Transformer-based de novo peptide sequencing for data-independent acquisition mass spectrometry

Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent years, substantial strides have been made in Data-Independent Acquisition (DIA) strategies, facilitating impartial and non-targeted fragmentation of precursor ions. The DIA-generated MS/MS spectra present a formidable obstacle due to their inherent high multiplexing nature. Each spectrum encapsulates fragmented product ions originating from multiple precursor peptides. This intricacy poses a particularly acute challenge in de novo peptide/protein sequencing, where current methods are ill-equipped to address the multiplexing conundrum. In this paper, we introduce Casanovo-DIA, a deep-learning model based on transformer architecture. It deciphers peptide sequences from DIA mass spectrometry data. Our results show significant improvements over existing STOA methods, including DeepNovo-DIA and PepNet. Casanovo-DIA enhances precision by 15.14% to 34.8%, recall by 11.62% to 31.94% at the amino acid level, and boosts precision by 59% to 81.36% at the peptide level. Integrating DIA data and our Casanovo-DIA model holds considerable promise to uncover novel peptides and more comprehensive profiling of biological samples. Casanovo-DIA is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/Casanovo-DIA.

Multi-teacher Distillation for Multilingual Spelling Correction

Accurate spelling correction is a critical step in modern search interfaces, especially in an era of mobile devices and speech-to-text interfaces. For services that are deployed around the world, this poses a significant challenge for multilingual NLP: spelling errors need to be caught and corrected in all languages, and even in queries that use multiple languages. In this paper, we tackle this challenge using multi-teacher distillation. On our approach, a monolingual teacher model is trained for each language/locale, and these individual models are distilled into a single multilingual student model intended to serve all languages/locales. In experiments using open-source data as well as user data from a worldwide search service, we show that this leads to highly effective spelling correction models that can meet the tight latency requirements of deployed services.

Representation Learning on Heterostructures via Heterogeneous Anonymous Walks

Capturing structural similarity has been a hot topic in the field of network embedding recently due to its great help in understanding the node functions and behaviors. However, existing works have paid very much attention to learning structures on homogeneous networks while the related study on heterogeneous networks is still a void. In this paper, we try to take the first step for representation learning on heterostructures, which is very challenging due to their highly diverse combinations of node types and underlying structures. To effectively distinguish diverse heterostructures, we firstly propose a theoretically guaranteed technique called heterogeneous anonymous walk (HAW) and its variant coarse HAW (CHAW). Then, we devise the heterogeneous anonymous walk embedding (HAWE) and its variant coarse HAWE in a data-driven manner to circumvent using an extremely large number of possible walks and train embeddings by predicting occurring walks in the neighborhood of each node. Finally, we design and apply extensive and illustrative experiments on synthetic and real-world networks to build a benchmark on heterostructure learning and evaluate the effectiveness of our methods. The results demonstrate our methods achieve outstanding performance compared with both homogeneous and heterogeneous classic methods, and can be applied on large-scale networks.

A Survey on Role-Oriented Network Embedding

Recently, Network Embedding (NE) has become one of the most attractive research topics in machine learning and data mining. NE approaches have achieved promising performance in various of graph mining tasks including link prediction and node clustering and classification. A wide variety of NE methods focus on the proximity of networks. They learn community-oriented embedding for each node, where the corresponding representations are similar if two nodes are closer to each other in the network. Meanwhile, there is another type of structural similarity, i.e., role-based similarity, which is usually complementary and completely different from the proximity. In order to preserve the role-based structural similarity, the problem of role-oriented NE is raised. However, compared to community-oriented NE problem, there are only a few role-oriented embedding approaches proposed recently. Although less explored, considering the importance of roles in analyzing networks and many applications that role-oriented NE can shed light on, it is necessary and timely to provide a comprehensive overview of existing role-oriented NE methods. In this review, we first clarify the differences between community-oriented and role-oriented network embedding. Afterwards, we propose a general framework for understanding role-oriented NE and a two-level categorization to better classify existing methods. Then, we select some representative methods according to the proposed categorization and briefly introduce them by discussing their motivation, development and differences. Moreover, we conduct comprehensive experiments to empirically evaluate these methods on a variety of role-related tasks including node classification and clustering (role discovery), top-k similarity search and visualization using some widely used synthetic and real-world datasets...

Automatic Generation of Multi-precision Multi-arithmetic CNN Accelerators for FPGAs

Modern deep Convolutional Neural Networks (CNNs) are computationally demanding, yet real applications often require high throughput and low latency. To help tackle these problems, we propose Tomato, a framework designed to automate the process of generating efficient CNN accelerators. The generated design is pipelined and each convolution layer uses different arithmetics at various precisions. Using Tomato, we showcase state-of-the-art multi-precision multi-arithmetic networks, including MobileNet-V1, running on FPGAs. To our knowledge, this is the first multi-precision multi-arithmetic auto-generation framework for CNNs. In software, Tomato fine-tunes pretrained networks to use a mixture of short powers-of-2 and fixed-point weights with a minimal loss in classification accuracy. The fine-tuned parameters are combined with the templated hardware designs to automatically produce efficient inference circuits in FPGAs. We demonstrate how our approach significantly reduces model sizes and computation complexities, and permits us to pack a complete ImageNet network onto a single FPGA without accessing off-chip memories for the first time. Furthermore, we show how Tomato produces implementations of networks with various sizes running on single or multiple FPGAs. To the best of our knowledge, our automatically generated accelerators outperform closest FPGA-based competitors by at least 2-4x for lantency and throughput; the generated accelerator runs ImageNet classification at a rate of more than 3000 frames per second.

Deep Convolutional Neural Network for Automated Detection of Mind Wandering using EEG Signals

Mind wandering (MW) is a ubiquitous phenomenon which reflects a shift in attention from task-related to task-unrelated thoughts. There is a need for intelligent interfaces that can reorient attention when MW is detected due to its detrimental effects on performance and productivity. In this paper, we propose a deep learning model for MW detection using Electroencephalogram (EEG) signals. Specifically, we develop a channel-wise deep convolutional neural network (CNN) model to classify the features of focusing state and MW extracted from EEG signals. This is the first study that employs CNN to automatically detect MW using only EEG data. The experimental results on the collected dataset demonstrate promising performance with 91.78% accuracy, 92.84% sensitivity, and 90.73% specificity.