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Dec 29

Learning Geometrically Disentangled Representations of Protein Folding Simulations

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

  • 5 authors
·
May 20, 2022

PlantBert: An Open Source Language Model for Plant Science

The rapid advancement of transformer-based language models has catalyzed breakthroughs in biomedical and clinical natural language processing; however, plant science remains markedly underserved by such domain-adapted tools. In this work, we present PlantBert, a high-performance, open-source language model specifically tailored for extracting structured knowledge from plant stress-response literature. Built upon the DeBERTa architecture-known for its disentangled attention and robust contextual encoding-PlantBert is fine-tuned on a meticulously curated corpus of expert-annotated abstracts, with a primary focus on lentil (Lens culinaris) responses to diverse abiotic and biotic stressors. Our methodology combines transformer-based modeling with rule-enhanced linguistic post-processing and ontology-grounded entity normalization, enabling PlantBert to capture biologically meaningful relationships with precision and semantic fidelity. The underlying corpus is annotated using a hierarchical schema aligned with the Crop Ontology, encompassing molecular, physiological, biochemical, and agronomic dimensions of plant adaptation. PlantBert exhibits strong generalization capabilities across entity types and demonstrates the feasibility of robust domain adaptation in low-resource scientific fields. By providing a scalable and reproducible framework for high-resolution entity recognition, PlantBert bridges a critical gap in agricultural NLP and paves the way for intelligent, data-driven systems in plant genomics, phenomics, and agronomic knowledge discovery. Our model is publicly released to promote transparency and accelerate cross-disciplinary innovation in computational plant science.

  • 8 authors
·
Jun 10

Robust Training Using Natural Transformation

Previous robustness approaches for deep learning models such as data augmentation techniques via data transformation or adversarial training cannot capture real-world variations that preserve the semantics of the input, such as a change in lighting conditions. To bridge this gap, we present NaTra, an adversarial training scheme that is designed to improve the robustness of image classification algorithms. We target attributes of the input images that are independent of the class identification, and manipulate those attributes to mimic real-world natural transformations (NaTra) of the inputs, which are then used to augment the training dataset of the image classifier. Specifically, we apply Batch Inverse Encoding and Shifting to map a batch of given images to corresponding disentangled latent codes of well-trained generative models. Latent Codes Expansion is used to boost image reconstruction quality through the incorporation of extended feature maps. Unsupervised Attribute Directing and Manipulation enables identification of the latent directions that correspond to specific attribute changes, and then produce interpretable manipulations of those attributes, thereby generating natural transformations to the input data. We demonstrate the efficacy of our scheme by utilizing the disentangled latent representations derived from well-trained GANs to mimic transformations of an image that are similar to real-world natural variations (such as lighting conditions or hairstyle), and train models to be invariant to these natural transformations. Extensive experiments show that our method improves generalization of classification models and increases its robustness to various real-world distortions

  • 6 authors
·
May 9, 2021

Gaitor: Learning a Unified Representation Across Gaits for Real-World Quadruped Locomotion

The current state-of-the-art in quadruped locomotion is able to produce a variety of complex motions. These methods either rely on switching between a discrete set of skills or learn a distribution across gaits using complex black-box models. Alternatively, we present Gaitor, which learns a disentangled and 2D representation across locomotion gaits. This learnt representation forms a planning space for closed-loop control delivering continuous gait transitions and perceptive terrain traversal. Gaitor's latent space is readily interpretable and we discover that during gait transitions, novel unseen gaits emerge. The latent space is disentangled with respect to footswing heights and lengths. This means that these gait characteristics can be varied independently in the 2D latent representation. Together with a simple terrain encoding and a learnt planner operating in the latent space, Gaitor can take motion commands including desired gait type and swing characteristics all while reacting to uneven terrain. We evaluate Gaitor in both simulation and the real world on the ANYmal C platform. To the best of our knowledge, this is the first work learning a unified and interpretable latent space for multiple gaits, resulting in continuous blending between different locomotion modes on a real quadruped robot. An overview of the methods and results in this paper is found at https://youtu.be/eVFQbRyilCA.

  • 5 authors
·
May 29, 2024

Geometry-Editable and Appearance-Preserving Object Compositon

General object composition (GOC) aims to seamlessly integrate a target object into a background scene with desired geometric properties, while simultaneously preserving its fine-grained appearance details. Recent approaches derive semantic embeddings and integrate them into advanced diffusion models to enable geometry-editable generation. However, these highly compact embeddings encode only high-level semantic cues and inevitably discard fine-grained appearance details. We introduce a Disentangled Geometry-editable and Appearance-preserving Diffusion (DGAD) model that first leverages semantic embeddings to implicitly capture the desired geometric transformations and then employs a cross-attention retrieval mechanism to align fine-grained appearance features with the geometry-edited representation, facilitating both precise geometry editing and faithful appearance preservation in object composition. Specifically, DGAD builds on CLIP/DINO-derived and reference networks to extract semantic embeddings and appearance-preserving representations, which are then seamlessly integrated into the encoding and decoding pipelines in a disentangled manner. We first integrate the semantic embeddings into pre-trained diffusion models that exhibit strong spatial reasoning capabilities to implicitly capture object geometry, thereby facilitating flexible object manipulation and ensuring effective editability. Then, we design a dense cross-attention mechanism that leverages the implicitly learned object geometry to retrieve and spatially align appearance features with their corresponding regions, ensuring faithful appearance consistency. Extensive experiments on public benchmarks demonstrate the effectiveness of the proposed DGAD framework.

  • 6 authors
·
May 27 2