After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are difficult to fit due to complex covariance structures between degrees of freedom in the protein chain, often causing models to either violate local or global structural constraints. In this paper, we present a new strategy for modelling protein densities in internal coordinates, which uses constraints in 3D space to induce covariance structure between the internal degrees of freedom. We illustrate the potential of the procedure by constructing a variational autoencoder with full covariance output induced by the constraints implied by the conditional mean in 3D, and demonstrate that our approach makes it possible to scale density models of internal coordinates to full protein backbones in two settings: 1) a unimodal setting for proteins exhibiting small fluctuations and limited amounts of available data, and 2) a multimodal setting for larger conformational changes in a high data regime.
We introduce CrossNet, a complex spectral mapping approach to speaker separation and enhancement in reverberant and noisy conditions. The proposed architecture comprises an encoder layer, a global multi-head self-attention module, a cross-band module, a narrow-band module, and an output layer. CrossNet captures global, cross-band, and narrow-band correlations in the time-frequency domain. To address performance degradation in long utterances, we introduce a random chunk positional encoding. Experimental results on multiple datasets demonstrate the effectiveness and robustness of CrossNet, achieving state-of-the-art performance in tasks including reverberant and noisy-reverberant speaker separation. Furthermore, CrossNet exhibits faster and more stable training in comparison to recent baselines. Additionally, CrossNet's high performance extends to multi-microphone conditions, demonstrating its versatility in various acoustic scenarios.
Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery. Our code and data are available at //github.com/SCIR-HI/ArtificiallyR2R.
Federated Learning (FL) thrives in training a global model with numerous clients by only sharing the parameters of their local models trained with their private training datasets. Therefore, without revealing the private dataset, the clients can obtain a deep learning (DL) model with high performance. However, recent research proposed poisoning attacks that cause a catastrophic loss in the accuracy of the global model when adversaries, posed as benign clients, are present in a group of clients. Therefore, recent studies suggested byzantine-robust FL methods that allow the server to train an accurate global model even with the adversaries present in the system. However, many existing methods require the knowledge of the number of malicious clients or the auxiliary (clean) dataset or the effectiveness reportedly decreased hugely when the private dataset was non-independently and identically distributed (non-IID). In this work, we propose FLGuard, a novel byzantine-robust FL method that detects malicious clients and discards malicious local updates by utilizing the contrastive learning technique, which showed a tremendous improvement as a self-supervised learning method. With contrastive models, we design FLGuard as an ensemble scheme to maximize the defensive capability. We evaluate FLGuard extensively under various poisoning attacks and compare the accuracy of the global model with existing byzantine-robust FL methods. FLGuard outperforms the state-of-the-art defense methods in most cases and shows drastic improvement, especially in non-IID settings. //github.com/201younghanlee/FLGuard
Distributed Stream Processing (DSP) systems are capable of processing large streams of unbounded data, offering high throughput and low latencies. To maintain a stable Quality of Service (QoS), these systems require a sufficient allocation of resources. At the same time, over-provisioning can result in wasted energy and high operating costs. Therefore, to maximize resource utilization, autoscaling methods have been proposed that aim to efficiently match the resource allocation with the incoming workload. However, determining when and by how much to scale remains a significant challenge. Given the long-running nature of DSP jobs, scaling actions need to be executed at runtime, and to maintain a good QoS, they should be both accurate and infrequent. To address the challenges of autoscaling, the concept of self-adaptive systems is particularly fitting. These systems monitor themselves and their environment, adapting to changes with minimal need for expert involvement. This paper introduces Daedalus, a self-adaptive manager for autoscaling in DSP systems, which draws on the principles of self-adaption to address the challenge of efficient autoscaling. Daedalus monitors a running DSP job and builds performance models, aiming to predict the maximum processing capacity at different scale-outs. When combined with time series forecasting to predict future workloads, Daedalus proactively scales DSP jobs, optimizing for maximum throughput and minimizing both latencies and resource usage. We conducted experiments using Apache Flink and Kafka Streams to evaluate the performance of Daedalus against two state-of-the-art approaches. Daedalus was able to achieve comparable latencies while reducing resource usage by up to 71%.
We present AlloyInEcore, a tool for specifying metamodels with their static semantics to facilitate automated, formal reasoning on models. Software development projects require that software systems be specified in various models (e.g., requirements models, architecture models, test models, and source code). It is crucial to reason about those models to ensure the correct and complete system specifications. AlloyInEcore allows the user to specify metamodels with their static semantics, while, using the semantics, it automatically detects inconsistent models, and completes partial models. It has been evaluated on three industrial case studies in the automotive domain (//modelwriter.github.io/AlloyInEcore/).
Exploring molecular spaces is crucial for advancing our understanding of chemical properties and reactions, leading to groundbreaking innovations in materials science, medicine, and energy. This paper explores an approach for active learning in molecular discovery using Deep Kernel Learning (DKL), a novel approach surpassing the limits of classical Variational Autoencoders (VAEs). Employing the QM9 dataset, we contrast DKL with traditional VAEs, which analyze molecular structures based on similarity, revealing limitations due to sparse regularities in latent spaces. DKL, however, offers a more holistic perspective by correlating structure with properties, creating latent spaces that prioritize molecular functionality. This is achieved by recalculating embedding vectors iteratively, aligning with the experimental availability of target properties. The resulting latent spaces are not only better organized but also exhibit unique characteristics such as concentrated maxima representing molecular functionalities and a correlation between predictive uncertainty and error. Additionally, the formation of exclusion regions around certain compounds indicates unexplored areas with potential for groundbreaking functionalities. This study underscores DKL's potential in molecular research, offering new avenues for understanding and discovering molecular functionalities beyond classical VAE limitations.
This study aims to address the pervasive challenge of quantifying uncertainty in large language models (LLMs) without logit-access. Conformal Prediction (CP), known for its model-agnostic and distribution-free features, is a desired approach for various LLMs and data distributions. However, existing CP methods for LLMs typically assume access to the logits, which are unavailable for some API-only LLMs. In addition, logits are known to be miscalibrated, potentially leading to degraded CP performance. To tackle these challenges, we introduce a novel CP method that (1) is tailored for API-only LLMs without logit-access; (2) minimizes the size of prediction sets; and (3) ensures a statistical guarantee of the user-defined coverage. The core idea of this approach is to formulate nonconformity measures using both coarse-grained (i.e., sample frequency) and fine-grained uncertainty notions (e.g., semantic similarity). Experimental results on both close-ended and open-ended Question Answering tasks show our approach can mostly outperform the logit-based CP baselines.
This research addresses a critical challenge in the field of generative models, particularly in the generation and evaluation of synthetic images. Given the inherent complexity of generative models and the absence of a standardized procedure for their comparison, our study introduces a pioneering algorithm to objectively assess the realism of synthetic images. This approach significantly enhances the evaluation methodology by refining the Fr\'echet Inception Distance (FID) score, allowing for a more precise and subjective assessment of image quality. Our algorithm is particularly tailored to address the challenges in generating and evaluating realistic images of Arabic handwritten digits, a task that has traditionally been near-impossible due to the subjective nature of realism in image generation. By providing a systematic and objective framework, our method not only enables the comparison of different generative models but also paves the way for improvements in their design and output. This breakthrough in evaluation and comparison is crucial for advancing the field of OCR, especially for scripts that present unique complexities, and sets a new standard in the generation and assessment of high-quality synthetic images.
With the breakthrough of AlphaGo, deep reinforcement learning becomes a recognized technique for solving sequential decision-making problems. Despite its reputation, data inefficiency caused by its trial and error learning mechanism makes deep reinforcement learning hard to be practical in a wide range of areas. Plenty of methods have been developed for sample efficient deep reinforcement learning, such as environment modeling, experience transfer, and distributed modifications, amongst which, distributed deep reinforcement learning has shown its potential in various applications, such as human-computer gaming, and intelligent transportation. In this paper, we conclude the state of this exciting field, by comparing the classical distributed deep reinforcement learning methods, and studying important components to achieve efficient distributed learning, covering single player single agent distributed deep reinforcement learning to the most complex multiple players multiple agents distributed deep reinforcement learning. Furthermore, we review recently released toolboxes that help to realize distributed deep reinforcement learning without many modifications of their non-distributed versions. By analyzing their strengths and weaknesses, a multi-player multi-agent distributed deep reinforcement learning toolbox is developed and released, which is further validated on Wargame, a complex environment, showing usability of the proposed toolbox for multiple players and multiple agents distributed deep reinforcement learning under complex games. Finally, we try to point out challenges and future trends, hoping this brief review can provide a guide or a spark for researchers who are interested in distributed deep reinforcement learning.
For deploying a deep learning model into production, it needs to be both accurate and compact to meet the latency and memory constraints. This usually results in a network that is deep (to ensure performance) and yet thin (to improve computational efficiency). In this paper, we propose an efficient method to train a deep thin network with a theoretic guarantee. Our method is motivated by model compression. It consists of three stages. In the first stage, we sufficiently widen the deep thin network and train it until convergence. In the second stage, we use this well-trained deep wide network to warm up (or initialize) the original deep thin network. This is achieved by letting the thin network imitate the immediate outputs of the wide network from layer to layer. In the last stage, we further fine tune this well initialized deep thin network. The theoretical guarantee is established by using mean field analysis, which shows the advantage of layerwise imitation over traditional training deep thin networks from scratch by backpropagation. We also conduct large-scale empirical experiments to validate our approach. By training with our method, ResNet50 can outperform ResNet101, and BERT_BASE can be comparable with BERT_LARGE, where both the latter models are trained via the standard training procedures as in the literature.