Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective peptide binders. First, not all residues contribute equally to peptide-target interactions. Second, the generated peptides must adopt valid geometries due to the constraints of peptide bonds. Third, realistic tasks for peptide drug development are still lacking. To address these challenges, we introduce PepHAR, a hot-spot-driven autoregressive generative model for designing peptides targeting specific proteins. Building on the observation that certain hot spot residues have higher interaction potentials, we first use an energy-based density model to fit and sample these key residues. Next, to ensure proper peptide geometry, we autoregressively extend peptide fragments by estimating dihedral angles between residue frames. Finally, we apply an optimization process to iteratively refine fragment assembly, ensuring correct peptide structures. By combining hot spot sampling with fragment-based extension, our approach enables de novo peptide design tailored to a target protein and allows the incorporation of key hot spot residues into peptide scaffolds. Extensive experiments, including peptide design and peptide scaffold generation, demonstrate the strong potential of PepHAR in computational peptide binder design.

GOPT: Generalizable Online 3D Bin Packing via Transformer-based Deep Reinforcement Learning

Robotic object packing has broad practical applications in the logistics and automation industry, often formulated by researchers as the online 3D Bin Packing Problem (3D-BPP). However, existing DRL-based methods primarily focus on enhancing performance in limited packing environments while neglecting the ability to generalize across multiple environments characterized by different bin dimensions. To this end, we propose GOPT, a generalizable online 3D Bin Packing approach via Transformer-based deep reinforcement learning (DRL). First, we design a Placement Generator module to yield finite subspaces as placement candidates and the representation of the bin. Second, we propose a Packing Transformer, which fuses the features of the items and bin, to identify the spatial correlation between the item to be packed and available sub-spaces within the bin. Coupling these two components enables GOPT's ability to perform inference on bins of varying dimensions. We conduct extensive experiments and demonstrate that GOPT not only achieves superior performance against the baselines, but also exhibits excellent generalization capabilities. Furthermore, the deployment with a robot showcases the practical applicability of our method in the real world. The source code will be publicly available at https://github.com/Xiong5Heng/GOPT.

FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames

Despite the striking success of general protein folding models such as AlphaFold2(AF2, Jumper et al. (2021)), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise a previously overlooked issue that FAPE tends to face gradient vanishing problem on high-rotational-error targets. To address this fundamental limitation, we propose a novel geodesic loss called Frame Aligned Frame Error (FAFE, denoted as F2E to distinguish from FAPE), which enables the model to better optimize both the rotational and translational errors between two frames. We then prove that F2E can be reformulated as a group-aware geodesic loss, which translates the optimization of the residue-to-residue error to optimizing group-to-group geodesic frame distance. By fine-tuning AF2 with our proposed new loss function, we attain a correct rate of 52.3\% (DockQ $>$ 0.23) on an evaluation set and 43.8\% correct rate on a subset with low homology, with substantial improvement over AF2 by 182\% and 100\% respectively.

Full-Atom Peptide Design based on Multi-modal Flow Matching

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first multi-modal deep generative model grounded in the flow-matching framework for the design of full-atom peptides that target specific protein receptors. Drawing inspiration from the crucial roles of residue backbone orientations and side-chain dynamics in protein-peptide interactions, we characterize the peptide structure using rigid backbone frames within the $\mathrm{SE}(3)$ manifold and side-chain angles on high-dimensional tori. Furthermore, we represent discrete residue types in the peptide sequence as categorical distributions on the probability simplex. By learning the joint distributions of each modality using derived flows and vector fields on corresponding manifolds, our method excels in the fine-grained design of full-atom peptides. Harnessing the multi-modal paradigm, our approach adeptly tackles various tasks such as fix-backbone sequence design and side-chain packing through partial sampling. Through meticulously crafted experiments, we demonstrate that PepFlow exhibits superior performance in comprehensive benchmarks, highlighting its significant potential in computational peptide design and analysis.

Categorical Flow Matching on Statistical Manifolds

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.

Equivariant Neural Operator Learning with Graphon Convolution

We propose a general architecture that combines the coefficient learning scheme with a residual operator layer for learning mappings between continuous functions in the 3D Euclidean space. Our proposed model is guaranteed to achieve SE(3)-equivariance by design. From the graph spectrum view, our method can be interpreted as convolution on graphons (dense graphs with infinitely many nodes), which we term InfGCN. By leveraging both the continuous graphon structure and the discrete graph structure of the input data, our model can effectively capture the geometric information while preserving equivariance. Through extensive experiments on large-scale electron density datasets, we observed that our model significantly outperformed the current state-of-the-art architectures. Multiple ablation studies were also carried out to demonstrate the effectiveness of the proposed architecture.

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation

Diffusion models have revolutionized text-to-image generation with its exceptional quality and creativity. However, its multi-step sampling process is known to be slow, often requiring tens of inference steps to obtain satisfactory results. Previous attempts to improve its sampling speed and reduce computational costs through distillation have been unsuccessful in achieving a functional one-step model. In this paper, we explore a recent method called Rectified Flow, which, thus far, has only been applied to small datasets. The core of Rectified Flow lies in its \emph{reflow} procedure, which straightens the trajectories of probability flows, refines the coupling between noises and images, and facilitates the distillation process with student models. We propose a novel text-conditioned pipeline to turn Stable Diffusion (SD) into an ultra-fast one-step model, in which we find reflow plays a critical role in improving the assignment between noise and images. Leveraging our new pipeline, we create, to the best of our knowledge, the first one-step diffusion-based text-to-image generator with SD-level image quality, achieving an FID (Frechet Inception Distance) of $23.3$ on MS COCO 2017-5k, surpassing the previous state-of-the-art technique, progressive distillation, by a significant margin ($37.2$ $\rightarrow$ $23.3$ in FID). By utilizing an expanded network with 1.7B parameters, we further improve the FID to $22.4$. We call our one-step models \emph{InstaFlow}. On MS COCO 2014-30k, InstaFlow yields an FID of $13.1$ in just $0.09$ second, the best in $\leq 0.1$ second regime, outperforming the recent StyleGAN-T ($13.9$ in $0.1$ second). Notably, the training of InstaFlow only costs 199 A100 GPU days. Project page:~\url{https://github.com/gnobitab/InstaFlow}.

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free models as the atomic interaction in the 3D space is explicitly modeled. However, current 3D target-aware models either rely on the voxelized atom densities or the autoregressive sampling process, which are not equivariant to rotation or easily violate geometric constraints resulting in unrealistic structures. In this work, we develop a 3D equivariant diffusion model to solve the above challenges. To achieve target-aware molecule design, our method learns a joint generative process of both continuous atom coordinates and categorical atom types with a SE(3)-equivariant network. Moreover, we show that our model can serve as an unsupervised feature extractor to estimate the binding affinity under proper parameterization, which provides an effective way for drug screening. To evaluate our model, we propose a comprehensive framework to evaluate the quality of sampled molecules from different dimensions. Empirical studies show our model could generate molecules with more realistic 3D structures and better affinities towards the protein targets, and improve binding affinity ranking and prediction without retraining.

Active Learning in Brain Tumor Segmentation with Uncertainty Sampling, Annotation Redundancy Restriction, and Data Initialization

Deep learning models have demonstrated great potential in medical 3D imaging, but their development is limited by the expensive, large volume of annotated data required. Active learning (AL) addresses this by training a model on a subset of the most informative data samples without compromising performance. We compared different AL strategies and propose a framework that minimizes the amount of data needed for state-of-the-art performance. 638 multi-institutional brain tumor MRI images were used to train a 3D U-net model and compare AL strategies. We investigated uncertainty sampling, annotation redundancy restriction, and initial dataset selection techniques. Uncertainty estimation techniques including Bayesian estimation with dropout, bootstrapping, and margins sampling were compared to random query. Strategies to avoid annotation redundancy by removing similar images within the to-be-annotated subset were considered as well. We determined the minimum amount of data necessary to achieve similar performance to the model trained on the full dataset ({\alpha} = 0.1). A variance-based selection strategy using radiomics to identify the initial training dataset is also proposed. Bayesian approximation with dropout at training and testing showed similar results to that of the full data model with less than 20% of the training data (p=0.293) compared to random query achieving similar performance at 56.5% of the training data (p=0.814). Annotation redundancy restriction techniques achieved state-of-the-art performance at approximately 40%-50% of the training data. Radiomics dataset initialization had higher Dice with initial dataset sizes of 20 and 80 images, but improvements were not significant. In conclusion, we investigated various AL strategies with dropout uncertainty estimation achieving state-of-the-art performance with the least annotated data.

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation

Learning new task-specific skills from a few trials is a fundamental challenge for artificial intelligence. Meta reinforcement learning (meta-RL) tackles this problem by learning transferable policies that support few-shot adaptation to unseen tasks. Despite recent advances in meta-RL, most existing methods require the access to the environmental reward function of new tasks to infer the task objective, which is not realistic in many practical applications. To bridge this gap, we study the problem of few-shot adaptation in the context of human-in-the-loop reinforcement learning. We develop a meta-RL algorithm that enables fast policy adaptation with preference-based feedback. The agent can adapt to new tasks by querying human's preference between behavior trajectories instead of using per-step numeric rewards. By extending techniques from information theory, our approach can design query sequences to maximize the information gain from human interactions while tolerating the inherent error of non-expert human oracle. In experiments, we extensively evaluate our method, Adaptation with Noisy OracLE (ANOLE), on a variety of meta-RL benchmark tasks and demonstrate substantial improvement over baseline algorithms in terms of both feedback efficiency and error tolerance.