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Limited availability of labeled data for machine learning on biomedical time-series hampers progress in the field. Self-supervised learning (SSL) is a promising approach to learning data representations without labels. However, current SSL methods require expensive computations for negative pairs and are designed for single modalities, limiting their versatility. To overcome these limitations, we introduce CroSSL (Cross-modal SSL). CroSSL introduces two novel concepts: masking intermediate embeddings from modality-specific encoders and aggregating them into a global embedding using a cross-modal aggregator. This enables the handling of missing modalities and end-to-end learning of cross-modal patterns without prior data preprocessing or time-consuming negative-pair sampling. We evaluate CroSSL on various multimodal time-series benchmarks, including both medical-grade and consumer biosignals. Our results demonstrate superior performance compared to previous SSL techniques and supervised benchmarks with minimal labeled data. We additionally analyze the impact of different masking ratios and strategies and assess the robustness of the learned representations to missing modalities. Overall, our work achieves state-of-the-art performance while highlighting the benefits of masking latent embeddings for cross-modal learning in temporal health data.

Video-to-speech synthesis is the task of reconstructing the speech signal from a silent video of a speaker. Most established approaches to date involve a two-step process, whereby an intermediate representation from the video, such as a spectrogram, is extracted first and then passed to a vocoder to produce the raw audio. Some recent work has focused on end-to-end synthesis, whereby the generation of raw audio and any intermediate representations is performed jointly. All such approaches involve training on data from almost exclusively audio-visual datasets, i.e. every audio sample has a corresponding video sample. This precludes the use of abundant audio-only datasets which may not have a corresponding visual modality (e.g. audiobooks, radio podcasts, speech recognition datasets etc.), as well as audio-only architectures that have been developed by the audio machine learning community over the years. In this paper we propose to train encoder-decoder models on more than 3,500 hours of audio data at 24kHz, and then use the pre-trained decoders to initialize the audio decoders for the video-to-speech synthesis task. The pre-training step uses audio samples only and does not require labels or corresponding samples from other modalities (visual, text). We demonstrate that this pre-training step improves the reconstructed speech and that it is an unexplored way to improve the quality of the generator in a cross-modal task while only requiring samples from one of the modalities. We conduct experiments using both raw audio and mel spectrograms as target outputs and benchmark our models with existing work.

Large language models (LLMs) have made significant progress in various domains, including healthcare. However, the specialized nature of clinical language understanding tasks presents unique challenges and limitations that warrant further investigation. In this study, we conduct a comprehensive evaluation of state-of-the-art LLMs, namely GPT-3.5, GPT-4, and Bard, within the realm of clinical language understanding tasks. These tasks span a diverse range, including named entity recognition, relation extraction, natural language inference, semantic textual similarity, document classification, and question-answering. We also introduce a novel prompting strategy, self-questioning prompting (SQP), tailored to enhance LLMs' performance by eliciting informative questions and answers pertinent to the clinical scenarios at hand. Our evaluation underscores the significance of task-specific learning strategies and prompting techniques for improving LLMs' effectiveness in healthcare-related tasks. Additionally, our in-depth error analysis on the challenging relation extraction task offers valuable insights into error distribution and potential avenues for improvement using SQP. Our study sheds light on the practical implications of employing LLMs in the specialized domain of healthcare, serving as a foundation for future research and the development of potential applications in healthcare settings.

Clinical trials are vital in advancing drug development and evidence-based medicine, but their success is often hindered by challenges in patient recruitment. In this work, we investigate the potential of large language models (LLMs) to assist individual patients and referral physicians in identifying suitable clinical trials from an extensive selection. Specifically, we introduce TrialGPT, a novel architecture employing LLMs to predict criterion-level eligibility with detailed explanations, which are then aggregated for ranking and excluding candidate clinical trials based on free-text patient notes. We evaluate TrialGPT on three publicly available cohorts of 184 patients and 18,238 annotated clinical trials. The experimental results demonstrate several key findings: First, TrialGPT achieves high criterion-level prediction accuracy with faithful explanations. Second, the aggregated trial-level TrialGPT scores are highly correlated with expert eligibility annotations. Third, these scores prove effective in ranking clinical trials and exclude ineligible candidates. Our error analysis suggests that current LLMs still make some mistakes due to limited medical knowledge and domain-specific context understanding. Nonetheless, we believe the explanatory capabilities of LLMs are highly valuable. Future research is warranted on how such AI assistants can be integrated into the routine trial matching workflow in real-world settings to improve its efficiency.

Recently, there has been a growing interest in text-to-speech (TTS) methods that can be trained with minimal supervision by combining two types of discrete speech representations and using two sequence-to-sequence tasks to decouple TTS. To address the challenges associated with high dimensionality and waveform distortion in discrete representations, we propose Diff-LM-Speech, which models semantic embeddings into mel-spectrogram based on diffusion models and introduces a prompt encoder structure based on variational autoencoders and prosody bottlenecks to improve prompt representation capabilities. Autoregressive language models often suffer from missing and repeated words, while non-autoregressive frameworks face expression averaging problems due to duration prediction models. To address these issues, we propose Tetra-Diff-Speech, which designs a duration diffusion model to achieve diverse prosodic expressions. While we expect the information content of semantic coding to be between that of text and acoustic coding, existing models extract semantic coding with a lot of redundant information and dimensionality explosion. To verify that semantic coding is not necessary, we propose Tri-Diff-Speech. Experimental results show that our proposed methods outperform baseline methods. We provide a website with audio samples.

This article provides a comprehensive synthesis of the recent developments in synthetic data generation via deep generative models, focusing on tabular datasets. We specifically outline the importance of synthetic data generation in the context of privacy-sensitive data. Additionally, we highlight the advantages of using deep generative models over other methods and provide a detailed explanation of the underlying concepts, including unsupervised learning, neural networks, and generative models. The paper covers the challenges and considerations involved in using deep generative models for tabular datasets, such as data normalization, privacy concerns, and model evaluation. This review provides a valuable resource for researchers and practitioners interested in synthetic data generation and its applications.

Recent advancements in surgical computer vision applications have been driven by fully-supervised methods, primarily using only visual data. These methods rely on manually annotated surgical videos to predict a fixed set of object categories, limiting their generalizability to unseen surgical procedures and downstream tasks. In this work, we put forward the idea that the surgical video lectures available through open surgical e-learning platforms can provide effective supervisory signals for multi-modal representation learning without relying on manual annotations. We address the surgery-specific linguistic challenges present in surgical video lectures by employing multiple complementary automatic speech recognition systems to generate text transcriptions. We then present a novel method, SurgVLP - Surgical Vision Language Pre-training, for multi-modal representation learning. SurgVLP constructs a new contrastive learning objective to align video clip embeddings with the corresponding multiple text embeddings by bringing them together within a joint latent space. To effectively show the representation capability of the learned joint latent space, we introduce several vision-and-language tasks for surgery, such as text-based video retrieval, temporal activity grounding, and video captioning, as benchmarks for evaluation. We further demonstrate that without using any labeled ground truth, our approach can be employed for traditional vision-only surgical downstream tasks, such as surgical tool, phase, and triplet recognition. The code will be made available at //github.com/CAMMA-public/SurgVLP

When learning tasks over time, artificial neural networks suffer from a problem known as Catastrophic Forgetting (CF). This happens when the weights of a network are overwritten during the training of a new task causing forgetting of old information. To address this issue, we propose MetA Reusable Knowledge or MARK, a new method that fosters weight reusability instead of overwriting when learning a new task. Specifically, MARK keeps a set of shared weights among tasks. We envision these shared weights as a common Knowledge Base (KB) that is not only used to learn new tasks, but also enriched with new knowledge as the model learns new tasks. Key components behind MARK are two-fold. On the one hand, a metalearning approach provides the key mechanism to incrementally enrich the KB with new knowledge and to foster weight reusability among tasks. On the other hand, a set of trainable masks provides the key mechanism to selectively choose from the KB relevant weights to solve each task. By using MARK, we achieve state of the art results in several popular benchmarks, surpassing the best performing methods in terms of average accuracy by over 10% on the 20-Split-MiniImageNet dataset, while achieving almost zero forgetfulness using 55% of the number of parameters. Furthermore, an ablation study provides evidence that, indeed, MARK is learning reusable knowledge that is selectively used by each task.

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.

It is always well believed that modeling relationships between objects would be helpful for representing and eventually describing an image. Nevertheless, there has not been evidence in support of the idea on image description generation. In this paper, we introduce a new design to explore the connections between objects for image captioning under the umbrella of attention-based encoder-decoder framework. Specifically, we present Graph Convolutional Networks plus Long Short-Term Memory (dubbed as GCN-LSTM) architecture that novelly integrates both semantic and spatial object relationships into image encoder. Technically, we build graphs over the detected objects in an image based on their spatial and semantic connections. The representations of each region proposed on objects are then refined by leveraging graph structure through GCN. With the learnt region-level features, our GCN-LSTM capitalizes on LSTM-based captioning framework with attention mechanism for sentence generation. Extensive experiments are conducted on COCO image captioning dataset, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, GCN-LSTM increases CIDEr-D performance from 120.1% to 128.7% on COCO testing set.