Gaze Estimation Based on Multi-view Geometric Neural Networks

Gaze and head pose estimation can play essential roles in various applications, such as human attention recognition and behavior analysis. Most of the deep neural network-based gaze estimation techniques use supervised regression techniques where features are extracted from eye images by neural networks and regress 3D gaze vectors. I plan to apply the geometric features of the eyes to determine the gaze vectors of observers relying on the concepts of 3D multiple view geometry. We develop an end to-end CNN framework for gaze estimation using 3D geometric constraints under semi-supervised and unsupervised settings and compare the results. We explore the mathematics behind the concepts of Homography and Structure-from- Motion and extend it to the gaze estimation problem using the eye region landmarks. We demonstrate the necessity of the application of 3D eye region landmarks for implementing the 3D geometry-based algorithms and address the problem when lacking the depth parameters in the gaze estimation datasets. We further explore the use of Convolutional Neural Networks (CNNs) to develop an end-to-end learning-based framework, which takes in sequential eye images to estimate the relative gaze changes of observers. We use a depth network for performing monocular image depth estimation of the eye region landmarks, which are further utilized by the pose network to estimate the relative gaze change using view synthesis constraints of the iris regions. We further explore CNN frameworks to estimate the relative changes in homography matrices between sequential eye images based on the eye region landmarks to estimate the pose of the iris and hence determine the relative change in the gaze of the observer. We compare and analyze the results obtained from mathematical calculations and deep neural network-based methods. We further compare the performance of the proposed CNN scheme with the state-of-the-art regression-based methods for gaze estimation. Future work involves extending the end-to-end pipeline as an unsupervised framework for gaze estimation in the wild

Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks

Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the limited quantity of structural data. Meanwhile, protein language models trained on substantial 1D sequences have shown burgeoning capabilities with scale in a broad range of applications. Several previous studies consider combining these different protein modalities to promote the representation power of geometric neural networks, but fail to present a comprehensive understanding of their benefits. In this work, we integrate the knowledge learned by well-trained protein language models into several state-of-the-art geometric networks and evaluate a variety of protein representation learning benchmarks, including protein-protein interface prediction, model quality assessment, protein-protein rigid-body docking, and binding affinity prediction. Our findings show an overall improvement of 20% over baselines. Strong evidence indicates that the incorporation of protein language models' knowledge enhances geometric networks' capacity by a significant margin and can be generalized to complex tasks

A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design

Therapeutic antibodies are an essential and rapidly expanding drug modality. The binding specificity between antibodies and antigens is decided by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a hierarchical training paradigm (HTP) for the antibody sequence-structure co-design. HTP consists of four levels of training stages, each corresponding to a specific protein modality within a particular protein domain. Through carefully crafted tasks in different stages, HTP seamlessly and effectively integrates geometric graph neural networks (GNNs) with large-scale protein language models to excavate evolutionary information from not only geometric structures but also vast antibody and non-antibody sequence databases, which determines ligand binding pose and strength. Empirical experiments show that HTP sets the new state-of-the-art performance in the co-design problem as well as the fix-backbone design. Our research offers a hopeful path to unleash the potential of deep generative architectures and seeks to illuminate the way forward for the antibody sequence and structure co-design challenge

Spectra of the Spike-Flow Graphs in Geometrically Embedded Neural Networks

Full article available at Springerlink: http://link.springer.com/chapter/10.1007%2F978-3-642-29347-4_17 DOI: 10.1007/978-3-642-29347-4_17In this work we study a simplified model of a neural activity flow in networks, whose connectivity is based on geometrical embedding, rather than being lattices or fully connected graphs. We present numerical results showing that as the spectrum (set of eigenvalues of adjacency matrix) of the resulting activity-based network develops a scale-free dependency. Moreover it strengthens and becomes valid for a wider segment along with the simulation progress, which implies a highly organised structure of the analysed graph

CNN based Cuneiform Sign Detection Learned from Annotated 3D Renderings and Mapped Photographs with Illumination Augmentation

Motivated by the challenges of the Digital Ancient Near Eastern Studies (DANES) community, we develop digital tools for processing cuneiform script being a 3D script imprinted into clay tablets used for more than three millennia and at least eight major languages. It consists of thousands of characters that have changed over time and space. Photographs are the most common representations usable for machine learning, while ink drawings are prone to interpretation. Best suited 3D datasets that are becoming available. We created and used the HeiCuBeDa and MaiCuBeDa datasets, which consist of around 500 annotated tablets. For our novel OCR-like approach to mixed image data, we provide an additional mapping tool for transferring annotations between 3D renderings and photographs. Our sign localization uses a RepPoints detector to predict the locations of characters as bounding boxes. We use image data from GigaMesh's MSII (curvature, see https://gigamesh.eu) based rendering, Phong-shaded 3D models, and photographs as well as illumination augmentation. The results show that using rendered 3D images for sign detection performs better than other work on photographs. In addition, our approach gives reasonably good results for photographs only, while it is best used for mixed datasets. More importantly, the Phong renderings, and especially the MSII renderings, improve the results on photographs, which is the largest dataset on a global scale.Comment: This paper was accepted to ICCV23 and includes the DOI for an Open Access Dataset with annotated cuneiform scrip

Adaptive Topological Feature via Persistent Homology: Filtration Learning for Point Clouds

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. To enhance the accuracy of such machine learning methods, it is known to be effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we need to choose a filtration for the point clouds, an increasing sequence of spaces. Because the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we theoretically show a finite-dimensional approximation result that justifies our architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.Comment: 17 pages with 4 figure

InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems

In the field of artificial intelligence for science, it is consistently an essential challenge to face a limited amount of labeled data for real-world problems. The prevailing approach is to pretrain a powerful task-agnostic model on a large unlabeled corpus but may struggle to transfer knowledge to downstream tasks. In this study, we propose InstructMol, a semi-supervised learning algorithm, to take better advantage of unlabeled examples. It introduces an instructor model to provide the confidence ratios as the measurement of pseudo-labels' reliability. These confidence scores then guide the target model to pay distinct attention to different data points, avoiding the over-reliance on labeled data and the negative influence of incorrect pseudo-annotations. Comprehensive experiments show that InstructBio substantially improves the generalization ability of molecular models, in not only molecular property predictions but also activity cliff estimations, demonstrating the superiority of the proposed method. Furthermore, our evidence indicates that InstructBio can be equipped with cutting-edge pretraining methods and used to establish large-scale and task-specific pseudo-labeled molecular datasets, which reduces the predictive errors and shortens the training process. Our work provides strong evidence that semi-supervised learning can be a promising tool to overcome the data scarcity limitation and advance molecular representation learning

DeepScribe: Localization and Classification of Elamite Cuneiform Signs Via Deep Learning

Twenty-five hundred years ago, the paperwork of the Achaemenid Empire was recorded on clay tablets. In 1933, archaeologists from the University of Chicago's Oriental Institute (OI) found tens of thousands of these tablets and fragments during the excavation of Persepolis. Many of these tablets have been painstakingly photographed and annotated by expert cuneiformists, and now provide a rich dataset consisting of over 5,000 annotated tablet images and 100,000 cuneiform sign bounding boxes. We leverage this dataset to develop DeepScribe, a modular computer vision pipeline capable of localizing cuneiform signs and providing suggestions for the identity of each sign. We investigate the difficulty of learning subtasks relevant to cuneiform tablet transcription on ground-truth data, finding that a RetinaNet object detector can achieve a localization mAP of 0.78 and a ResNet classifier can achieve a top-5 sign classification accuracy of 0.89. The end-to-end pipeline achieves a top-5 classification accuracy of 0.80. As part of the classification module, DeepScribe groups cuneiform signs into morphological clusters. We consider how this automatic clustering approach differs from the organization of standard, printed sign lists and what we may learn from it. These components, trained individually, are sufficient to produce a system that can analyze photos of cuneiform tablets from the Achaemenid period and provide useful transliteration suggestions to researchers. We evaluate the model's end-to-end performance on locating and classifying signs, providing a roadmap to a linguistically-aware transliteration system, then consider the model's potential utility when applied to other periods of cuneiform writing.Comment: Currently under review in the ACM JOCC