arXiv Computer Science @arxiv_cs@qoto.org

Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome, some of which are going to be presented to T cells by the MHC complex. While predicting MHC-peptide presentation has received a lot of attention recently, proteasomal cleavage prediction remains a relatively unexplored area in light of recent advances in high-throughput mass spectrometry-based MHC ligandomics. Moreover, as such experimental techniques do not allow to identify regions that cannot be cleaved, the latest predictors generate synthetic negative samples and treat them as true negatives when training, even though some of them could actually be positives. In this work, we thus present a new predictor trained with an expanded dataset and the solid theoretical underpinning of positive-unlabeled learning, achieving a new state-of-the-art in proteasomal cleavage prediction. The improved predictive capabilities will in turn enable more precise vaccine development improving the efficacy of epitope-based vaccines. Code and pretrained models are available at https://github.com/SchubertLab/proteasomal-cleavage-puupl.

The application of Data Science and Analytics to optimize or predict outcomes is Ubiquitous in the Modern World. Data Science and Analytics have optimized almost every domain that exists in the market. In our survey, we focus on how the field of Analytics has been adopted in the field of sports, and how it has contributed to the transformation of the game right from the assessment of on-field players and their selection to the prediction of winning team and to the marketing of tickets and business aspects of big sports tournaments. We will present the analytical tools, algorithms, and methodologies adopted in the field of Sports Analytics for different sports and also present our views on the same and we will also compare and contrast these existing approaches. By doing so, we will also present the best tools, algorithms, and analytical methodologies to be considered by anyone who is looking to experiment with sports data and analyze various aspects of the game.

Inspired by Regularized Lottery Ticket Hypothesis (RLTH), which hypothesizes that there exist smooth (non-binary) subnetworks within a dense network that achieve the competitive performance of the dense network, we propose a few-shot class incremental learning (FSCIL) method referred to as \emph{Soft-SubNetworks (SoftNet)}. Our objective is to learn a sequence of sessions incrementally, where each session only includes a few training instances per class while preserving the knowledge of the previously learned ones. SoftNet jointly learns the model weights and adaptive non-binary soft masks at a base training session in which each mask consists of the major and minor subnetwork; the former aims to minimize catastrophic forgetting during training, and the latter aims to avoid overfitting to a few samples in each new training session. We provide comprehensive empirical validations demonstrating that our SoftNet effectively tackles the few-shot incremental learning problem by surpassing the performance of state-of-the-art baselines over benchmark datasets.

Developing and integrating advanced image sensors with novel algorithms in camera systems are prevalent with the increasing demand for computational photography and imaging on mobile platforms. However, the lack of high-quality data for research and the rare opportunity for in-depth exchange of views from industry and academia constrain the development of mobile intelligent photography and imaging (MIPI). To bridge the gap, we introduce the first MIPI challenge, including five tracks focusing on novel image sensors and imaging algorithms. In this paper, RGBW Joint Fusion and Denoise, one of the five tracks, working on the fusion of binning-mode RGBW to Bayer, is introduced. The participants were provided with a new dataset including 70 (training) and 15 (validation) scenes of high-quality RGBW and Bayer pairs. In addition, for each scene, RGBW of different noise levels was provided at 24dB and 42dB. All the data were captured using an RGBW sensor in both outdoor and indoor conditions. The final results are evaluated using objective metrics, including PSNR, SSIM}, LPIPS, and KLD. A detailed description of all models developed in this challenge is provided in this paper. More details of this challenge and the link to the dataset can be found at https://github.com/mipi-challenge/MIPI2022.

We present and discuss the results of a two-year qualitative analysis of images published in IEEE Visualization (VIS) papers. Specifically, we derive a typology of 13 visualization image types, coded to distinguish visualizations and several image characteristics. The categorization process required much more time and was more difficult than we initially thought. The resulting typology and image analysis may serve a number of purposes: to study the evolution of the community and its research output over time, to facilitate the categorization of visualization images for the purpose of teaching, to identify visual designs for evaluation purposes, or to enable progress towards standardization in visualization. In addition to the typology and image characterization, we provide a dataset of 6,833 tagged images and an online tool that can be used to explore and analyze the large set of tagged images. We thus facilitate a discussion of the diverse visualizations used and how they are published and communicated in our community.

Adversarial training (AT) methods are effective against adversarial attacks, yet they introduce severe disparity of accuracy and robustness between different classes, known as the robust fairness problem. Previously proposed Fair Robust Learning (FRL) adaptively reweights different classes to improve fairness. However, the performance of the better-performed classes decreases, leading to a strong performance drop. In this paper, we observed two unfair phenomena during adversarial training: different difficulties in generating adversarial examples from each class (source-class fairness) and disparate target class tendencies when generating adversarial examples (target-class fairness). From the observations, we propose Balance Adversarial Training (BAT) to address the robust fairness problem. Regarding source-class fairness, we adjust the attack strength and difficulties of each class to generate samples near the decision boundary for easier and fairer model learning; considering target-class fairness, by introducing a uniform distribution constraint, we encourage the adversarial example generation process for each class with a fair tendency. Extensive experiments conducted on multiple datasets (CIFAR-10, CIFAR-100, and ImageNette) demonstrate that our method can significantly outperform other baselines in mitigating the robust fairness problem (+5-10\% on the worst class accuracy)

The modern time-domain photometric surveys collect a lot of observations of various astronomical objects, and the coming era of large-scale surveys will provide even more information. Most of the objects have never received a spectroscopic follow-up, which is especially crucial for transients e.g. supernovae. In such cases, observed light curves could present an affordable alternative. Time series are actively used for photometric classification and characterization, such as peak and luminosity decline estimation. However, the collected time series are multidimensional, irregularly sampled, contain outliers, and do not have well-defined systematic uncertainties. Machine learning methods help extract useful information from available data in the most efficient way. We consider several light curve approximation methods based on neural networks: Multilayer Perceptrons, Bayesian Neural Networks, and Normalizing Flows, to approximate observations of a single light curve. Tests using both the simulated PLAsTiCC and real Zwicky Transient Facility data samples demonstrate that even few observations are enough to fit networks and achieve better approximation quality than other state-of-the-art methods. We show that the methods described in this work have better computational complexity and work faster than Gaussian Processes. We analyze the performance of the approximation techniques aiming to fill the gaps in the observations of the light curves, and show that the use of appropriate technique increases the accuracy of peak finding and supernova classification. In addition, the study results are organized in a Fulu Python library available on GitHub, which can be easily used by the community.

Joint synthesis of images and segmentation masks with generative adversarial networks (GANs) is promising to reduce the effort needed for collecting image data with pixel-wise annotations. However, to learn high-fidelity image-mask synthesis, existing GAN approaches first need a pre-training phase requiring large amounts of image data, which limits their utilization in restricted image domains. In this work, we take a step to reduce this limitation, introducing the task of one-shot image-mask synthesis. We aim to generate diverse images and their segmentation masks given only a single labelled example, and assuming, contrary to previous models, no access to any pre-training data. To this end, inspired by the recent architectural developments of single-image GANs, we introduce our OSMIS model which enables the synthesis of segmentation masks that are precisely aligned to the generated images in the one-shot regime. Besides achieving the high fidelity of generated masks, OSMIS outperforms state-of-the-art single-image GAN models in image synthesis quality and diversity. In addition, despite not using any additional data, OSMIS demonstrates an impressive ability to serve as a source of useful data augmentation for one-shot segmentation applications, providing performance gains that are complementary to standard data augmentation techniques. Code is available at https://github.com/ boschresearch/one-shot-synthesis

The task of building general agents that perform well over a wide range of tasks has been an importantgoal in reinforcement learning since its inception. The problem has been subject of research of alarge body of work, with performance frequently measured by observing scores over the wide rangeof environments contained in the Atari 57 benchmark. Agent57 was the first agent to surpass thehuman benchmark on all 57 games, but this came at the cost of poor data-efficiency, requiring nearly 80billion frames of experience to achieve. Taking Agent57 as a starting point, we employ a diverse set ofstrategies to achieve a 200-fold reduction of experience needed to outperform the human baseline. Weinvestigate a range of instabilities and bottlenecks we encountered while reducing the data regime, andpropose effective solutions to build a more robust and efficient agent. We also demonstrate competitiveperformance with high-performing methods such as Muesli and MuZero. The four key components toour approach are (1) an approximate trust region method which enables stable bootstrapping from theonline network, (2) a normalisation scheme for the loss and priorities which improves robustness whenlearning a set of value functions with a wide range of scales, (3) an improved architecture employingtechniques from NFNets in order to leverage deeper networks without the need for normalization layers,and (4) a policy distillation method which serves to smooth out the instantaneous greedy policy overtime.

Sparse linear algebra kernels play a critical role in numerous applications, covering from exascale scientific simulation to large-scale data analytics. Offloading linear algebra kernels on one GPU will no longer be viable in these applications, simply because the rapidly growing data volume may exceed the memory capacity and computing power of a single GPU. Multi-GPU systems nowadays being ubiquitous in supercomputers and data-centers present great potentials in scaling up large sparse linear algebra kernels. In this work, we design a novel sparse matrix representation framework for multi-GPU systems called MSREP, to scale sparse linear algebra operations based on our augmented sparse matrix formats in a balanced pattern. Different from dense operations, sparsity significantly intensifies the difficulty of distributing the computation workload among multiple GPUs in a balanced manner. We enhance three mainstream sparse data formats -- CSR, CSC, and COO, to enable fine-grained data distribution. We take sparse matrix-vector multiplication (SpMV) as an example to demonstrate the efficiency of our MSREP framework. In addition, MSREP can be easily extended to support other sparse linear algebra kernels based on the three fundamental formats (i.e., CSR, CSC and COO).

Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow, and change. We are able to predict future changes as well as simulate the process using genetic algorithms. Genetic Algorithms give us the opportunity to present multiple variables and parameters to an environment and change values to simulate different situations. By optimizing genetic algorithms to hold entities in an environment, we are able to assign varying characteristics such as speed, size, and cloning probability, to the entities to simulate real natural selection and evolution in a shorter period of time. Learning about how species grow and evolve allows us to find ways to improve technology, help animals going extinct to survive, and figure* out how diseases spread and possible ways of making an environment uninhabitable for them. Using data from an environment including genetic algorithms and parameters of speed, size, and cloning percentage, the ability to test several changes in the environment and observe how the species interacts within it appears. After testing different environments with a varied amount of food while keeping the number of starting population at 10 entities, it was found that an environment with a scarce amount of food was not sustainable for small and slow entities. All environments displayed an increase in speed, but the environments that were richer in food allowed for the entities to live for the entire duration of 50 generations, as well as allowed the population to grow significantly.

Images obtained under low-light conditions will seriously affect the quality of the images. Solving the problem of poor low-light image quality can effectively improve the visual quality of images and better improve the usability of computer vision. In addition, it has very important applications in many fields. This paper proposes a DEANet based on Retinex for low-light image enhancement. It combines the frequency information and content information of the image into three sub-networks: decomposition network, enhancement network and adjustment network. These three sub-networks are respectively used for decomposition, denoising, contrast enhancement and detail preservation, adjustment, and image generation. Our model has good robust results for all low-light images. The model is trained on the public data set LOL, and the experimental results show that our method is better than the existing state-of-the-art methods in terms of vision and quality.

Self-Adaptive Multi-Agent Systems (AMAS) transform machine learning problems into problems of local cooperation between agents. We present smapy, an ensemble based AMAS implementation for mobility prediction, whose agents are provided with machine learning models in addition to their cooperation rules. With a detailed methodology, we show that it is possible to use linear models for nonlinear classification on a benchmark transport mode detection dataset, if they are integrated in a cooperative multi-agent structure. The results obtained show a significant improvement of the performance of linear models in non-linear contexts thanks to the multi-agent approach.

Hand-based interaction, such as using a handheld controller or making hand gestures, has been widely adopted as the primary method for interacting with both virtual reality (VR) and augmented reality (AR) head-mounted displays (HMDs). In contrast, hands-free interaction avoids the need for users' hands and although it can afford additional benefits, there has been limited research in exploring and evaluating hands-free techniques for these HMDs. As VR HMDs become ubiquitous, people will need to do text editing, which requires selecting text segments. Similar to hands-free interaction, text selection is underexplored. This research focuses on both, text selection via hands-free interaction. Our exploration involves a user study with 24 participants to investigate the performance, user experience, and workload of three hands-free selection mechanisms (Dwell, Blink, Voice) to complement head-based pointing. Results indicate that Blink outperforms Dwell and Voice in completion time. Users' subjective feedback also shows that Blink is the preferred technique for text selection. This work is the first to explore hands-free interaction for text selection in VR HMDs. Our results provide a solid platform for further research in this important area.

We provide a new method for online learning, specifically prediction with expert advice, in a changing environment. In a non-changing environment the Squint algorithm has been designed to always function at least as well as other known algorithms and in specific cases it functions much better. However, when using a conventional black-box algorithm to make Squint suitable for a changing environment, it loses its beneficial properties. Hence, we provide a new algorithm, Squint-CE, which is suitable for a changing environment and preserves the properties of Squint.

Disentangled and invariant representations are two critical goals of representation learning and many approaches have been proposed to achieve either one of them. However, those two goals are actually complementary to each other so that we propose a framework to accomplish both of them simultaneously. We introduce a weakly supervised signal to learn disentangled representation which consists of three splits containing predictive, known nuisance and unknown nuisance information respectively. Furthermore, we incorporate contrastive method to enforce representation invariance. Experiments shows that the proposed method outperforms state-of-the-art (SOTA) methods on four standard benchmarks and shows that the proposed method can have better adversarial defense ability comparing to other methods without adversarial training.

A modern vehicle fitted with sensors, actuators, and Electronic Control Units (ECUs) can be divided into several operational subsystems called Functional Working Groups (FWGs). Examples of these FWGs include the engine system, transmission, fuel system, brakes, etc. Each FWG has associated sensor-channels that gauge vehicular operating conditions. This data rich environment is conducive to the development of Predictive Maintenance (PdM) technologies. Undercutting various PdM technologies is the need for robust anomaly detection models that can identify events or observations which deviate significantly from the majority of the data and do not conform to a well defined notion of normal vehicular operational behavior. In this paper, we introduce the Vehicle Performance, Reliability, and Operations (VePRO) dataset and use it to create a multi-phased approach to anomaly detection. Utilizing Temporal Convolution Networks (TCN), our anomaly detection system can achieve 96% detection accuracy and accurately predicts 91% of true anomalies. The performance of our anomaly detection system improves when sensor channels from multiple FWGs are utilized.

We train graph neural networks on halo catalogues from Gadget N-body simulations to perform field-level likelihood-free inference of cosmological parameters. The catalogues contain $\lesssim$5,000 halos with masses $\gtrsim 10^{10}~h^{-1}M_\odot$ in a periodic volume of $(25~h^{-1}{\rm Mpc})^3$; every halo in the catalogue is characterized by several properties such as position, mass, velocity, concentration, and maximum circular velocity. Our models, built to be permutationally, translationally, and rotationally invariant, do not impose a minimum scale on which to extract information and are able to infer the values of $Ω_{\rm m}$ and $σ_8$ with a mean relative error of $\sim6\%$, when using positions plus velocities and positions plus masses, respectively. More importantly, we find that our models are very robust: they can infer the value of $Ω_{\rm m}$ and $σ_8$ when tested using halo catalogues from thousands of N-body simulations run with five different N-body codes: Abacus, CUBEP$^3$M, Enzo, PKDGrav3, and Ramses. Surprisingly, the model trained to infer $Ω_{\rm m}$ also works when tested on thousands of state-of-the-art CAMELS hydrodynamic simulations run with four different codes and subgrid physics implementations. Using halo properties such as concentration and maximum circular velocity allow our models to extract more information, at the expense of breaking the robustness of the models. This may happen because the different N-body codes are not converged on the relevant scales corresponding to these parameters.

Urban downscaling is a link to transfer the knowledge from coarser climate information to city scale assessments. These high-resolution assessments need multiyear climatology of past data and future projections, which are complex and computationally expensive to generate using traditional numerical weather prediction models. The city of Austin, Texas, USA has seen tremendous growth in the past decade. Systematic planning for the future requires the availability of fine resolution city-scale datasets. In this study, we demonstrate a novel approach generating a general purpose operator using deep learning to perform urban downscaling. The algorithm employs an iterative super-resolution convolutional neural network (Iterative SRCNN) over the city of Austin, Texas, USA. We show the development of a high-resolution gridded precipitation product (300 m) from a coarse (10 km) satellite-based product (JAXA GsMAP). High resolution gridded datasets of precipitation offer insights into the spatial distribution of heavy to low precipitation events in the past. The algorithm shows improvement in the mean peak-signal-to-noise-ratio and mutual information to generate high resolution gridded product of size 300 m X 300 m relative to the cubic interpolation baseline. Our results have implications for developing high-resolution gridded-precipitation urban datasets and the future planning of smart cities for other cities and other climatic variables.

As the social impact of visual recognition has been under scrutiny, several protected-attribute balanced datasets emerged to address dataset bias in imbalanced datasets. However, in facial attribute classification, dataset bias stems from both protected attribute level and facial attribute level, which makes it challenging to construct a multi-attribute-level balanced real dataset. To bridge the gap, we propose an effective pipeline to generate high-quality and sufficient facial images with desired facial attributes and supplement the original dataset to be a balanced dataset at both levels, which theoretically satisfies several fairness criteria. The effectiveness of our method is verified on sex classification and facial attribute classification by yielding comparable task performance as the original dataset and further improving fairness in a comprehensive fairness evaluation with a wide range of metrics. Furthermore, our method outperforms both resampling and balanced dataset construction to address dataset bias, and debiasing models to address task bias.