人蛋白质组包含一个庞大的相互作用激酶和底物网络。即使某些激酶被证明是治疗靶标的非常有用的，但大多数仍在研究中。在这项工作中，我们提出了一种新颖的知识图表示方法，以预测研究研究的新型相互作用伙伴。我们的方法使用通过整合IPTMNET，蛋白质本体论，基因本体论和BIOKG的数据构建的磷蛋白知识图。通过在三元组上进行定向的随机步行，与修改后的Skipgram或CBOW模型一起进行定向的随机步行，从而学习了该知识图中激酶和底物的表示。然后，这些表示形式被用作监督分类模型的输入，以预测研究不细的激酶的新型相互作用。我们还提供了对预测相互作用的后预测分析和对磷酸蛋白质学知识图的消融研究，以了解对研究的激酶的生物学的见解。

Periocular refers to the region of the face that surrounds the eye socket. This is a feature-rich area that can be used by itself to determine the identity of an individual. It is especially useful when the iris or the face cannot be reliably acquired. This can be the case of unconstrained or uncooperative scenarios, where the face may appear partially occluded, or the subject-to-camera distance may be high. However, it has received revived attention during the pandemic due to masked faces, leaving the ocular region as the only visible facial area, even in controlled scenarios. This paper discusses the state-of-the-art of periocular biometrics, giving an overall framework of its most significant research aspects.

The task of reconstructing 3D human motion has wideranging applications. The gold standard Motion capture (MoCap) systems are accurate but inaccessible to the general public due to their cost, hardware and space constraints. In contrast, monocular human mesh recovery (HMR) methods are much more accessible than MoCap as they take single-view videos as inputs. Replacing the multi-view Mo- Cap systems with a monocular HMR method would break the current barriers to collecting accurate 3D motion thus making exciting applications like motion analysis and motiondriven animation accessible to the general public. However, performance of existing HMR methods degrade when the video contains challenging and dynamic motion that is not in existing MoCap datasets used for training. This reduces its appeal as dynamic motion is frequently the target in 3D motion recovery in the aforementioned applications. Our study aims to bridge the gap between monocular HMR and multi-view MoCap systems by leveraging information shared across multiple video instances of the same action. We introduce the Neural Motion (NeMo) field. It is optimized to represent the underlying 3D motions across a set of videos of the same action. Empirically, we show that NeMo can recover 3D motion in sports using videos from the Penn Action dataset, where NeMo outperforms existing HMR methods in terms of 2D keypoint detection. To further validate NeMo using 3D metrics, we collected a small MoCap dataset mimicking actions in Penn Action,and show that NeMo achieves better 3D reconstruction compared to various baselines.

Neural compression offers a domain-agnostic approach to creating codecs for lossy or lossless compression via deep generative models. For sequence compression, however, most deep sequence models have costs that scale with the sequence length rather than the sequence complexity. In this work, we instead treat data sequences as observations from an underlying continuous-time process and learn how to efficiently discretize while retaining information about the full sequence. As a consequence of decoupling sequential information from its temporal discretization, our approach allows for greater compression rates and smaller computational complexity. Moreover, the continuous-time approach naturally allows us to decode at different time intervals. We empirically verify our approach on multiple domains involving compression of video and motion capture sequences, showing that our approaches can automatically achieve reductions in bit rates by learning how to discretize.

Detecting actions in untrimmed videos should not be limited to a small, closed set of classes. We present a simple, yet effective strategy for open-vocabulary temporal action detection utilizing pretrained image-text co-embeddings. Despite being trained on static images rather than videos, we show that image-text co-embeddings enable openvocabulary performance competitive with fully-supervised models. We show that the performance can be further improved by ensembling the image-text features with features encoding local motion, like optical flow based features, or other modalities, like audio. In addition, we propose a more reasonable open-vocabulary evaluation setting for the ActivityNet data set, where the category splits are based on similarity rather than random assignment.

Spoken language understanding (SLU) tasks have been studied for many decades in the speech research community, but have not received as much attention as lower-level tasks like speech and speaker recognition. In particular, there are not nearly as many SLU task benchmarks, and many of the existing ones use data that is not freely available to all researchers. Recent work has begun to introduce such benchmark datasets for several tasks. In this work, we introduce several new annotated SLU benchmark tasks based on freely available speech data, which complement existing benchmarks and address gaps in the SLU evaluation landscape. We contribute four tasks: question answering and summarization involve inference over longer speech sequences; named entity localization addresses the speech-specific task of locating the targeted content in the signal; dialog act classification identifies the function of a given speech utterance. We follow the blueprint of the Spoken Language Understanding Evaluation (SLUE) benchmark suite. In order to facilitate the development of SLU models that leverage the success of pre-trained speech representations, we will be publishing for each task (i) annotations for a relatively small fine-tuning set, (ii) annotated development and test sets, and (iii) baseline models for easy reproducibility and comparisons. In this work, we present the details of data collection and annotation and the performance of the baseline models. We also perform sensitivity analysis of pipeline models' performance (speech recognizer + text model) to the speech recognition accuracy, using more than 20 state-of-the-art speech recognition models.

Self-supervised pre-trained transformers have improved the state of the art on a variety of speech tasks. Due to the quadratic time and space complexity of self-attention, they usually operate at the level of relatively short (e.g., utterance) segments. In this paper, we study the use of context, i.e., surrounding segments, during fine-tuning and propose a new approach called context-aware fine-tuning. We attach a context module on top of the last layer of a pre-trained model to encode the whole segment into a context embedding vector which is then used as an additional feature for the final prediction. During the fine-tuning stage, we introduce an auxiliary loss that encourages this context embedding vector to be similar to context vectors of surrounding segments. This allows the model to make predictions without access to these surrounding segments at inference time and requires only a tiny overhead compared to standard fine-tuned models. We evaluate the proposed approach using the SLUE and Librilight benchmarks for several downstream tasks: Automatic speech recognition (ASR), named entity recognition (NER), and sentiment analysis (SA). The results show that context-aware fine-tuning not only outperforms a standard fine-tuning baseline but also rivals a strong context injection baseline that uses neighboring speech segments during inference.

Recent neural compression methods have been based on the popular hyperprior framework. It relies on Scalar Quantization and offers a very strong compression performance. This contrasts from recent advances in image generation and representation learning, where Vector Quantization is more commonly employed. In this work, we attempt to bring these lines of research closer by revisiting vector quantization for image compression. We build upon the VQ-VAE framework and introduce several modifications. First, we replace the vanilla vector quantizer by a product quantizer. This intermediate solution between vector and scalar quantization allows for a much wider set of rate-distortion points: It implicitly defines high-quality quantizers that would otherwise require intractably large codebooks. Second, inspired by the success of Masked Image Modeling (MIM) in the context of self-supervised learning and generative image models, we propose a novel conditional entropy model which improves entropy coding by modelling the co-dependencies of the quantized latent codes. The resulting PQ-MIM model is surprisingly effective: its compression performance on par with recent hyperprior methods. It also outperforms HiFiC in terms of FID and KID metrics when optimized with perceptual losses (e.g. adversarial). Finally, since PQ-MIM is compatible with image generation frameworks, we show qualitatively that it can operate under a hybrid mode between compression and generation, with no further training or finetuning. As a result, we explore the extreme compression regime where an image is compressed into 200 bytes, i.e., less than a tweet.

Scaling up neural networks has led to remarkable performance across a wide range of tasks. Moreover, performance often follows reliable scaling laws as a function of training set size, model size, and compute, which offers valuable guidance as large-scale experiments are becoming increasingly expensive. However, previous work on scaling laws has primarily used private data \& models or focused on uni-modal language or vision learning. To address these limitations, we investigate scaling laws for contrastive language-image pre-training (CLIP) with the public LAION dataset and the open-source OpenCLIP repository. Our large-scale experiments involve models trained on up to two billion image-text pairs and identify power law scaling for multiple downstream tasks including zero-shot classification, retrieval, linear probing, and end-to-end fine-tuning. We find that the training distribution plays a key role in scaling laws as the OpenAI and OpenCLIP models exhibit different scaling behavior despite identical model architectures and similar training recipes. We open-source our evaluation workflow and all models, including the largest public CLIP models, to ensure reproducibility and make scaling laws research more accessible. Source code and instructions to reproduce this study will be available at https://github.com/LAION-AI/scaling-laws-openclip

Electronic Health Records (EHRs) hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Temporal modelling of this medical history, which considers the sequence of events, can be used to forecast and simulate future events, estimate risk, suggest alternative diagnoses or forecast complications. While most prediction approaches use mainly structured data or a subset of single-domain forecasts and outcomes, we processed the entire free-text portion of EHRs for longitudinal modelling. We present Foresight, a novel GPT3-based pipeline that uses NER+L tools (i.e. MedCAT) to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, medications, symptoms and interventions. Since large portions of EHR data are in text form, such an approach benefits from a granular and detailed view of a patient while introducing modest additional noise. On tests in two large UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by 5 clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. Foresight can be easily trained and deployed locally as it only requires free-text data (as a minimum). As a generative model, it can simulate follow-on disorders, medications and interventions for as many steps as required. Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk estimation, virtual trials and clinical research to study the progression of diseases, simulate interventions and counterfactuals, and for educational purposes.