activity recorded while bilingual participants read stories in English and Chinese. We then evaluate how well these representations generalize to the bilingual participants’ first language, their second language, and several other languages that the participants are not fluent in. We assess the fine-tuned language models on brain encoding performance and downstream NLP tasks. Our results show that bilingual brain-informed fine-tuned language models outperform their vanilla (pretrained) counterparts in both brain encoding performance and most downstream NLP tasks across multiple languages. These findings suggest that brain-informed fine-tuning improves multilingual understanding in language models, offering a bridge between cognitive neuroscience and NLP research. We make our code publicly available.

Poster
MoleBridge: Synthetic Space Projecting with Discrete Markov Bridges

Rongchao Zhang, Yu Huang, Yongzhi Cao, Hanpin Wang

展开摘要

Molecular synthetic space projecting is a critical technique in de novo molecular design, which aims to rectify molecules without synthesizability guarantee by converting them into synthetic postfix notations. However, the vast synthesizable chemical space and the discrete data modalities involved pose significant challenges to postfix notation conversion benchmarking. In this paper, we exploit conditional probability transitions in discrete state space and introduce MoleBridge, a deep generative model built on the Markov bridge approach for designing postfix notations of molecular synthesis pathways. MoleBridge consists of two iterative optimizations: i) Autoregressive extending of notation tokens from molecular graphs, and ii) generation of discrete reaction postfix notations through Markov bridge, where noisy token blocks are progressively denoised over multi-step iterations. For the challenging second iteration, which demands sensitivity to incorrect generative probability paths within intricate chemical spaces, we employ a thinking and denoising separation approach to denoise. Empirically, we find that MoleBridge is capable of accurately predicting synthesis pathways while exhibiting excellent performance in a variety of application scenarios.

Poster
Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Aditya Sengar, Ali Hariri, Daniel Probst, PATRICK BARTH, Pierre Vandergheynst

展开摘要

Generating diverse, all‐atom conformational ensembles of dynamic proteins such as G‐protein‐coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational diversity altogether. We present latent diffusion for full protein generation (LD-FPG), a framework that constructs complete all‐atom protein structures, including every side‐chain heavy atom, directly from molecular dynamics (MD) trajectories. LD-FPG employs a Chebyshev graph neural network (ChebNet) to obtain low‐dimensional latent embeddings of protein conformations, which are processed using three pooling strategies: blind, sequential and residue‐based. A diffusion model trained on these latent representations generates new samples that a decoder, optionally regularized by dihedral‐angle losses, maps back to Cartesian coordinates. Using D2R-MD, a $2\mu\text{s}$ MD trajectory (12 000 frames) of the human dopamine D$2$ receptor in a membrane environment, the sequential and residue-based pooling strategies reproduce the reference ensemble with high structural fidelity (all‐atom lDDT \~ $0.7$; $C\alpha$-lDDT \~ $0.8$) and recovers backbone and side‐chain dihedral‐angle distributions with a Jensen–Shannon divergence $<0.03$ compared to the MD data. LD-FPG thereby offers a practical route to system‐specific, all‐atom ensemble generation for large proteins, providing a promising tool for structure‐based therapeutic design on complex, dynamic targets. The D2R-MD dataset and our implementation are freely available to facilitate further research.

Poster
Feature Unlearning: Theoretical Foundations and Practical Applications with Shuffling

Yue Yang, Jinhao Li, Hao Wang

展开摘要

Machine unlearning has become a focal point in recent research, yet the specific area of feature unlearning has not been thoroughly explored. Feature unlearning involves the elimination of specific features' effects from an already trained model, presenting distinct challenges that are still not comprehensively addressed. This paper presents a novel and straightforward approach to feature unlearning that employs a tactical shuffling of the features designated for removal. By redistributing the values of the features targeted for unlearning throughout the original training dataset and subsequently fine-tuning the model with this shuffled data, our proposed method provides a theoretical guarantee for effective feature unlearning. Under mild assumptions, our method can effectively disrupt the established correlations between unlearned features and the target outcomes, while preserving the relationships between the remaining features and the predicted outcomes. Our empirical studies across various datasets,validate that our approach not only successfully removes the effects of specified features but also maintains the informational integrity of the remaining features while achieving a faster convergence rate.

Poster
Unified all-atom molecule generation with neural fields

Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew Martin Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi

展开摘要

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

Poster