Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery

In this work, we propose MEDICO, a Multi-viEw Deep generative model for molecule generation, structural optimization, and the SARS-CoV-2 Inhibitor disCOvery. To the best of our knowledge, MEDICO is the first-of-this-kind graph generative model that can generate molecular graphs similar to the structure of targeted molecules, with a multi-view representation learning framework to sufficiently and adaptively learn comprehensive structural semantics from targeted molecular topology and geometry. We show that our MEDICO significantly outperforms the state-of-the-art methods in generating valid, unique, and novel molecules under benchmarking comparisons. In particular, we showcase the multi-view deep learning model enables us to generate not only the molecules structurally similar to the targeted molecules but also the molecules with desired chemical properties, demonstrating the strong capability of our model in exploring the chemical space deeply. Moreover, case study results on targeted molecule generation for the SARS-CoV-2 main protease (Mpro) show that by integrating molecule docking into our model as chemical priori, we successfully generate new small molecules with desired drug-like properties for the Mpro, potentially accelerating the de novo design of Covid-19 drugs. Further, we apply MEDICO to the structural optimization of three well-known Mpro inhibitors (N3, 11a, and GC376) and achieve ~88% improvement in their binding affinity to Mpro, demonstrating the application value of our model for the development of therapeutics for SARS-CoV-2 infection.

Attentional Ptycho-Tomography (APT) for three-dimensional nanoscale X-ray imaging with minimal data acquisition and computation time

Noninvasive X-ray imaging of nanoscale three-dimensional objects, e.g. integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of complex electromagnetic field through ICs; and tomographic scanning, which collects complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach trained to provide accurate reconstructions of ICs despite incomplete measurements, using a dramatically reduced amount of angular scanning. Training process includes regularizing priors based on typical IC patterns and the physics of X-ray propagation. We demonstrate that APT with 12-time reduced angles achieves fidelity comparable to the gold standard with the original set of angles. With the same set of reduced angles, APT also outperforms baseline reconstruction methods. In our experiments, APT achieves 108-time aggregate reduction in data acquisition and computation without compromising quality. We expect our physics-assisted machine learning framework could also be applied to other branches of nanoscale imaging.

Learning Object-Language Alignments for Open-Vocabulary Object Detection

Existing object detection methods are bounded in a fixed-set vocabulary by costly labeled data. When dealing with novel categories, the model has to be retrained with more bounding box annotations. Natural language supervision is an attractive alternative for its annotation-free attributes and broader object concepts. However, learning open-vocabulary object detection from language is challenging since image-text pairs do not contain fine-grained object-language alignments. Previous solutions rely on either expensive grounding annotations or distilling classification-oriented vision models. In this paper, we propose a novel open-vocabulary object detection framework directly learning from image-text pair data. We formulate object-language alignment as a set matching problem between a set of image region features and a set of word embeddings. It enables us to train an open-vocabulary object detector on image-text pairs in a much simple and effective way. Extensive experiments on two benchmark datasets, COCO and LVIS, demonstrate our superior performance over the competing approaches on novel categories, e.g. achieving 32.0% mAP on COCO and 21.7% mask mAP on LVIS. Code is available at: https://github.com/clin1223/VLDet.

RIS-Assisted Self-Interference Mitigation for In-Band Full-Duplex Transceivers

The wireless in-band full-duplex (IBFD) technology can in theory double the system capacity over the conventional frequency division duplex (FDD) or time-division duplex (TDD) alternatives. But the strong self-interference of the IBFD can cause excessive quantization noise in the analog-to-digital converters (ADC), which represents the hurdle for its real implementation. In this paper, we consider employing a reconfigurable intelligent surface (RIS) for IBFD communications. While the BS transmits and receives the signals to and from the users simultaneously on the same frequency band, it can adjust the reflection coefficients of the RIS to configure the wireless channel so that the self-interference of the BS is sufficiently mitigated in the propagation domain. Taking the impact of the quantization noise into account, we propose to jointly design the downlink (DL) precoding matrix and the RIS coefficients to maximize the sum of uplink (UL) and DL rates. The effectiveness of the proposed RIS-assisted in-band full-duplex (RAIBFD) system is verified by simulation studies, even taking into considerations that the phases of the RIS have only finite resolution.

The Runner-up Solution for YouTube-VIS Long Video Challenge 2022

This technical report describes our 2nd-place solution for the ECCV 2022 YouTube-VIS Long Video Challenge. We adopt the previously proposed online video instance segmentation method IDOL for this challenge. In addition, we use pseudo labels to further help contrastive learning, so as to obtain more temporally consistent instance embedding to improve tracking performance between frames. The proposed method obtains 40.2 AP on the YouTube-VIS 2022 long video dataset and was ranked second place in this challenge. We hope our simple and effective method could benefit further research.

Periodic Artifact Reduction in Fourier transforms of Full Field Atomic Resolution Images

The discrete Fourier transform is among the most routine tools used in high-resolution scanning / transmission electron microscopy (S/TEM). However, when calculating a Fourier transform, periodic boundary conditions are imposed and sharp discontinuities between the edges of an image cause a cross patterned artifact along the reciprocal space axes. This artifact can interfere with the analysis of reciprocal lattice peaks of an atomic resolution image. Here we demonstrate that the recently developed Periodic Plus Smooth Decomposition technique provides a simple, efficient method for reliable removal of artifacts caused by edge discontinuities. In this method, edge artifacts are reduced by subtracting a smooth background that solves Poisson's equation with boundary conditions set by the image's edges. Unlike the traditional windowed Fourier transforms, Periodic Plus Smooth Decomposition maintains sharp reciprocal lattice peaks from the image's entire field of view.

Self-supervised Video Representation Learning with Motion-Aware Masked Autoencoders

Masked autoencoders (MAEs) have emerged recently as art self-supervised spatiotemporal representation learners. Inheriting from the image counterparts, however, existing video MAEs still focus largely on static appearance learning whilst are limited in learning dynamic temporal information hence less effective for video downstream tasks. To resolve this drawback, in this work we present a motion-aware variant -- MotionMAE. Apart from learning to reconstruct individual masked patches of video frames, our model is designed to additionally predict the corresponding motion structure information over time. This motion information is available at the temporal difference of nearby frames. As a result, our model can extract effectively both static appearance and dynamic motion spontaneously, leading to superior spatiotemporal representation learning capability. Extensive experiments show that our MotionMAE outperforms significantly both supervised learning baseline and state-of-the-art MAE alternatives, under both domain-specific and domain-generic pretraining-then-finetuning settings. In particular, when using ViT-B as the backbone our MotionMAE surpasses the prior art model by a margin of 1.2% on Something-Something V2 and 3.2% on UCF101 in domain-specific pretraining setting. Encouragingly, it also surpasses the competing MAEs by a large margin of over 3% on the challenging video object segmentation task. The code is available at https://github.com/happy-hsy/MotionMAE.

MechRetro is a chemical-mechanism-driven graph learning framework for interpretable retrosynthesis prediction and pathway planning

Leveraging artificial intelligence for automatic retrosynthesis speeds up organic pathway planning in digital laboratories. However, existing deep learning approaches are unexplainable, like "black box" with few insights, notably limiting their applications in real retrosynthesis scenarios. Here, we propose MechRetro, a chemical-mechanism-driven graph learning framework for interpretable retrosynthetic prediction and pathway planning, which learns several retrosynthetic actions to simulate a reverse reaction via elaborate self-adaptive joint learning. By integrating chemical knowledge as prior information, we design a novel Graph Transformer architecture to adaptively learn discriminative and chemically meaningful molecule representations, highlighting the strong capacity in molecule feature representation learning. We demonstrate that MechRetro outperforms the state-of-the-art approaches for retrosynthetic prediction with a large margin on large-scale benchmark datasets. Extending MechRetro to the multi-step retrosynthesis analysis, we identify efficient synthetic routes via an interpretable reasoning mechanism, leading to a better understanding in the realm of knowledgeable synthetic chemists. We also showcase that MechRetro discovers a novel pathway for protokylol, along with energy scores for uncertainty assessment, broadening the applicability for practical scenarios. Overall, we expect MechRetro to provide meaningful insights for high-throughput automated organic synthesis in drug discovery.

Rethinking Resolution in the Context of Efficient Video Recognition

In this paper, we empirically study how to make the most of low-resolution frames for efficient video recognition. Existing methods mainly focus on developing compact networks or alleviating temporal redundancy of video inputs to increase efficiency, whereas compressing frame resolution has rarely been considered a promising solution. A major concern is the poor recognition accuracy on low-resolution frames. We thus start by analyzing the underlying causes of performance degradation on low-resolution frames. Our key finding is that the major cause of degradation is not information loss in the down-sampling process, but rather the mismatch between network architecture and input scale. Motivated by the success of knowledge distillation (KD), we propose to bridge the gap between network and input size via cross-resolution KD (ResKD). Our work shows that ResKD is a simple but effective method to boost recognition accuracy on low-resolution frames. Without bells and whistles, ResKD considerably surpasses all competitive methods in terms of efficiency and accuracy on four large-scale benchmark datasets, i.e., ActivityNet, FCVID, Mini-Kinetics, Something-Something V2. In addition, we extensively demonstrate its effectiveness over state-of-the-art architectures, i.e., 3D-CNNs and Video Transformers, and scalability towards super low-resolution frames. The results suggest ResKD can serve as a general inference acceleration method for state-of-the-art video recognition. Our code will be available at https://github.com/CVMI-Lab/ResKD.

Deep learning at the edge enables real-time streaming ptychographic imaging

Coherent microscopy techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent X-ray microscopy methods like ptychography are poised to revolutionize nanoscale materials characterization. However, associated significant increases in data and compute needs mean that conventional approaches no longer suffice for recovering sample images in real-time from high-speed coherent imaging experiments. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the sampling constraints imposed by traditional ptychography, allowing low dose imaging using orders of magnitude less data than required by traditional methods.