pwc-archive/papers-with-abstracts huggingface dataset:
The Fundamental Theorem of Phyllotaxis revisited
Authors: Jonathan Swinton
Date: 2012-01-08 00:00:00

Jean's `Fundamental Theorem of Phyllotaxis' (\emph{Phyllotaxis: a systematic study in Plant Morphogenesis}, CUP 1994) describes the relationship between the count numbers of observed spirals in cylindrical lattices and the horizontal angle between vertically successive spots in the lattice. It is indeed fundamental to observational studies of phyllotactic counts, and especially to the evaluation of hypotheses about the origin of Fibonacci structure within lattices. Unfortunately the textbook version of the theorem is incomplete in that it is incorrect for an important special case. This paper provides a complete statement and proof of the Theorem.
Computer-Assisted Retrosynthesis Based on Molecular Similarity
Authors: Connor W. Coley, Luke Rogers, William H. Green, and Klavs F. Jensen
Date: 2017-11-16 00:00:00
Proceeding: ACS Cent. Sci. 2017 11
Tasks: Retrosynthesis, Single-step retrosynthesis

We demonstrate molecular similarity to be a surprisingly effective metric for proposing and ranking one-step retrosynthetic disconnections based on analogy to precedent reactions. The developed approach mimics the retrosynthetic strategy defined implicitly by a corpus of known reactions without the need to encode any chemical knowledge. Using 40 000 reactions from the patent literature as a knowledge base, the recorded reactants are among the top 10 proposed precursors in 74.1% of 5000 test reactions, providing strong quantitative support for our methodology. Extension of the one-step strategy to multistep pathway planning is demonstrated and discussed for two exemplary drug products.
DeepMol: An Automated Machine and Deep Learning Framework for Computational Chemistr
Authors: João Correia, João Capela, Miguel Rocha
Date: 2024-06-01 00:00:00
Proceeding: bioRxiv 2024 6
Tasks: Activity Prediction, AutoML, Computational chemistry, Deep Learning, Feature Engineering, TDC ADMET Benchmarking Group

The domain of computational chemistry has experienced a significant evolution due to the introduction of Machine Learning (ML) technologies. Despite its potential to revolutionize the field, researchers are often encumbered by obstacles, such as the complexity of selecting optimal algorithms, the automation of data pre-processing steps, the necessity for adaptive feature engineering, and the assurance of model performance consistency across different datasets. Addressing these issues head-on, DeepMol stands out as an Automated ML (AutoML) tool by automating critical steps of the ML pipeline. DeepMol rapidly and automatically identifies the most effective data representation, pre-processing methods and model configurations for a specific molecular property/activity prediction problem. On 22 benchmark datasets, DeepMol obtained competitive pipelines compared with those requiring time-consuming feature engineering, model design and selection processes. As one of the first AutoML tools specifically developed for the computational chemistry domain, DeepMol stands out with its open-source code, in-depth tutorials, detailed documentation, and examples of real-world applications, all available at https://github.com/BioSystemsUM/DeepMol and https://deepmol.readthedocs.io/en/latest/. By introducing AutoML as a ground-breaking feature in computational chemistry, DeepMol establishes itself as the pioneering state-of-the-art tool in the field.
A Complex-Coefficient Voltage Control for Virtual Synchronous Generators for Dynamic Enhancement and Power-Voltage Decoupling
Authors: Jingzhe Xu, Weihua Zhou, Behrooz Bahrani
Date: 2024-07-05 00:00:00

As electric power systems evolve towards decarbonization, the transition to inverter-based resources (IBRs) presents challenges to grid stability, necessitating innovative control solutions. Virtual synchronous generator (VSG) emerges as a prominent solution. However, conventional VSGs are prone to instability in strong grids, slow voltage regulation, and coupled power-voltage response. To address these issues, this paper introduces an advanced VSG control strategy. A novel analysis of the VSG control dynamics is presented through a second-order closed-loop complex single-input single-output system, employing a vectorized geometrical pole analysis technique for enhanced voltage stability and dynamics. The proposed comprehensive controller design mitigates issues related to control interacted subsynchronous resonance and $dq \leftrightarrow 3\phi$ transformation-induced voltage-coupled power transients, achieving improved system robustness and simplified control tuning. Key contributions include a two-fold design: optimized voltage transition characteristics through direct pole placement and transient power overshoot correction via a compensator. Validated by simulation and experiments, the findings offer a pragmatic solution for integrating VSG technology into decarbonizing power systems, ensuring reliability and efficiency.
SCSA: Exploring the Synergistic Effects Between Spatial and Channel Attention
Authors: Yunzhong Si, Huiying Xu, Xinzhong Zhu, WenHao Zhang, Yao Dong, Yuxing Chen, Hongbo Li
Date: 2024-07-06 00:00:00
Tasks: Classification, object-detection, Object Detection, Segmentation

Channel and spatial attentions have respectively brought significant improvements in extracting feature dependencies and spatial structure relations for various downstream vision tasks. While their combination is more beneficial for leveraging their individual strengths, the synergy between channel and spatial attentions has not been fully explored, lacking in fully harness the synergistic potential of multi-semantic information for feature guidance and mitigation of semantic disparities. Our study attempts to reveal the synergistic relationship between spatial and channel attention at multiple semantic levels, proposing a novel Spatial and Channel Synergistic Attention module (SCSA). Our SCSA consists of two parts: the Shareable Multi-Semantic Spatial Attention (SMSA) and the Progressive Channel-wise Self-Attention (PCSA). SMSA integrates multi-semantic information and utilizes a progressive compression strategy to inject discriminative spatial priors into PCSA's channel self-attention, effectively guiding channel recalibration. Additionally, the robust feature interactions based on the self-attention mechanism in PCSA further mitigate the disparities in multi-semantic information among different sub-features within SMSA. We conduct extensive experiments on seven benchmark datasets, including classification on ImageNet-1K, object detection on MSCOCO 2017, segmentation on ADE20K, and four other complex scene detection datasets. Our results demonstrate that our proposed SCSA not only surpasses the current state-of-the-art attention but also exhibits enhanced generalization capabilities across various task scenarios. The code and models are available at: https://github.com/HZAI-ZJNU/SCSA.
OvSW: Overcoming Silent Weights for Accurate Binary Neural Networks
Authors: Jingyang Xiang, Zuohui Chen, Siqi Li, Qing Wu, Yong liu
Date: 2024-07-07 00:00:00
Tasks: Quantization

Binary Neural Networks~(BNNs) have been proven to be highly effective for deploying deep neural networks on mobile and embedded platforms. Most existing works focus on minimizing quantization errors, improving representation ability, or designing gradient approximations to alleviate gradient mismatch in BNNs, while leaving the weight sign flipping, a critical factor for achieving powerful BNNs, untouched. In this paper, we investigate the efficiency of weight sign updates in BNNs. We observe that, for vanilla BNNs, over 50\% of the weights remain their signs unchanged during training, and these weights are not only distributed at the tails of the weight distribution but also universally present in the vicinity of zero. We refer to these weights as ``silent weights'', which slow down convergence and lead to a significant accuracy degradation. Theoretically, we reveal this is due to the independence of the BNNs gradient from the latent weight distribution. To address the issue, we propose Overcome Silent Weights~(OvSW). OvSW first employs Adaptive Gradient Scaling~(AGS) to establish a relationship between the gradient and the latent weight distribution, thereby improving the overall efficiency of weight sign updates. Additionally, we design Silence Awareness Decaying~(SAD) to automatically identify ``silent weights'' by tracking weight flipping state, and apply an additional penalty to ``silent weights'' to facilitate their flipping. By efficiently updating weight signs, our method achieves faster convergence and state-of-the-art performance on CIFAR10 and ImageNet1K dataset with various architectures. For example, OvSW obtains 61.6\% and 65.5\% top-1 accuracy on the ImageNet1K using binarized ResNet18 and ResNet34 architecture respectively. Codes are available at \url{https://github.com/JingyangXiang/OvSW}.
qlty: handling large tensors in scientific imaging
Authors: Petrus Zwart
Date: 2024-07-06 00:00:00
Tasks: Deep Learning, Management

In scientific imaging, deep learning has become a pivotal tool for image analytics. However, handling large volumetric datasets, which often exceed the memory capacity of standard GPUs, require special attention when subjected to deep learning efforts. This paper introduces qlty, a toolkit designed to address these challenges through tensor management techniques. qlty offers robust methods for subsampling, cleaning, and stitching of large-scale spatial data, enabling effective training and inference even in resource-limited environments.
TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery
Authors: Kun Wu, Zixu Wang, Xiulong Yang, Yangyang Chen, Zhenqi Han, Jialu Zhang, Lizhuang Liu
Date: 2024-07-08 00:00:00
Tasks: Mamba

As the primary mRNA delivery vehicles, ionizable lipid nanoparticles (LNPs) exhibit excellent safety, high transfection efficiency, and strong immune response induction. However, the screening process for LNPs is time-consuming and costly. To expedite the identification of high-transfection-efficiency mRNA drug delivery systems, we propose an explainable LNPs transfection efficiency prediction model, called TransMA. TransMA employs a multi-modal molecular structure fusion architecture, wherein the fine-grained atomic spatial relationship extractor named molecule 3D Transformer captures three-dimensional spatial features of the molecule, and the coarse-grained atomic sequence extractor named molecule Mamba captures one-dimensional molecular features. We design the mol-attention mechanism block, enabling it to align coarse and fine-grained atomic features and captures relationships between atomic spatial and sequential structures. TransMA achieves state-of-the-art performance in predicting transfection efficiency using the scaffold and cliff data splitting methods on the current largest LNPs dataset, including Hela and RAW cell lines. Moreover, we find that TransMA captures the relationship between subtle structural changes and significant transfection efficiency variations, providing valuable insights for LNPs design. Additionally, TransMA's predictions on external transfection efficiency data maintain a consistent order with actual transfection efficiencies, demonstrating its robust generalization capability. The code, model and data are made publicly available at https://github.com/wklix/TransMA/tree/master. We hope that high-accuracy transfection prediction models in the future can aid in LNPs design and initial screening, thereby assisting in accelerating the mRNA design process.
Greener GRASS: Enhancing GNNs with Encoding, Rewiring, and Attention
Authors: Tongzhou Liao, Barnabás Póczos
Date: 2024-07-08 00:00:00
Tasks: Graph Attention, Inductive Bias

Graph Neural Networks (GNNs) have become important tools for machine learning on graph-structured data. In this paper, we explore the synergistic combination of graph encoding, graph rewiring, and graph attention, by introducing Graph Attention with Stochastic Structures (GRASS), a novel GNN architecture. GRASS utilizes relative random walk probabilities (RRWP) encoding and a novel decomposed variant (D-RRWP) to efficiently capture structural information. It rewires the input graph by superimposing a random regular graph to enhance long-range information propagation. It also employs a novel additive attention mechanism tailored for graph-structured data. Our empirical evaluations demonstrate that GRASS achieves state-of-the-art performance on multiple benchmark datasets, including a 20.3% reduction in mean absolute error on the ZINC dataset.
Fostering Trust and Quantifying Value of AI and ML
Authors: Dalmo Cirne, Veena Calambur
Date: 2024-07-08 00:00:00

Artificial Intelligence (AI) and Machine Learning (ML) providers have a responsibility to develop valid and reliable systems. Much has been discussed about trusting AI and ML inferences (the process of running live data through a trained AI model to make a prediction or solve a task), but little has been done to define what that means. Those in the space of ML- based products are familiar with topics such as transparency, explainability, safety, bias, and so forth. Yet, there are no frameworks to quantify and measure those. Producing ever more trustworthy machine learning inferences is a path to increase the value of products (i.e., increased trust in the results) and to engage in conversations with users to gather feedback to improve products. In this paper, we begin by examining the dynamic of trust between a provider (Trustor) and users (Trustees). Trustors are required to be trusting and trustworthy, whereas trustees need not be trusting nor trustworthy. The challenge for trustors is to provide results that are good enough to make a trustee increase their level of trust above a minimum threshold for: 1- doing business together; 2- continuation of service. We conclude by defining and proposing a framework, and a set of viable metrics, to be used for computing a trust score and objectively understand how trustworthy a machine learning system can claim to be, plus their behavior over time.
MSTF: Multiscale Transformer for Incomplete Trajectory Prediction
Authors: Zhanwen Liu, Chao Li, Nan Yang, Yang Wang, Jiaqi Ma, Guangliang Cheng, Xiangmo Zhao
Date: 2024-07-08 00:00:00
Tasks: Autonomous Driving, Missing Values, Motion Forecasting, Prediction, Trajectory Prediction

Motion forecasting plays a pivotal role in autonomous driving systems, enabling vehicles to execute collision warnings and rational local-path planning based on predictions of the surrounding vehicles. However, prevalent methods often assume complete observed trajectories, neglecting the potential impact of missing values induced by object occlusion, scope limitation, and sensor failures. Such oversights inevitably compromise the accuracy of trajectory predictions. To tackle this challenge, we propose an end-to-end framework, termed Multiscale Transformer (MSTF), meticulously crafted for incomplete trajectory prediction. MSTF integrates a Multiscale Attention Head (MAH) and an Information Increment-based Pattern Adaptive (IIPA) module. Specifically, the MAH component concurrently captures multiscale motion representation of trajectory sequence from various temporal granularities, utilizing a multi-head attention mechanism. This approach facilitates the modeling of global dependencies in motion across different scales, thereby mitigating the adverse effects of missing values. Additionally, the IIPA module adaptively extracts continuity representation of motion across time steps by analyzing missing patterns in the data. The continuity representation delineates motion trend at a higher level, guiding MSTF to generate predictions consistent with motion continuity. We evaluate our proposed MSTF model using two large-scale real-world datasets. Experimental results demonstrate that MSTF surpasses state-of-the-art (SOTA) models in the task of incomplete trajectory prediction, showcasing its efficacy in addressing the challenges posed by missing values in motion forecasting for autonomous driving systems.
P2P: Part-to-Part Motion Cues Guide a Strong Tracking Framework for LiDAR Point Clouds
Authors: Jiahao Nie, Fei Xie, Sifan Zhou, Xueyi Zhou, Dong-Kyu Chae, Zhiwei He
Date: 2024-07-07 00:00:00
Tasks: 3D Single Object Tracking, GPU, Object Tracking

3D single object tracking (SOT) methods based on appearance matching has long suffered from insufficient appearance information incurred by incomplete, textureless and semantically deficient LiDAR point clouds. While motion paradigm exploits motion cues instead of appearance matching for tracking, it incurs complex multi-stage processing and segmentation module. In this paper, we first provide in-depth explorations on motion paradigm, which proves that (\textbf{i}) it is feasible to directly infer target relative motion from point clouds across consecutive frames; (\textbf{ii}) fine-grained information comparison between consecutive point clouds facilitates target motion modeling. We thereby propose to perform part-to-part motion modeling for consecutive point clouds and introduce a novel tracking framework, termed \textbf{P2P}. The novel framework fuses each corresponding part information between consecutive point clouds, effectively exploring detailed information changes and thus modeling accurate target-related motion cues. Following this framework, we present P2P-point and P2P-voxel models, incorporating implicit and explicit part-to-part motion modeling by point- and voxel-based representation, respectively. Without bells and whistles, P2P-voxel sets a new state-of-the-art performance ($\sim$\textbf{89\%}, \textbf{72\%} and \textbf{63\%} precision on KITTI, NuScenes and Waymo Open Dataset, respectively). Moreover, under the same point-based representation, P2P-point outperforms the previous motion tracker M$^2$Track by \textbf{3.3\%} and \textbf{6.7\%} on the KITTI and NuScenes, while running at a considerably high speed of \textbf{107 Fps} on a single RTX3090 GPU. The source code and pre-trained models are available at \url{https://github.com/haooozi/P2P}.
Edge-guided and Cross-scale Feature Fusion Network for Efficient Multi-contrast MRI Super-Resolution
Authors: Zhiyuan Yang, Bo Zhang, Zhiqiang Zeng, Si Yong Yeo
Date: 2024-07-07 00:00:00
Tasks: Super-Resolution

In recent years, MRI super-resolution techniques have achieved great success, especially multi-contrast methods that extract texture information from reference images to guide the super-resolution reconstruction. However, current methods primarily focus on texture similarities at the same scale, neglecting cross-scale similarities that provide comprehensive information. Moreover, the misalignment between features of different scales impedes effective aggregation of information flow. To address the limitations, we propose a novel edge-guided and cross-scale feature fusion network, namely ECFNet. Specifically, we develop a pipeline consisting of the deformable convolution and the cross-attention transformer to align features of different scales. The cross-scale fusion strategy fully integrates the texture information from different scales, significantly enhancing the super-resolution. In addition, a novel structure information collaboration module is developed to guide the super-resolution reconstruction with implicit structure priors. The structure information enables the network to focus on high-frequency components of the image, resulting in sharper details. Extensive experiments on the IXI and BraTS2020 datasets demonstrate that our method achieves state-of-the-art performance compared to other multi-contrast MRI super-resolution methods, and our method is robust in terms of different super-resolution scales. We would like to release our code and pre-trained model after the paper is accepted.
Entropy-Informed Weighting Channel Normalizing Flow
Authors: Wei Chen, Shian Du, Shigui Li, Delu Zeng, John Paisley
Date: 2024-07-06 00:00:00
Tasks: Density Estimation

Normalizing Flows (NFs) have gained popularity among deep generative models due to their ability to provide exact likelihood estimation and efficient sampling. However, a crucial limitation of NFs is their substantial memory requirements, arising from maintaining the dimension of the latent space equal to that of the input space. Multi-scale architectures bypass this limitation by progressively reducing the dimension of latent variables while ensuring reversibility. Existing multi-scale architectures split the latent variables in a simple, static manner at the channel level, compromising NFs' expressive power. To address this issue, we propose a regularized and feature-dependent $\mathtt{Shuffle}$ operation and integrate it into vanilla multi-scale architecture. This operation heuristically generates channel-wise weights and adaptively shuffles latent variables before splitting them with these weights. We observe that such operation guides the variables to evolve in the direction of entropy increase, hence we refer to NFs with the $\mathtt{Shuffle}$ operation as \emph{Entropy-Informed Weighting Channel Normalizing Flow} (EIW-Flow). Experimental results indicate that the EIW-Flow achieves state-of-the-art density estimation results and comparable sample quality on CIFAR-10, CelebA and ImageNet datasets, with negligible additional computational overhead.
MMIS: Multimodal Dataset for Interior Scene Visual Generation and Recognition
Authors: Hozaifa Kassab, Ahmed Mahmoud, Mohamed Bahaa, Ammar Mohamed, Ali Hamdi
Date: 2024-07-08 00:00:00
Tasks: Image Generation, Representation Learning, Retrieval, Scene Generation

We introduce MMIS, a novel dataset designed to advance MultiModal Interior Scene generation and recognition. MMIS consists of nearly 160,000 images. Each image within the dataset is accompanied by its corresponding textual description and an audio recording of that description, providing rich and diverse sources of information for scene generation and recognition. MMIS encompasses a wide range of interior spaces, capturing various styles, layouts, and furnishings. To construct this dataset, we employed careful processes involving the collection of images, the generation of textual descriptions, and corresponding speech annotations. The presented dataset contributes to research in multi-modal representation learning tasks such as image generation, retrieval, captioning, and classification.