OpenRaiser/Intern-Atlas huggingface dataset:
Transformer-based Time-to-Event Prediction for Chronic Kidney Disease Deterioration
Venue: arXiv cs.LG 2023
Year: 2023

Deep-learning techniques, particularly the transformer model, have shown great potential in enhancing the prediction performance of longitudinal health records. While previous methods have mainly focused on fixed-time risk prediction, time-to-event prediction (also known as survival analysis) is often more appropriate for clinical scenarios. Here, we present a novel deep-learning architecture we named STRAFE, a generalizable survival analysis transformer-based architecture for electronic health records. The performance of STRAFE was evaluated using a real-world claim dataset of over 130,000 individuals with stage 3 chronic kidney disease (CKD) and was found to outperform other time-to-event prediction algorithms in predicting the exact time of deterioration to stage 5. Additionally, STRAFE was found to outperform binary outcome algorithms in predicting fixed-time risk, possibly due to its ability to train on censored data. We show that STRAFE predictions can improve the positive predictive value of high-risk patients by 3-fold, demonstrating possible usage to improve targeting for intervention programs. Finally, we suggest a novel visualization approach to predictions on a per-patient basis. In conclusion, STRAFE is a cutting-edge time-to-event prediction algorithm that has the potential to enhance risk predictions in large claims datasets.
End-to-End Neural Network Compression via $\frac{\ell_1}{\ell_2}$ Regularized Latency Surrogates
Venue: arXiv cs.LG 2023
Year: 2023

Neural network (NN) compression via techniques such as pruning, quantization requires setting compression hyperparameters (e.g., number of channels to be pruned, bitwidths for quantization) for each layer either manually or via neural architecture search (NAS) which can be computationally expensive. We address this problem by providing an end-to-end technique that optimizes for model's Floating Point Operations (FLOPs) or for on-device latency via a novel $\frac{\ell_1}{\ell_2}$ latency surrogate. Our algorithm is versatile and can be used with many popular compression methods including pruning, low-rank factorization, and quantization. Crucially, it is fast and runs in almost the same amount of time as single model training; which is a significant training speed-up over standard NAS methods. For BERT compression on GLUE fine-tuning tasks, we achieve $50\%$ reduction in FLOPs with only $1\%$ drop in performance. For compressing MobileNetV3 on ImageNet-1K, we achieve $15\%$ reduction in FLOPs, and $11\%$ reduction in on-device latency without drop in accuracy, while still requiring $3\times$ less training compute than SOTA compression techniques. Finally, for transfer learning on smaller datasets, our technique identifies $1.2\times$-$1.4\times$ cheaper architectures than standard MobileNetV3, EfficientNet suite of architectures at almost the same training cost and accuracy.
Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders
Venue: arXiv cs.LG 2023
Year: 2023

Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower degree of interpretability. Furthermore, very few methods deal with trying to translate interpretability in biologically relevant terms, such as known pathway cascades. Biological pathways reflecting signalling events or metabolic conversions are Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. Determining which pathways are implicated in disease and incorporating such pathway data as prior knowledge may enhance predictive modelling and personalised strategies for diagnosis, treatment and prevention of disease. Results: We propose a novel prior-knowledge-based deep auto-encoding framework, PAAE, together with its accompanying generative variant, PAVAE, for RNA-seq data in cancer. Through comprehensive comparisons among various learning models, we show that, despite having access to a smaller set of features, our PAAE and PAVAE models achieve better out-of-set reconstruction results compared to common methodologies. Furthermore, we compare our model with equivalent baselines on a classification task and show that they achieve better results than models which have access to the full input gene set. Another result is that using vanilla variational frameworks might negatively impact both reconstruction outputs as well as classification performance. Finally, our work directly contributes by providing comprehensive interpretability analyses on our models on top of improving prognostication for translational medicine.
Complexity of Reachability Problems in Neural Networks
Venue: arXiv cs.CC 2023
Year: 2023

In this paper we investigate formal verification problems for Neural Network computations. Various reachability problems will be in the focus, such as: Given symbolic specifications of allowed inputs and outputs in form of Linear Programming instances, one question is whether valid inputs exist such that the given network computes a valid output? Does this property hold for all valid inputs? The former question's complexity has been investigated recently by Sälzer and Lange for nets using the Rectified Linear Unit and the identity function as their activation functions. We complement their achievements by showing that the problem is NP-complete for piecewise linear functions with rational coefficients that are not linear, NP-hard for almost all suitable activation functions including non-linear ones that are continuous on an interval, complete for the Existential Theory of the Reals $\exists \mathbb R$ for every non-linear polynomial and $\exists \mathbb R$-hard for the exponential function and various sigmoidal functions. For the completeness results, linking the verification tasks with the theory of Constraint Satisfaction Problems turns out helpful.
How Object Information Improves Skeleton-based Human Action Recognition in Assembly Tasks
Venue: arXiv cs.CV 2023
Year: 2023

As the use of collaborative robots (cobots) in industrial manufacturing continues to grow, human action recognition for effective human-robot collaboration becomes increasingly important. This ability is crucial for cobots to act autonomously and assist in assembly tasks. Recently, skeleton-based approaches are often used as they tend to generalize better to different people and environments. However, when processing skeletons alone, information about the objects a human interacts with is lost. Therefore, we present a novel approach of integrating object information into skeleton-based action recognition. We enhance two state-of-the-art methods by treating object centers as further skeleton joints. Our experiments on the assembly dataset IKEA ASM show that our approach improves the performance of these state-of-the-art methods to a large extent when combining skeleton joints with objects predicted by a state-of-the-art instance segmentation model. Our research sheds light on the benefits of combining skeleton joints with object information for human action recognition in assembly tasks. We analyze the effect of the object detector on the combination for action classification and discuss the important factors that must be taken into account.
Meta-Learning Based Few Pilots Demodulation and Interference Cancellation For NOMA Uplink
Venue: arXiv cs.IT 2023
Year: 2023

Non-Orthogonal Multiple Access (NOMA) is at the heart of a paradigm shift towards non-orthogonal communication due to its potential to scale well in massive deployments. Nevertheless, the overhead of channel estimation remains a key challenge in such scenarios. This paper introduces a data-driven, meta-learning-aided NOMA uplink model that minimizes the channel estimation overhead and does not require perfect channel knowledge. Unlike conventional deep learning successive interference cancellation (SICNet), Meta-Learning aided SIC (meta-SICNet) is able to share experience across different devices, facilitating learning for new incoming devices while reducing training overhead. Our results confirm that meta-SICNet outperforms classical SIC and conventional SICNet as it can achieve a lower symbol error rate with fewer pilots.
Efficient parallelization strategy for real-time FE simulations
Venue: arXiv cs.DC 2023
Year: 2023

This paper introduces an efficient and generic framework for finite-element simulations under an implicit time integration scheme. Being compatible with generic constitutive models, a fast matrix assembly method exploits the fact that system matrices are created in a deterministic way as long as the mesh topology remains constant. Using the sparsity pattern of the assembled system brings about significant optimizations on the assembly stage. As a result, developed techniques of GPU-based parallelization can be directly applied with the assembled system. Moreover, an asynchronous Cholesky precondition scheme is used to improve the convergence of the system solver. On this basis, a GPU-based Cholesky preconditioner is developed, significantly reducing the data transfer between the CPU/GPU during the solving stage. We evaluate the performance of our method with different mesh elements and hyperelastic models and compare it with typical approaches on the CPU and the GPU.
Augmenting Off-the-Shelf Grippers with Tactile Sensing
Venue: arXiv cs.RO 2023
Year: 2023

The development of tactile sensing and its fusion with computer vision is expected to enhance robotic systems in handling complex tasks like deformable object manipulation. However, readily available industrial grippers typically lack tactile feedback, which has led researchers to develop and integrate their own tactile sensors. This has resulted in a wide range of sensor hardware, making it difficult to compare performance between different systems. We highlight the value of accessible open-source sensors and present a set of fingertips specifically designed for fine object manipulation, with readily interpretable data outputs. The fingertips are validated through two difficult tasks: cloth edge tracing and cable tracing. Videos of these demonstrations, as well as design files and readout code can be found at https://github.com/RemkoPr/icra-2023-workshop-tactile-fingertips.
Towards Universally Optimal Shortest Paths Algorithms in the Hybrid Model
Venue: arXiv cs.DC 2023
Year: 2023

A drawback of the classic approach for complexity analysis of distributed graph problems is that it mostly informs about the complexity of notorious classes of ``worst case'' graphs. Algorithms that are used to prove a tight (existential) bound are essentially optimized to perform well on such worst case graphs. However, such graphs are often either unlikely or actively avoided in practice, where benign graph instances usually admit much faster solutions. To circumnavigate these drawbacks, the concept of universal complexity analysis in the distributed setting was suggested by [Kutten and Peleg, PODC'95] and actively pursued by [Haeupler et al., STOC'21]. Here, the aim is to gauge the complexity of a distributed graph problem depending on the given graph instance. The challenge is to identify and understand the graph property that allows to accurately quantify the complexity of a distributed problem on a given graph. In the present work, we consider distributed shortest paths problems in the HYBRID model of distributed computing, where nodes have simultaneous access to two different modes of communication: one is restricted by locality and the other is restricted by congestion. We identify the graph parameter of neighborhood quality and show that it accurately describes a universal bound for the complexity of certain class of shortest paths problems in the HYBRID model.
State of Refactoring Adoption: Better Understanding Developer Perception of Refactoring
Venue: arXiv cs.SE 2023
Year: 2023

We aim to explore how developers document their refactoring activities during the software life cycle. We call such activity Self-Affirmed Refactoring (SAR), which indicates developers' documentation of their refactoring activities. SAR is crucial in understanding various aspects of refactoring, including the motivation, procedure, and consequences of the performed code change. After that, we propose an approach to identify whether a commit describes developer-related refactoring events to classify them according to the refactoring common quality improvement categories. To complement this goal, we aim to reveal insights into how reviewers decide to accept or reject a submitted refactoring request and what makes such a review challenging.Our SAR taxonomy and model can work with refactoring detectors to report any early inconsistency between refactoring types and their documentation. They can serve as a solid background for various empirical investigations. Our survey with code reviewers has revealed several difficulties related to understanding the refactoring intent and implications on the functional and non-functional aspects of the software. In light of our findings from the industrial case study, we recommended a procedure to properly document refactoring activities, as part of our survey feedback.
HiTZ@Antidote: Argumentation-driven Explainable Artificial Intelligence for Digital Medicine
Venue: arXiv cs.CL 2023
Year: 2023

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.
Reconstructing Human Expressiveness in Piano Performances with a Transformer Network
Venue: arXiv cs.SD 2023
Year: 2023

Capturing intricate and subtle variations in human expressiveness in music performance using computational approaches is challenging. In this paper, we propose a novel approach for reconstructing human expressiveness in piano performance with a multi-layer bi-directional Transformer encoder. To address the needs for large amounts of accurately captured and score-aligned performance data in training neural networks, we use transcribed scores obtained from an existing transcription model to train our model. We integrate pianist identities to control the sampling process and explore the ability of our system to model variations in expressiveness for different pianists. The system is evaluated through statistical analysis of generated expressive performances and a listening test. Overall, the results suggest that our method achieves state-of-the-art in generating human-like piano performances from transcribed scores, while fully and consistently reconstructing human expressiveness poses further challenges.
Problematic Advertising and its Disparate Exposure on Facebook
Venue: arXiv cs.CY 2023
Year: 2023

Targeted advertising remains an important part of the free web browsing experience, where advertisers' targeting and personalization algorithms together find the most relevant audience for millions of ads every day. However, given the wide use of advertising, this also enables using ads as a vehicle for problematic content, such as scams or clickbait. Recent work that explores people's sentiments toward online ads, and the impacts of these ads on people's online experiences, has found evidence that online ads can indeed be problematic. Further, there is the potential for personalization to aid the delivery of such ads, even when the advertiser targets with low specificity. In this paper, we study Facebook -- one of the internet's largest ad platforms -- and investigate key gaps in our understanding of problematic online advertising: (a) What categories of ads do people find problematic? (b) Are there disparities in the distribution of problematic ads to viewers? and if so, (c) Who is responsible -- advertisers or advertising platforms? To answer these questions, we empirically measure a diverse sample of user experiences with Facebook ads via a 3-month longitudinal panel. We categorize over 32,000 ads collected from this panel ($n=132$); and survey participants' sentiments toward their own ads to identify four categories of problematic ads. Statistically modeling the distribution of problematic ads across demographics, we find that older people and minority groups are especially likely to be shown such ads. Further, given that 22% of problematic ads had no specific targeting from advertisers, we infer that ad delivery algorithms (advertising platforms themselves) played a significant role in the biased distribution of these ads.
Multi-level Cross-modal Feature Alignment via Contrastive Learning towards Zero-shot Classification of Remote Sensing Image Scenes
Venue: arXiv cs.CV 2023
Year: 2023

Zero-shot classification of image scenes which can recognize the image scenes that are not seen in the training stage holds great promise of lowering the dependence on large numbers of labeled samples. To address the zero-shot image scene classification, the cross-modal feature alignment methods have been proposed in recent years. These methods mainly focus on matching the visual features of each image scene with their corresponding semantic descriptors in the latent space. Less attention has been paid to the contrastive relationships between different image scenes and different semantic descriptors. In light of the challenge of large intra-class difference and inter-class similarity among image scenes and the potential noisy samples, these methods are susceptible to the influence of the instances which are far from these of the same classes and close to these of other classes. In this work, we propose a multi-level cross-modal feature alignment method via contrastive learning for zero-shot classification of remote sensing image scenes. While promoting the single-instance level positive alignment between each image scene with their corresponding semantic descriptors, the proposed method takes the cross-instance contrastive relationships into consideration,and learns to keep the visual and semantic features of different classes in the latent space apart from each other. Extensive experiments have been done to evaluate the performance of the proposed method. The results show that our proposed method outperforms state of the art methods for zero-shot remote sensing image scene classification. All the code and data are available at github https://github.com/masuqiang/MCFA-Pytorch
SAM-helps-Shadow:When Segment Anything Model meet shadow removal
Venue: arXiv cs.CV 2023
Year: 2023

The challenges surrounding the application of image shadow removal to real-world images and not just constrained datasets like ISTD/SRD have highlighted an urgent need for zero-shot learning in this field. In this study, we innovatively adapted the SAM (Segment anything model) for shadow removal by introducing SAM-helps-Shadow, effectively integrating shadow detection and removal into a single stage. Our approach utilized the model's detection results as a potent prior for facilitating shadow detection, followed by shadow removal using a second-order deep unfolding network. The source code of SAM-helps-Shadow can be obtained from https://github.com/zhangbaijin/SAM-helps-Shadow.
Using R-functions to Control the Shape of Soft Robots
Venue: arXiv cs.RO 2023
Year: 2023

In this paper, we introduce a new approach for soft robot shape formation and morphing using approximate distance fields. The method uses concepts from constructive solid geometry, R-functions, to construct an approximate distance function to the boundary of a domain in $\Re^d$. The gradients of the R-functions can then be used to generate control algorithms for shape formation tasks for soft robots. By construction, R-functions are smooth and convex everywhere, possess precise differential properties, and easily extend from $\Re^2$ to $\Re^3$ if needed. Furthermore, R-function theory provides a straightforward method to creating composite distance functions for any desired shape by combining subsets of distance functions. The process is highly efficient since the shape description is an analytical expression, and in this sense, it is better than competing control algorithms such as those based on potential fields. Although the method could also apply to swarm robots, in this paper it is applied to soft robots to demonstrate shape formation and morphing in 2-D (simulation and experimentation) and 3-D (simulation).
Artificial intelligence and radiation protection. A game changer or an update?
Venue: arXiv cs.LG 2023
Year: 2023

Artificial intelligence (AI) is regarded as one of the most disruptive technology of the century and with countless applications. What does it mean for radiation protection? This article describes the fundamentals of machine learning (ML) based methods and presents the inaugural applications in different fields of radiation protection. It is foreseen that the usage of AI will increase in radiation protection. Consequently, this article explores some of the benefits and also the potential barriers and questions, including ethical ones, that can come out. The article proposes that collaboration between radiation protection professionals and data scientist experts can accelerate and guide the development of the algorithms for effective scientific and technological outcomes.
EfficientBioAI: Making Bioimaging AI Models Efficient in Energy, Latency and Representation
Venue: arXiv cs.LG 2023
Year: 2023

Artificial intelligence (AI) has been widely used in bioimage image analysis nowadays, but the efficiency of AI models, like the energy consumption and latency is not ignorable due to the growing model size and complexity, as well as the fast-growing analysis needs in modern biomedical studies. Like we can compress large images for efficient storage and sharing, we can also compress the AI models for efficient applications and deployment. In this work, we present EfficientBioAI, a plug-and-play toolbox that can compress given bioimaging AI models for them to run with significantly reduced energy cost and inference time on both CPU and GPU, without compromise on accuracy. In some cases, the prediction accuracy could even increase after compression, since the compression procedure could remove redundant information in the model representation and therefore reduce over-fitting. From four different bioimage analysis applications, we observed around 2-5 times speed-up during inference and 30-80$\%$ saving in energy. Cutting the runtime of large scale bioimage analysis from days to hours or getting a two-minutes bioimaging AI model inference done in near real-time will open new doors for method development and biomedical discoveries. We hope our toolbox will facilitate resource-constrained bioimaging AI and accelerate large-scale AI-based quantitative biological studies in an eco-friendly way, as well as stimulate further research on the efficiency of bioimaging AI.