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.

Generative modeling is increasingly important for data-driven computational design. Conventional approaches pair a generative model with a discriminative model to select or guide samples toward optimized designs. Yet discriminative models often struggle in data-scarce settings, common in scientific applications, and are unreliable in the tails of the distribution where optimal designs typically lie. We introduce generative property enhancer (GPE), an approach that implicitly guides generation by matching samples with lower property values to higher-value ones. Formulated as conditional density estimation, our framework defines a target distribution with improved properties, compelling the generative model to produce enhanced, diverse designs without auxiliary predictors. GPE is simple, scalable, end-to-end, modality-agnostic, and integrates seamlessly with diverse generative model architectures and losses. We demonstrate competitive empirical results on standard _in silico_ offline (non-sequential) protein fitness optimization benchmarks. Finally, we propose iterative training on a combination of limited real data and self-generated synthetic data, enabling extrapolation beyond the original property ranges.

We presents VoxBind, a new score-based generative model for 3D molecules conditioned on protein structures. Our approach represents molecules as 3D atomic density grids and leverages a 3D voxel-denoising network for learning and generation. We extend the neural empirical Bayes formalism (Saremi & Hyvärinen, 2019) to the conditional setting and generate structure-conditioned molecules with a two-step procedure: (i) sample noisy molecules from the Gaussian-smoothed conditional distribution with underdamped Langevin MCMC using the learned score function and (ii) estimate clean molecules from the noisy samples with single-step denoising. Compared to the current state of the art, our model is simpler to train, significantly faster to sample from, and achieves better results on extensive in silico benchmarks—the generated molecules are more diverse, exhibit fewer steric clashes, and bind with higher affinity to protein pockets.

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields. Our model, FuncMol, encodes molecular fields into latent codes using a conditional neural field, samples noisy codes from a Gaussian-smoothed distribution with Langevin MCMC (walk), denoises these samples in a single step (jump), and finally decodes them into molecular fields. FuncMol performs all-atom generation of 3D molecules without assumptions on the molecular structure and scales well with the size of molecules, unlike most approaches. Our method achieves competitive results on drug-like molecules and easily scales to macro-cyclic peptides, with at least one order of magnitude faster sampling. The code is available at https://github.com/prescient-design/funcmol.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the _neural empirical Bayes_ framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the "clean" molecule by denoising the noisy grid with a single step. Our method, _VoxMol_, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

Instance segmentation methods often require costly per-pixel labels. We propose a method called WISE-Net that only requires point-level annotations. During training, the model only has access to a single pixel label per object, yet the task is to output full segmentation masks. To address this challenge, we construct a network with two branches: (1) a 10-calization network (L-Net) that predicts the location of each object; and (2) an embedding network (E-Net) that learns an embedding space where pixels of the same object are close. The segmentation masks for the located objects are obtained by grouping pixels with similar embeddings. We evaluate our approach on PASCAL VOC, COCO, KITTI and CityScapes datasets. The experiments show that our method (1) obtains competitive results compared to fully-supervised methods in certain scenarios; (2) outperforms fully-and weakly-supervised methods with a fixed annotation budget; and (3) establishes a first strong baseline for instance segmentation with point-level supervision.

Contrastive self-supervised learning has emerged as a promising approach to unsupervised visual representation learning. In general, these methods learn global (image-level) representations that are invariant to different views (i.e., compositions of data augmentation) of the same image. However, many visual understanding tasks require dense (pixel-level) representations. In this paper, we propose View-Agnostic Dense Representation (VADeR) for unsupervised learning of dense representations. VADeR learns pixelwise representations by forcing local features to remain constant over different viewing conditions. Specifically, this is achieved through pixel-level contrastive learning: matching features (that is, features that describes the same location of the scene on different views) should be close in an embedding space, while non-matching features should be apart. VADeR provides a natural representation for dense prediction tasks and transfers well to downstream tasks. Our method outperforms ImageNet supervised pretraining (and strong unsupervised baselines) in multiple dense prediction tasks.

Neural networks are prone to adversarial attacks. In general, such attacks deteriorate the quality of the input by either slightly modifying most of its pixels, or by occluding it with a patch. In this paper, we propose a method that keeps the image unchanged and only adds an adversarial framing on the border of the image. We show empirically that our method is able to successfully attack state-of-theart methods on both image and video classification problems. Notably, the proposed method results in a universal attack which is very fast at test time. Source code can be found at github.com/zajaczajac/adv_framing.

Single-view 3D shape reconstruction is an important but challenging problem, mainly for two reasons. First, as shape annotation is very expensive to acquire, current methods rely on synthetic data, in which ground-truth 3D annotation is easy to obtain. However, this results in domain adaptation problem when applied to natural images. The second challenge is that there are multiple shapes that can explain a given 2D image. In this paper, we propose a framework to improve over these challenges using adversarial training. On one hand, we impose domain confusion between natural and synthetic image representations to reduce the distribution gap. On the other hand, we impose the reconstruction to be `realistic' by forcing it to lie on a (learned) manifold of realistic object shapes. Our experiments show that these constraints improve performance by a large margin over baseline reconstruction models. We achieve results competitive with the state of the art with a much simpler architecture.

For embodied agents to infer representations of the underlying 3D physical world they inhabit, they should efficiently combine multisensory cues from numerous trials, e.g., by looking at and touching objects. Despite its importance, multisensory 3D scene representation learning has received less attention compared to the unimodal setting. In this paper, we propose the Generative Multisensory Network (GMN) for learning latent representations of 3D scenes which are partially observable through multiple sensory modalities. We also introduce a novel method, called the Amortized Product-of-Experts, to improve the computational efficiency and the robustness to unseen combinations of modalities at test time. Experimental results demonstrate that the proposed model can efficiently infer robust modality-invariant 3D-scene representations from arbitrary combinations of modalities and perform accurate cross-modal generation. To perform this exploration we have also developed a novel multi-sensory simulation environment for embodied agents.

Metric-based meta-learning techniques have successfully been applied to few-shot classification problems. In this paper, we propose to leverage cross-modal information to enhance metric-based few-shot learning methods. Visual and semantic feature spaces have different structures by definition. For certain concepts, visual features might be richer and more discriminative than text ones. While for others, the inverse might be true. Moreover, when the support from visual information is limited in image classification, semantic representations (learned from unsupervised text corpora) can provide strong prior knowledge and context to help learning. Based on these two intuitions, we propose a mechanism that can adaptively combine information from both modalities according to new image categories to be learned. Through a series of experiments, we show that by this adaptive combination of the two modalities, our model outperforms current uni-modality few-shot learning methods and modality-alignment methods by a large margin on all benchmarks and few-shot scenarios tested. Experiments also show that our model can effectively adjust its focus on the two modalities. The improvement in performance is particularly large when the number of shots is very small.

The objective of unsupervised domain adaptation is to leverage features from a labeled source domain and learn a classifier for an unlabeled target domain, with a similar but different data distribution. Most deep learning approaches to domain adaptation consist of two steps: (i) learn features that preserve a low risk on labeled samples (source domain) and (ii) make the features from both domains to be as indistinguishable as possible, so that a classifier trained on the source can also be applied on the target domain. In general, the classifiers in step (i) consist of fully-connected layers applied directly on the indistinguishable features learned in (ii). In this paper, we propose a different way to do the classification, using similarity learning. The proposed method learns a pairwise similarity function in which classification can be performed by computing similarity between prototype representations of each category. The domain-invariant features and the categorical prototype representations are learned jointly and in an end-to-end fashion. At inference time, images from the target domain are compared to the prototypes and the label associated with the one that best matches the image is outputed. The approach is simple, scalable and effective. We show that our model achieves state-of-the-art performance in different unsupervised domain adaptation scenarios.