Efficient Prediction of Peptide Self-assembly through Sequential and Graphical Encoding

In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the efficient collection of large peptide datasets, providing reliable training data for deep learning. However, the lack of systematic analysis of the peptide encoding, which is essential for AI-assisted peptide-related tasks, makes it an urgent problem to be solved for the improvement of prediction accuracy. To address this issue, we first collect a high-quality, colossal simulation dataset of peptide self-assembly containing over 62,000 samples generated by coarse-grained molecular dynamics (CGMD). Then, we systematically investigate the effect of peptide encoding of amino acids into sequences and molecular graphs using state-of-the-art sequential (i.e., RNN, LSTM, and Transformer) and structural deep learning models (i.e., GCN, GAT, and GraphSAGE), on the accuracy of peptide self-assembly prediction, an essential physiochemical process prior to any peptide-related applications. Extensive benchmarking studies have proven Transformer to be the most powerful sequence-encoding-based deep learning model, pushing the limit of peptide self-assembly prediction to decapeptides. In summary, this work provides a comprehensive benchmark analysis of peptide encoding with advanced deep learning models, serving as a guide for a wide range of peptide-related predictions such as isoelectric points, hydration free energy, etc.

Unleashing Realistic Air Quality Forecasting: Introducing the Ready-to-Use PurpleAirSF Dataset

Air quality forecasting has garnered significant attention recently, with data-driven models taking center stage due to advancements in machine learning and deep learning models. However, researchers face challenges with complex data acquisition and the lack of open-sourced datasets, hindering efficient model validation. This paper introduces PurpleAirSF, a comprehensive and easily accessible dataset collected from the PurpleAir network. With its high temporal resolution, various air quality measures, and diverse geographical coverage, this dataset serves as a useful tool for researchers aiming to develop novel forecasting models, study air pollution patterns, and investigate their impacts on health and the environment. We present a detailed account of the data collection and processing methods employed to build PurpleAirSF. Furthermore, we conduct preliminary experiments using both classic and modern spatio-temporal forecasting models, thereby establishing a benchmark for future air quality forecasting tasks.

Causal Discovery from Temporal Data: An Overview and New Perspectives

Temporal data, representing chronological observations of complex systems, has always been a typical data structure that can be widely generated by many domains, such as industry, medicine and finance. Analyzing this type of data is extremely valuable for various applications. Thus, different temporal data analysis tasks, eg, classification, clustering and prediction, have been proposed in the past decades. Among them, causal discovery, learning the causal relations from temporal data, is considered an interesting yet critical task and has attracted much research attention. Existing casual discovery works can be divided into two highly correlated categories according to whether the temporal data is calibrated, ie, multivariate time series casual discovery, and event sequence casual discovery. However, most previous surveys are only focused on the time series casual discovery and ignore the second category. In this paper, we specify the correlation between the two categories and provide a systematical overview of existing solutions. Furthermore, we provide public datasets, evaluation metrics and new perspectives for temporal data casual discovery.

RotoGBML: Towards Out-of-Distribution Generalization for Gradient-Based Meta-Learning

Gradient-based meta-learning (GBML) algorithms are able to fast adapt to new tasks by transferring the learned meta-knowledge, while assuming that all tasks come from the same distribution (in-distribution, ID). However, in the real world, they often suffer from an out-of-distribution (OOD) generalization problem, where tasks come from different distributions. OOD exacerbates inconsistencies in magnitudes and directions of task gradients, which brings challenges for GBML to optimize the meta-knowledge by minimizing the sum of task gradients in each minibatch. To address this problem, we propose RotoGBML, a novel approach to homogenize OOD task gradients. RotoGBML uses reweighted vectors to dynamically balance diverse magnitudes to a common scale and uses rotation matrixes to rotate conflicting directions close to each other. To reduce overhead, we homogenize gradients with the features rather than the network parameters. On this basis, to avoid the intervention of non-causal features (e.g., backgrounds), we also propose an invariant self-information (ISI) module to extract invariant causal features (e.g., the outlines of objects). Finally, task gradients are homogenized based on these invariant causal features. Experiments show that RotoGBML outperforms other state-of-the-art methods on various few-shot image classification benchmarks.

A Visual SLAM with Moving Object Trajectory Prediction

Visual Simultaneous Localization and Mapping (SLAM) has received significant attention in recent years due to its ability to estimate camera trajectory and create an environment map using visual data alone, making a substantial contribution to autonomous driving applications, in particular, a real-world scenario with moving crowds and vehicles. In this work, we propose a visual SLAM system that incorporates moving object trajectory tracking and prediction. We take into account the motion clues of the pedestrians to track and predict their movement, as long as mapping the environment. Such an integrated system solves the localization of the camera and other moving objects in the scene, and further creates a sparse map to support the potential navigation of the vehicle. In the experiment, we demonstrate the effectiveness and robustness of our approach through a comprehensive evaluation on both our simulation and real-world KITTI datasets.

Resource-Constrained Station-Keeping for Helium Balloons using Reinforcement Learning

High altitude balloons have proved useful for ecological aerial surveys, atmospheric monitoring, and communication relays. However, due to weight and power constraints, there is a need to investigate alternate modes of propulsion to navigate in the stratosphere. Very recently, reinforcement learning has been proposed as a control scheme to maintain the balloon in the region of a fixed location, facilitated through diverse opposing wind-fields at different altitudes. Although air-pump based station keeping has been explored, there is no research on the control problem for venting and ballasting actuated balloons, which is commonly used as a low-cost alternative. We show how reinforcement learning can be used for this type of balloon. Specifically, we use the soft actor-critic algorithm, which on average is able to station-keep within 50\;km for 25\% of the flight, consistent with state-of-the-art. Furthermore, we show that the proposed controller effectively minimises the consumption of resources, thereby supporting long duration flights. We frame the controller as a continuous control reinforcement learning problem, which allows for a more diverse range of trajectories, as opposed to current state-of-the-art work, which uses discrete action spaces. Furthermore, through continuous control, we can make use of larger ascent rates which are not possible using air-pumps. The desired ascent-rate is decoupled into desired altitude and time-factor to provide a more transparent policy, compared to low-level control commands used in previous works. Finally, by applying the equations of motion, we establish appropriate thresholds for venting and ballasting to prevent the agent from exploiting the environment. More specifically, we ensure actions are physically feasible by enforcing constraints on venting and ballasting.

A Review and a Taxonomy of Edge Machine Learning: Requirements, Paradigms, and Techniques

The union of Edge Computing (EC) and Artificial Intelligence (AI) has brought forward the Edge AI concept to provide intelligent solutions close to end-user environment, for privacy preservation, low latency to real-time performance, as well as resource optimization. Machine Learning (ML), as the most advanced branch of AI in the past few years, has shown encouraging results and applications in the edge environment. Nevertheless, edge powered ML solutions are more complex to realize due to the joint constraints from both edge computing and AI domains, and the corresponding solutions are expected to be efficient and adapted in technologies such as data processing, model compression, distributed inference, and advanced learning paradigms for Edge ML requirements. Despite that a great attention of Edge ML is gained in both academic and industrial communities, we noticed the lack of a complete survey on existing Edge ML technologies to provide a common understanding of this concept. To tackle this, this paper aims at providing a comprehensive taxonomy and a systematic review of Edge ML techniques: we start by identifying the Edge ML requirements driven by the joint constraints. We then survey more than twenty paradigms and techniques along with their representative work, covering two main parts: edge inference, and edge learning. In particular, we analyze how each technique fits into Edge ML by meeting a subset of the identified requirements. We also summarize Edge ML open issues to shed light on future directions for Edge ML.

A Unified Framework for Contrastive Learning from a Perspective of Affinity Matrix

In recent years, a variety of contrastive learning based unsupervised visual representation learning methods have been designed and achieved great success in many visual tasks. Generally, these methods can be roughly classified into four categories: (1) standard contrastive methods with an InfoNCE like loss, such as MoCo and SimCLR; (2) non-contrastive methods with only positive pairs, such as BYOL and SimSiam; (3) whitening regularization based methods, such as W-MSE and VICReg; and (4) consistency regularization based methods, such as CO2. In this study, we present a new unified contrastive learning representation framework (named UniCLR) suitable for all the above four kinds of methods from a novel perspective of basic affinity matrix. Moreover, three variants, i.e., SimAffinity, SimWhitening and SimTrace, are presented based on UniCLR. In addition, a simple symmetric loss, as a new consistency regularization term, is proposed based on this framework. By symmetrizing the affinity matrix, we can effectively accelerate the convergence of the training process. Extensive experiments have been conducted to show that (1) the proposed UniCLR framework can achieve superior results on par with and even be better than the state of the art, (2) the proposed symmetric loss can significantly accelerate the convergence of models, and (3) SimTrace can avoid the mode collapse problem by maximizing the trace of a whitened affinity matrix without relying on asymmetry designs or stop-gradients.

Deep object detection for waterbird monitoring using aerial imagery

Monitoring of colonial waterbird nesting islands is essential to tracking waterbird population trends, which are used for evaluating ecosystem health and informing conservation management decisions. Recently, unmanned aerial vehicles, or drones, have emerged as a viable technology to precisely monitor waterbird colonies. However, manually counting waterbirds from hundreds, or potentially thousands, of aerial images is both difficult and time-consuming. In this work, we present a deep learning pipeline that can be used to precisely detect, count, and monitor waterbirds using aerial imagery collected by a commercial drone. By utilizing convolutional neural network-based object detectors, we show that we can detect 16 classes of waterbird species that are commonly found in colonial nesting islands along the Texas coast. Our experiments using Faster R-CNN and RetinaNet object detectors give mean interpolated average precision scores of 67.9% and 63.1% respectively.

Learning Credit Assignment for Cooperative Reinforcement Learning

Cooperative multi-agent policy gradient (MAPG) algorithms have recently attracted wide attention and are regarded as a general scheme for the multi-agent system. Credit assignment plays an important role in MAPG and can induce cooperation among multiple agents. However, most MAPG algorithms cannot achieve good credit assignment because of the game-theoretic pathology known as \textit{centralized-decentralized mismatch}. To address this issue, this paper presents a novel method, \textit{\underline{M}ulti-\underline{A}gent \underline{P}olarization \underline{P}olicy \underline{G}radient} (MAPPG). MAPPG takes a simple but efficient polarization function to transform the optimal consistency of joint and individual actions into easily realized constraints, thus enabling efficient credit assignment in MAPG. Theoretically, we prove that individual policies of MAPPG can converge to the global optimum. Empirically, we evaluate MAPPG on the well-known matrix game and differential game, and verify that MAPPG can converge to the global optimum for both discrete and continuous action spaces. We also evaluate MAPPG on a set of StarCraft II micromanagement tasks and demonstrate that MAPPG outperforms the state-of-the-art MAPG algorithms.