OpenRaiser/Intern-Atlas huggingface dataset:
Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity
Venue: arXiv cs.LG 2022
Year: 2022

Development of new drugs is an expensive and time-consuming process. Due to the world-wide SARS-CoV-2 outbreak, it is essential that new drugs for SARS-CoV-2 are developed as soon as possible. Drug repurposing techniques can reduce the time span needed to develop new drugs by probing the list of existing FDA-approved drugs and their properties to reuse them for combating the new disease. We propose a novel architecture DeepGLSTM, which is a Graph Convolutional network and LSTM based method that predicts binding affinity values between the FDA-approved drugs and the viral proteins of SARS-CoV-2. Our proposed model has been trained on Davis, KIBA (Kinase Inhibitor Bioactivity), DTC (Drug Target Commons), Metz, ToxCast and STITCH datasets. We use our novel architecture to predict a Combined Score (calculated using Davis and KIBA score) of 2,304 FDA-approved drugs against 5 viral proteins. On the basis of the Combined Score, we prepare a list of the top-18 drugs with the highest binding affinity for 5 viral proteins present in SARS-CoV-2. Subsequently, this list may be used for the creation of new useful drugs.
Temperature Field Inversion of Heat-Source Systems via Physics-Informed Neural Networks
Venue: arXiv cs.LG 2022
Year: 2022

Temperature field inversion of heat-source systems (TFI-HSS) with limited observations is essential to monitor the system health. Although some methods such as interpolation have been proposed to solve TFI-HSS, those existing methods ignore correlations between data constraints and physics constraints, causing the low precision. In this work, we develop a physics-informed neural network-based temperature field inversion (PINN-TFI) method to solve the TFI-HSS task and a coefficient matrix condition number based position selection of observations (CMCN-PSO) method to select optima positions of noise observations. For the TFI-HSS task, the PINN-TFI method encodes constrain terms into the loss function, thus the task is transformed into an optimization problem of minimizing the loss function. In addition, we have found that noise observations significantly affect reconstruction performances of the PINN-TFI method. To alleviate the effect of noise observations, the CMCN-PSO method is proposed to find optimal positions, where the condition number of observations is used to evaluate positions. The results demonstrate that the PINN-TFI method can significantly improve prediction precisions and the CMCN-PSO method can find good positions to acquire a more robust temperature field.
Autoencoding Video Latents for Adversarial Video Generation
Venue: arXiv cs.CV 2022
Year: 2022

Given the three dimensional complexity of a video signal, training a robust and diverse GAN based video generative model is onerous due to large stochasticity involved in data space. Learning disentangled representations of the data help to improve robustness and provide control in the sampling process. For video generation, there is a recent progress in this area by considering motion and appearance as orthogonal information and designing architectures that efficiently disentangle them. These approaches rely on handcrafting architectures that impose structural priors on the generator to decompose appearance and motion codes in the latent space. Inspired from the recent advancements in the autoencoder based image generation, we present AVLAE (Adversarial Video Latent AutoEncoder) which is a two stream latent autoencoder where the video distribution is learned by adversarial training. In particular, we propose to autoencode the motion and appearance latent vectors of the video generator in the adversarial setting. We demonstrate that our approach learns to disentangle motion and appearance codes even without the explicit structural composition in the generator. Several experiments with qualitative and quantitative results demonstrate the effectiveness of our method.
Improve Sentence Alignment by Divide-and-conquer
Venue: arXiv cs.CL 2022
Year: 2022

In this paper, we introduce a divide-and-conquer algorithm to improve sentence alignment speed. We utilize external bilingual sentence embeddings to find accurate hard delimiters for the parallel texts to be aligned. We use Monte Carlo simulation to show experimentally that using this divide-and-conquer algorithm, we can turn any quadratic time complexity sentence alignment algorithm into an algorithm with average time complexity of O(NlogN). On a standard OCR-generated dataset, our method improves the Bleualign baseline by 3 F1 points. Besides, when computational resources are restricted, our algorithm is faster than Vecalign in practice.
ZeroPrompt: Scaling Prompt-Based Pretraining to 1,000 Tasks Improves Zero-Shot Generalization
Venue: arXiv cs.LG 2022
Year: 2022

We propose a multitask pretraining approach ZeroPrompt for zero-shot generalization, focusing on task scaling and zero-shot prompting. While previous models are trained on only a few dozen tasks, we scale to 1,000 tasks for the first time using real-world data. This leads to a crucial discovery that task scaling can be an efficient alternative to model scaling; i.e., the model size has little impact on performance with an extremely large number of tasks. Our results show that task scaling can substantially improve training efficiency by 30 times in FLOPs. Moreover, we present a prompting method that incorporates a genetic algorithm to automatically search for the best prompt for unseen tasks, along with a few other improvements. Empirically, ZeroPrompt substantially improves both the efficiency and the performance of zero-shot learning across a variety of academic and production datasets.
Secure IoT Routing: Selective Forwarding Attacks and Trust-based Defenses in RPL Network
Venue: arXiv cs.NI 2022
Year: 2022

IPv6 Routing Protocol for Low Power and Lossy Networks (RPL) is an essential routing protocol to enable communications for IoT networks with low power devices. RPL uses an objective function and routing constraints to find an optimized routing path for each node in the network. However, recent research has shown that topological attacks, such as selective forwarding attacks, pose great challenges to the secure routing of IoT networks. Many conventional secure routing solutions, on the other hand, are computationally heavy to be directly applied in resource-constrained IoT networks. There is an urgent need to develop lightweight secure routing solutions for IoT networks. In this paper, we first design and implement a series of advanced selective forwarding attacks from the attack perspective, which can flexibly select the type and percentage of forwarding packets in an energy efficient way, and even bad-mouth other innocent nodes in the network. Experiment results show that the proposed attacks can maximize the attack consequences (i.e. number of dropped packets) while maintaining undetected. Moreover, we propose a lightweight trust-based defense solution to detect and eliminate malicious selective forwarding nodes from the network. The results show that the proposed defense solution can achieve high detection accuracy with very limited extra energy usage (i.e. 3.4%).
It's All in the Head: Representation Knowledge Distillation through Classifier Sharing
Venue: arXiv cs.CV 2022
Year: 2022

Representation knowledge distillation aims at transferring rich information from one model to another. Common approaches for representation distillation mainly focus on the direct minimization of distance metrics between the models' embedding vectors. Such direct methods may be limited in transferring high-order dependencies embedded in the representation vectors, or in handling the capacity gap between the teacher and student models. Moreover, in standard knowledge distillation, the teacher is trained without awareness of the student's characteristics and capacity. In this paper, we explore two mechanisms for enhancing representation distillation using classifier sharing between the teacher and student. We first investigate a simple scheme where the teacher's classifier is connected to the student backbone, acting as an additional classification head. Then, we propose a student-aware mechanism that asks to tailor the teacher model to a student with limited capacity by training the teacher with a temporary student's head. We analyze and compare these two mechanisms and show their effectiveness on various datasets and tasks, including image classification, fine-grained classification, and face verification. In particular, we achieve state-of-the-art results for face verification on the IJB-C dataset for a MobileFaceNet model: TAR@(FAR=1e-5)=93.7\%. Code is available at https://github.com/Alibaba-MIIL/HeadSharingKD.
Understanding COVID-19 Effects on Mobility: A Community-Engaged Approach
Venue: arXiv cs.CY 2022
Year: 2022

Given aggregated mobile device data, the goal is to understand the impact of COVID-19 policy interventions on mobility. This problem is vital due to important societal use cases, such as safely reopening the economy. Challenges include understanding and interpreting questions of interest to policymakers, cross-jurisdictional variability in choice and time of interventions, the large data volume, and unknown sampling bias. The related work has explored the COVID-19 impact on travel distance, time spent at home, and the number of visitors at different points of interest. However, many policymakers are interested in long-duration visits to high-risk business categories and understanding the spatial selection bias to interpret summary reports. We provide an Entity Relationship diagram, system architecture, and implementation to support queries on long-duration visits in addition to fine resolution device count maps to understand spatial bias. We closely collaborated with policymakers to derive the system requirements and evaluate the system components, the summary reports, and visualizations.
Finding Shortest Path on a Terrain Surface by Using Finite Element Method
Venue: arXiv cs.CE 2022
Year: 2022

The solution of the shortest path problem on a surface is not only a theoretical problem to be solved in the field of mathematics, but also problems that need to be solved in very different fields such as medicine, defense and construction technologies. When it comes to the land specific, solution algorithms for these problems are also of great importance in terms of determination of the shortest path in an open area where the road will pass in the field of civil engineering, or route determination of manned or unmanned vehicles for various logistic needs, especially in raw terrains. In addition, path finding problems in the raw terrains are also important for manned and unmanned ground vehicles (UGV) used in the defense industry. Within the scope of this study, a method that can be used for instant route determinations within sight range or for route determinations covering wider areas is proposed. Although the examples presented within the scope of the study are land-based, the method can be applied to almost all problem types of similar nature. The approach used in the study can be briefly described as the mechanical analysis of a surface transformed into a structural load bearing system based on mechanical analogies. In this approach, the determination of the shortest path connecting two points can be realized by following the stress-strain values that will occur by moving the points away from each other or by following a linear line that will be formed between two points during the mechanical analysis. If the proposed approach is to be carried out with multiple rigid body dynamics approaches instead of flexible bodies mechanics, it can be carried out easily and very quickly by determining the shortest path between two points or by tracking the forces. However, the proposed approach in this study is presented by simulating examples of flexible bodies using FEM.
PyHHMM: A Python Library for Heterogeneous Hidden Markov Models
Venue: arXiv cs.MS 2022
Year: 2022

We introduce PyHHMM, an object-oriented open-source Python implementation of Heterogeneous-Hidden Markov Models (HHMMs). In addition to HMM's basic core functionalities, such as different initialization algorithms and classical observations models, i.e., continuous and multinoulli, PyHHMM distinctively emphasizes features not supported in similar available frameworks: a heterogeneous observation model, missing data inference, different model order selection criterias, and semi-supervised training. These characteristics result in a feature-rich implementation for researchers working with sequential data. PyHHMM relies on the numpy, scipy, scikit-learn, and seaborn Python packages, and is distributed under the Apache-2.0 License. PyHHMM's source code is publicly available on Github (https://github.com/fmorenopino/HeterogeneousHMM) to facilitate adoptions and future contributions. A detailed documentation (https://pyhhmm.readthedocs.io/en/latest), which covers examples of use and models' theoretical explanation, is available. The package can be installed through the Python Package Index (PyPI), via 'pip install pyhhmm'.
Adversarial vulnerability of powerful near out-of-distribution detection
Venue: arXiv cs.LG 2022
Year: 2022

There has been a significant progress in detecting out-of-distribution (OOD) inputs in neural networks recently, primarily due to the use of large models pretrained on large datasets, and an emerging use of multi-modality. We show a severe adversarial vulnerability of even the strongest current OOD detection techniques. With a small, targeted perturbation to the input pixels, we can change the image assignment from an in-distribution to an out-distribution, and vice versa, easily. In particular, we demonstrate severe adversarial vulnerability on the challenging near OOD CIFAR-100 vs CIFAR-10 task, as well as on the far OOD CIFAR-100 vs SVHN. We study the adversarial robustness of several post-processing techniques, including the simple baseline of Maximum of Softmax Probabilities (MSP), the Mahalanobis distance, and the newly proposed \textit{Relative} Mahalanobis distance. By comparing the loss of OOD detection performance at various perturbation strengths, we demonstrate the beneficial effect of using ensembles of OOD detectors, and the use of the \textit{Relative} Mahalanobis distance over other post-processing methods. In addition, we show that even strong zero-shot OOD detection using CLIP and multi-modality suffers from a severe lack of adversarial robustness as well. Our code is available at https://github.com/stanislavfort/adversaries_to_OOD_detection
Cooperative Multi-UAV Coverage Mission Planning Platform for Remote Sensing Applications
Venue: arXiv cs.RO 2022
Year: 2022

This paper proposes a novel mission planning platform, capable of efficiently deploying a team of UAVs to cover complex-shaped areas, in various remote sensing applications. Under the hood lies a novel optimization scheme for grid-based methods, utilizing Simulated Annealing algorithm, that significantly increases the achieved percentage of coverage and improves the qualitative features of the generated paths. Extensive simulated evaluation in comparison with a state-of-the-art alternative methodology, for coverage path planning (CPP) operations, establishes the performance gains in terms of achieved coverage and overall duration of the generated missions. On top of that, DARP algorithm is employed to allocate sub-tasks to each member of the swarm, taking into account each UAV's sensing and operational capabilities, their initial positions and any no-fly-zones possibly defined inside the operational area. This feature is of paramount importance in real-life applications, as it has the potential to achieve tremendous performance improvements in terms of time demanded to complete a mission, while at the same time it unlocks a wide new range of applications, that was previously not feasible due to the limited battery life of UAVs. In order to investigate the actual efficiency gains that are introduced by the multi-UAV utilization, a simulated study is performed as well. All of these capabilities are packed inside an end-to-end platform that eases the utilization of UAVs' swarms in remote sensing applications. Its versatility is demonstrated via two different real-life applications: (i) a photogrametry for precision agriculture and (ii) an indicative search and rescue for first responders missions, that were performed utilizing a swarm of commercial UAVs. The source code can be found at: https://github.com/savvas-ap/mCPP-optimized-DARP
Temporal Characterization of XR Traffic with Application to Predictive Network Slicing
Venue: arXiv cs.NI 2022
Year: 2022

Over the past few years, eXtended Reality (XR) has attracted increasing interest thanks to its extensive industrial and commercial applications, and its popularity is expected to rise exponentially over the next decade. However, the stringent Quality of Service (QoS) constraints imposed by XR's interactive nature require Network Slicing (NS) solutions to support its use over wireless connections: in this context, quasi-Constant Bit Rate (CBR) encoding is a promising solution, as it can increase the predictability of the stream, making the network resource allocation easier. However, traffic characterization of XR streams is still a largely unexplored subject, particularly with this encoding. In this work, we characterize XR streams from more than 4 hours of traces captured in a real setup, analyzing their temporal correlation and proposing two prediction models for future frame size. Our results show that even the state-of-the-art H.264 CBR mode can have significant frame size fluctuations, which can impact the NS optimization. Our proposed prediction models can be applied to different traces, and even to different contents, achieving very similar performance. We also show the trade-off between network resource efficiency and XR QoS in a simple NS use case.
Combining Fast and Slow Thinking for Human-like and Efficient Navigation in Constrained Environments
Venue: arXiv cs.AI 2022
Year: 2022

Current AI systems lack several important human capabilities, such as adaptability, generalizability, self-control, consistency, common sense, and causal reasoning. We believe that existing cognitive theories of human decision making, such as the thinking fast and slow theory, can provide insights on how to advance AI systems towards some of these capabilities. In this paper, we propose a general architecture that is based on fast/slow solvers and a metacognitive component. We then present experimental results on the behavior of an instance of this architecture, for AI systems that make decisions about navigating in a constrained environment. We show how combining the fast and slow decision modalities allows the system to evolve over time and gradually pass from slow to fast thinking with enough experience, and that this greatly helps in decision quality, resource consumption, and efficiency.
Differentially Private Reinforcement Learning with Linear Function Approximation
Venue: arXiv cs.LG 2022
Year: 2022

Motivated by the wide adoption of reinforcement learning (RL) in real-world personalized services, where users' sensitive and private information needs to be protected, we study regret minimization in finite-horizon Markov decision processes (MDPs) under the constraints of differential privacy (DP). Compared to existing private RL algorithms that work only on tabular finite-state, finite-actions MDPs, we take the first step towards privacy-preserving learning in MDPs with large state and action spaces. Specifically, we consider MDPs with linear function approximation (in particular linear mixture MDPs) under the notion of joint differential privacy (JDP), where the RL agent is responsible for protecting users' sensitive data. We design two private RL algorithms that are based on value iteration and policy optimization, respectively, and show that they enjoy sub-linear regret performance while guaranteeing privacy protection. Moreover, the regret bounds are independent of the number of states, and scale at most logarithmically with the number of actions, making the algorithms suitable for privacy protection in nowadays large-scale personalized services. Our results are achieved via a general procedure for learning in linear mixture MDPs under changing regularizers, which not only generalizes previous results for non-private learning, but also serves as a building block for general private reinforcement learning.
A Min-Max Fair Resource Allocation Framework for Optical x-haul and DU/CU in Multi-tenant O-RANs
Venue: arXiv cs.NI 2022
Year: 2022

The recently proposed open-radio access network (O-RAN) architecture embraces cloudification and network function virtualization techniques to perform the base-band function processing by dis-aggregated radio units (RUs), distributed units (DUs), and centralized units (CUs). This enables the cloud-RAN vision in full, where mobile network operators (MNOs) could install their own RUs, but then lease on-demand computational resources for the processing of DU and CU functions from commonly available open-cloud (O-Cloud) servers via open x-haul interfaces due to variation of load over the day. This creates a multi-tenant scenario where multiple MNOs share networking as well as computational resources. In this paper, we propose a framework that dynamically allocates x-haul and DU/CU resources in a multi-tenant O-RAN ecosystem with min-max fairness guarantees. This framework ensures that a maximum number of RUs get sufficient resources while minimizing the OPEX for their MNOs. Moreover, in order to provide an access network architecture capable of sustaining low-latency and high capacity between RUs and edge-computing devices, we consider time-wavelength division multiplexed (TWDM) passive optical network (PON)-based x-haul interfaces where the PON virtualization technique is used to provide a direct optical connection between end-points. This creates a virtual mesh interconnection among all the nodes such that the RUs can be connected to the Edge-Clouds at macro-cell RU locations as well as to the O-Cloud servers at the central office locations. Furthermore, we analyze the system performance with our proposed framework and show that MNOs can operate with a better cost-efficiency than baseline greedy resource allocation with uniform cost-sharing.
Sectioning of Biomedical Abstracts: A Sequence of Sequence Classification Task
Venue: arXiv cs.CL 2022
Year: 2022

Rapid growth of the biomedical literature has led to many advances in the biomedical text mining field. Among the vast amount of information, biomedical article abstracts are the easily accessible sources. However, the number of the structured abstracts, describing the rhetorical sections with one of Background, Objective, Method, Result and Conclusion categories is still not considerable. Exploration of valuable information in the biomedical abstracts can be expedited with the improvements in the sequential sentence classification task. Deep learning based models has great performance/potential in achieving significant results in this task. However, they can often be overly complex and overfit to specific data. In this project, we study a state-of-the-art deep learning model, which we called SSN-4 model here. We investigate different components of the SSN-4 model to study the trade-off between the performance and complexity. We explore how well this model generalizes to a new data set beyond Randomized Controlled Trials (RCT) dataset. We address the question that whether word embeddings can be adjusted to the task to improve the performance. Furthermore, we develop a second model that addresses the confusion pairs in the first model. Results show that SSN-4 model does not appear to generalize well beyond RCT dataset.