OpenRaiser/Intern-Atlas huggingface dataset:
Carbohydrate NMR chemical shift predictions using E(3) equivariant graph neural networks
Venue: arXiv cs.LG 2023
Year: 2023

Carbohydrates, vital components of biological systems, are well-known for their structural diversity. Nuclear Magnetic Resonance (NMR) spectroscopy plays a crucial role in understanding their intricate molecular arrangements and is essential in assessing and verifying the molecular structure of organic molecules. An important part of this process is to predict the NMR chemical shift from the molecular structure. This work introduces a novel approach that leverages E(3) equivariant graph neural networks to predict carbohydrate NMR spectra. Notably, our model achieves a substantial reduction in mean absolute error, up to threefold, compared to traditional models that rely solely on two-dimensional molecular structure. Even with limited data, the model excels, highlighting its robustness and generalization capabilities. The implications are far-reaching and go beyond an advanced understanding of carbohydrate structures and spectral interpretation. For example, it could accelerate research in pharmaceutical applications, biochemistry, and structural biology, offering a faster and more reliable analysis of molecular structures. Furthermore, our approach is a key step towards a new data-driven era in spectroscopy, potentially influencing spectroscopic techniques beyond NMR.
Towards a more inductive world for drug repurposing approaches
Venue: arXiv cs.LG 2023
Year: 2023

Drug-target interaction (DTI) prediction is a challenging, albeit essential task in drug repurposing. Learning on graph models have drawn special attention as they can significantly reduce drug repurposing costs and time commitment. However, many current approaches require high-demanding additional information besides DTIs that complicates their evaluation process and usability. Additionally, structural differences in the learning architecture of current models hinder their fair benchmarking. In this work, we first perform an in-depth evaluation of current DTI datasets and prediction models through a robust benchmarking process, and show that DTI prediction methods based on transductive models lack generalization and lead to inflated performance when evaluated as previously done in the literature, hence not being suited for drug repurposing approaches. We then propose a novel biologically-driven strategy for negative edge subsampling and show through in vitro validation that newly discovered interactions are indeed true. We envision this work as the underpinning for future fair benchmarking and robust model design. All generated resources and tools are publicly available as a python package.
Investigating Weight-Perturbed Deep Neural Networks With Application in Iris Presentation Attack Detection
Venue: arXiv cs.CV 2023
Year: 2023

Deep neural networks (DNNs) exhibit superior performance in various machine learning tasks, e.g., image classification, speech recognition, biometric recognition, object detection, etc. However, it is essential to analyze their sensitivity to parameter perturbations before deploying them in real-world applications. In this work, we assess the sensitivity of DNNs against perturbations to their weight and bias parameters. The sensitivity analysis involves three DNN architectures (VGG, ResNet, and DenseNet), three types of parameter perturbations (Gaussian noise, weight zeroing, and weight scaling), and two settings (entire network and layer-wise). We perform experiments in the context of iris presentation attack detection and evaluate on two publicly available datasets: LivDet-Iris-2017 and LivDet-Iris-2020. Based on the sensitivity analysis, we propose improved models simply by perturbing parameters of the network without undergoing training. We further combine these perturbed models at the score-level and at the parameter-level to improve the performance over the original model. The ensemble at the parameter-level shows an average improvement of 43.58% on the LivDet-Iris-2017 dataset and 9.25% on the LivDet-Iris-2020 dataset. The source code is available at https://github.com/redwankarimsony/WeightPerturbation-MSU.
Finding Adversarial Inputs for Heuristics using Multi-level Optimization
Venue: arXiv cs.NI 2023
Year: 2023

Production systems use heuristics because they are faster or scale better than their optimal counterparts. Yet, practitioners are often unaware of the performance gap between a heuristic and the optimum or between two heuristics in realistic scenarios. We present MetaOpt, a system that helps analyze heuristics. Users specify the heuristic and the optimal (or another heuristic) as input, and MetaOpt automatically encodes these efficiently for a solver to find performance gaps and their corresponding adversarial inputs. Its suite of built-in optimizations helps it scale its analysis to practical problem sizes. To show it is versatile, we used MetaOpt to analyze heuristics from three domains (traffic engineering, vector bin packing, and packet scheduling). We found a production traffic engineering heuristic can require 30% more capacity than the optimal to satisfy realistic demands. Based on the patterns in the adversarial inputs MetaOpt produced, we modified the heuristic to reduce its performance gap by 12.5$\times$. We examined adversarial inputs to a vector bin packing heuristic and proved a new lower bound on its performance.
Quantifying Impairment and Disease Severity Using AI Models Trained on Healthy Subjects
Venue: arXiv cs.LG 2023
Year: 2023

Automatic assessment of impairment and disease severity is a key challenge in data-driven medicine. We propose a novel framework to address this challenge, which leverages AI models trained exclusively on healthy individuals. The COnfidence-Based chaRacterization of Anomalies (COBRA) score exploits the decrease in confidence of these models when presented with impaired or diseased patients to quantify their deviation from the healthy population. We applied the COBRA score to address a key limitation of current clinical evaluation of upper-body impairment in stroke patients. The gold-standard Fugl-Meyer Assessment (FMA) requires in-person administration by a trained assessor for 30-45 minutes, which restricts monitoring frequency and precludes physicians from adapting rehabilitation protocols to the progress of each patient. The COBRA score, computed automatically in under one minute, is shown to be strongly correlated with the FMA on an independent test cohort for two different data modalities: wearable sensors ($ρ= 0.845$, 95% CI [0.743,0.908]) and video ($ρ= 0.746$, 95% C.I [0.594, 0.847]). To demonstrate the generalizability of the approach to other conditions, the COBRA score was also applied to quantify severity of knee osteoarthritis from magnetic-resonance imaging scans, again achieving significant correlation with an independent clinical assessment ($ρ= 0.644$, 95% C.I [0.585,0.696]).
Reducing the Environmental Impact of Wireless Communication via Probabilistic Machine Learning
Venue: arXiv cs.NI 2023
Year: 2023

Machine learning methods are increasingly adopted in communications problems, particularly those arising in next generation wireless settings. Though seen as a key climate mitigation and societal adaptation enabler, communications related energy consumption is high and is expected to grow in future networks in spite of anticipated efficiency gains in 6G due to exponential communications traffic growth. To make meaningful climate mitigation impact in the communications sector, a mindset shift away from maximizing throughput at all cost and towards prioritizing energy efficiency is needed. Moreover, this must be adopted in both existing (without incurring further embodied carbon costs through equipment replacement) and future network infrastructure, given the long development time of mobile generations. To that end, we present summaries of two such problems, from both current and next generation network specifications, where probabilistic inference methods were used to great effect: using Bayesian parameter tuning we are able to safely reduce the energy consumption of existing hardware on a live communications network by $11\%$ whilst maintaining operator specified performance envelopes; through spatiotemporal Gaussian process surrogate modeling we reduce the overhead in a next generation hybrid beamforming system by over $60\%$, greatly improving the networks' ability to target highly mobile users such as autonomous vehicles. The Bayesian paradigm is itself helpful in terms of energy usage, since training a Bayesian optimization model can require much less computation than, say, training a deep neural network.
Evolution of Convolutional Neural Network (CNN): Compute vs Memory bandwidth for Edge AI
Venue: arXiv cs.CV 2023
Year: 2023

Convolutional Neural Networks (CNNs) have greatly influenced the field of Embedded Vision and Edge Artificial Intelligence (AI), enabling powerful machine learning capabilities on resource-constrained devices. This article explores the relationship between CNN compute requirements and memory bandwidth in the context of Edge AI. We delve into the historical progression of CNN architectures, from the early pioneering models to the current state-of-the-art designs, highlighting the advancements in compute-intensive operations. We examine the impact of increasing model complexity on both computational requirements and memory access patterns. The paper presents a comparison analysis of the evolving trade-off between compute demands and memory bandwidth requirements in CNNs. This analysis provides insights into designing efficient architectures and potential hardware accelerators in enhancing CNN performance on edge devices.
A Review of Deep Reinforcement Learning in Serverless Computing: Function Scheduling and Resource Auto-Scaling
Venue: arXiv cs.DC 2023
Year: 2023

In the rapidly evolving field of serverless computing, efficient function scheduling and resource scaling are critical for optimizing performance and cost. This paper presents a comprehensive review of the application of Deep Reinforcement Learning (DRL) techniques in these areas. We begin by providing an overview of serverless computing, highlighting its benefits and challenges, with a particular focus on function scheduling and resource scaling. We then delve into the principles of deep reinforcement learning (DRL) and its potential for addressing these challenges. A systematic review of recent studies applying DRL to serverless computing is presented, covering various algorithms, models, and performances. Our analysis reveals that DRL, with its ability to learn and adapt from an environment, shows promising results in improving the efficiency of function scheduling and resource scaling in serverless computing. However, several challenges remain, including the need for more realistic simulation environments, handling of cold starts, and the trade-off between learning time and scheduling performance. We conclude by discussing potential future directions for this research area, emphasizing the need for more robust DRL models, better benchmarking methods, and the exploration of multi-agent reinforcement learning for more complex serverless architectures. This review serves as a valuable resource for researchers and practitioners aiming to understand and advance the application of DRL in serverless computing.
Wafer Map Defect Patterns Semi-Supervised Classification Using Latent Vector Representation
Venue: arXiv cs.CV 2023
Year: 2023

As the globalization of semiconductor design and manufacturing processes continues, the demand for defect detection during integrated circuit fabrication stages is becoming increasingly critical, playing a significant role in enhancing the yield of semiconductor products. Traditional wafer map defect pattern detection methods involve manual inspection using electron microscopes to collect sample images, which are then assessed by experts for defects. This approach is labor-intensive and inefficient. Consequently, there is a pressing need to develop a model capable of automatically detecting defects as an alternative to manual operations. In this paper, we propose a method that initially employs a pre-trained VAE model to obtain the fault distribution information of the wafer map. This information serves as guidance, combined with the original image set for semi-supervised model training. During the semi-supervised training, we utilize a teacher-student network for iterative learning. The model presented in this paper is validated on the benchmark dataset WM-811K wafer dataset. The experimental results demonstrate superior classification accuracy and detection performance compared to state-of-the-art models, fulfilling the requirements for industrial applications. Compared to the original architecture, we have achieved significant performance improvement.
On the stability, correctness and plausibility of visual explanation methods based on feature importance
Venue: arXiv cs.CV 2023
Year: 2023

In the field of Explainable AI, multiples evaluation metrics have been proposed in order to assess the quality of explanation methods w.r.t. a set of desired properties. In this work, we study the articulation between the stability, correctness and plausibility of explanations based on feature importance for image classifiers. We show that the existing metrics for evaluating these properties do not always agree, raising the issue of what constitutes a good evaluation metric for explanations. Finally, in the particular case of stability and correctness, we show the possible limitations of some evaluation metrics and propose new ones that take into account the local behaviour of the model under test.
Modular Blended Attention Network for Video Question Answering
Venue: arXiv cs.CV 2023
Year: 2023

In multimodal machine learning tasks, it is due to the complexity of the assignments that the network structure, in most cases, is assembled in a sophisticated way. The holistic architecture can be separated into several logical parts according to the respective ends that the modules are devised to achieve. As the number of modalities of information representation increases, constructing ad hoc subnetworks for processing the data from divergent modalities while mediating the fusion of different information types has become a cumbersome and expensive problem. In this paper, we present an approach to facilitate the question with a reusable and composable neural unit; by connecting the units in series or parallel, the arduous network constructing of multimodal machine learning tasks will be accomplished in a much straightforward way. Additionally, through parameter sharing (weights replication) among the units, the space complexity will be significantly reduced. We have conducted experiments on three commonly used datasets; our method achieves impressive performance compared to several video QA baselines.
Long-MIL: Scaling Long Contextual Multiple Instance Learning for Histopathology Whole Slide Image Analysis
Venue: arXiv cs.CV 2023
Year: 2023

Histopathology image analysis is the golden standard of clinical diagnosis for Cancers. In doctors daily routine and computer-aided diagnosis, the Whole Slide Image (WSI) of histopathology tissue is used for analysis. Because of the extremely large scale of resolution, previous methods generally divide the WSI into a large number of patches, then aggregate all patches within a WSI by Multi-Instance Learning (MIL) to make the slide-level prediction when developing computer-aided diagnosis tools. However, most previous WSI-MIL models using global-attention without pairwise interaction and any positional information, or self-attention with absolute position embedding can not well handle shape varying large WSIs, e.g. testing WSIs after model deployment may be larger than training WSIs, since the model development set is always limited due to the difficulty of histopathology WSIs collection. To deal with the problem, in this paper, we propose to amend position embedding for shape varying long-contextual WSI by introducing Linear Bias into Attention, and adapt it from 1-d long sequence into 2-d long-contextual WSI which helps model extrapolate position embedding to unseen or under-fitted positions. We further utilize Flash-Attention module to tackle the computational complexity of Transformer, which also keep full self-attention performance compared to previous attention approximation work. Our method, Long-contextual MIL (Long-MIL) are evaluated on extensive experiments including 4 dataset including WSI classification and survival prediction tasks to validate the superiority on shape varying WSIs. The source code will be open-accessed soon.
AnimateAnything: Fine-Grained Open Domain Image Animation with Motion Guidance
Venue: arXiv cs.CV 2023
Year: 2023

Image animation is a key task in computer vision which aims to generate dynamic visual content from static image. Recent image animation methods employ neural based rendering technique to generate realistic animations. Despite these advancements, achieving fine-grained and controllable image animation guided by text remains challenging, particularly for open-domain images captured in diverse real environments. In this paper, we introduce an open domain image animation method that leverages the motion prior of video diffusion model. Our approach introduces targeted motion area guidance and motion strength guidance, enabling precise control the movable area and its motion speed. This results in enhanced alignment between the animated visual elements and the prompting text, thereby facilitating a fine-grained and interactive animation generation process for intricate motion sequences. We validate the effectiveness of our method through rigorous experiments on an open-domain dataset, with the results showcasing its superior performance. Project page can be found at https://animationai.github.io/AnimateAnything.
A Safer Vision-based Autonomous Planning System for Quadrotor UAVs with Dynamic Obstacle Trajectory Prediction and Its Application with LLMs
Venue: arXiv cs.RO 2023
Year: 2023

For intelligent quadcopter UAVs, a robust and reliable autonomous planning system is crucial. Most current trajectory planning methods for UAVs are suitable for static environments but struggle to handle dynamic obstacles, which can pose challenges and even dangers to flight. To address this issue, this paper proposes a vision-based planning system that combines tracking and trajectory prediction of dynamic obstacles to achieve efficient and reliable autonomous flight. We use a lightweight object detection algorithm to identify dynamic obstacles and then use Kalman Filtering to track and estimate their motion states. During the planning phase, we not only consider static obstacles but also account for the potential movements of dynamic obstacles. For trajectory generation, we use a B-spline-based trajectory search algorithm, which is further optimized with various constraints to enhance safety and alignment with the UAV's motion characteristics. We conduct experiments in both simulation and real-world environments, and the results indicate that our approach can successfully detect and avoid obstacles in dynamic environments in real-time, offering greater reliability compared to existing approaches. Furthermore, with the advancements in Natural Language Processing (NLP) technology demonstrating exceptional zero-shot generalization capabilities, more user-friendly human-machine interactions have become feasible, and this study also explores the integration of autonomous planning systems with Large Language Models (LLMs).
SPOT! Revisiting Video-Language Models for Event Understanding
Venue: arXiv cs.CV 2023
Year: 2023

Understanding videos is an important research topic for multimodal learning. Leveraging large-scale datasets of web-crawled video-text pairs as weak supervision has become a pre-training paradigm for learning joint representations and showcased remarkable potential in video understanding tasks. However, videos can be multi-event and multi-grained, while these video-text pairs usually contain only broad-level video captions. This raises a question: with such weak supervision, can video representation in video-language models gain the ability to distinguish even factual discrepancies in textual description and understand fine-grained events? To address this, we introduce SPOT Prober, to benchmark existing video-language models's capacities of distinguishing event-level discrepancies as an indicator of models' event understanding ability. Our approach involves extracting events as tuples (<Subject, Predicate, Object, Attribute, Timestamps>) from videos and generating false event tuples by manipulating tuple components systematically. We reevaluate the existing video-language models with these positive and negative captions and find they fail to distinguish most of the manipulated events. Based on our findings, we propose to plug in these manipulated event captions as hard negative samples and find them effective in enhancing models for event understanding.
PINNs-Based Uncertainty Quantification for Transient Stability Analysis
Venue: arXiv cs.AI 2023
Year: 2023

This paper addresses the challenge of transient stability in power systems with missing parameters and uncertainty propagation in swing equations. We introduce a novel application of Physics-Informed Neural Networks (PINNs), specifically an Ensemble of PINNs (E-PINNs), to estimate critical parameters like rotor angle and inertia coefficient with enhanced accuracy and reduced computational load. E-PINNs capitalize on the underlying physical principles of swing equations to provide a robust solution. Our approach not only facilitates efficient parameter estimation but also quantifies uncertainties, delivering probabilistic insights into the system behavior. The efficacy of E-PINNs is demonstrated through the analysis of $1$-bus and $2$-bus systems, highlighting the model's ability to handle parameter variability and data scarcity. The study advances the application of machine learning in power system stability, paving the way for reliable and computationally efficient transient stability analysis.
NERIF: GPT-4V for Automatic Scoring of Drawn Models
Venue: arXiv cs.AI 2023
Year: 2023

Scoring student-drawn models is time-consuming. Recently released GPT-4V provides a unique opportunity to advance scientific modeling practices by leveraging the powerful image processing capability. To test this ability specifically for automatic scoring, we developed a method NERIF (Notation-Enhanced Rubric Instruction for Few-shot Learning) employing instructional note and rubrics to prompt GPT-4V to score students' drawn models for science phenomena. We randomly selected a set of balanced data (N = 900) that includes student-drawn models for six modeling assessment tasks. Each model received a score from GPT-4V ranging at three levels: 'Beginning,' 'Developing,' or 'Proficient' according to scoring rubrics. GPT-4V scores were compared with human experts' scores to calculate scoring accuracy. Results show that GPT-4V's average scoring accuracy was mean =.51, SD = .037. Specifically, average scoring accuracy was .64 for the 'Beginning' class, .62 for the 'Developing' class, and .26 for the 'Proficient' class, indicating that more proficient models are more challenging to score. Further qualitative study reveals how GPT-4V retrieves information from image input, including problem context, example evaluations provided by human coders, and students' drawing models. We also uncovered how GPT-4V catches the characteristics of student-drawn models and narrates them in natural language. At last, we demonstrated how GPT-4V assigns scores to student-drawn models according to the given scoring rubric and instructional notes. Our findings suggest that the NERIF is an effective approach for employing GPT-4V to score drawn models. Even though there is space for GPT-4V to improve scoring accuracy, some mis-assigned scores seemed interpretable to experts. The results of this study show that utilizing GPT-4V for automatic scoring of student-drawn models is promising.