Self-Supervised Clustering of Multivariate Time-Series Data for Identifying TBI Physiological States

Determining clinically relevant physiological states from multivariate time series data with missing values is essential for providing appropriate treatment for acute conditions such as Traumatic Brain Injury (TBI), respiratory failure, and heart failure. Utilizing non-temporal clustering or data imputation and aggregation techniques may lead to loss of valuable information and biased analyses. In our study, we apply the SLAC-Time algorithm, an innovative self-supervision-based approach that maintains data integrity by avoiding imputation or aggregation, offering a more useful representation of acute patient states. By using SLAC-Time to cluster data in a large research dataset, we identified three distinct TBI physiological states and their specific feature profiles. We employed various clustering evaluation metrics and incorporated input from a clinical domain expert to validate and interpret the identified physiological states. Further, we discovered how specific clinical events and interventions can influence patient states and state transitions.

Transformer-based Planning for Symbolic Regression

Symbolic regression (SR) is a challenging task in machine learning that involves finding a mathematical expression for a function based on its values. Recent advancements in SR have demonstrated the efficacy of pretrained transformer-based models for generating equations as sequences, which benefit from large-scale pretraining on synthetic datasets and offer considerable advantages over GP-based methods in terms of inference time. However, these models focus on supervised pretraining goals borrowed from text generation and ignore equation-specific objectives like accuracy and complexity. To address this, we propose TPSR, a Transformer-based Planning strategy for Symbolic Regression that incorporates Monte Carlo Tree Search into the transformer decoding process. TPSR, as opposed to conventional decoding strategies, allows for the integration of non-differentiable feedback, such as fitting accuracy and complexity, as external sources of knowledge into the equation generation process. Extensive experiments on various datasets show that our approach outperforms state-of-the-art methods, enhancing the model's fitting-complexity trade-off, extrapolation abilities, and robustness to noise. We also demonstrate that the utilization of various caching mechanisms can further enhance the efficiency of TPSR.

A Self-Supervised Learning-based Approach to Clustering Multivariate Time-Series Data with Missing Values (SLAC-Time): An Application to Traumatic Brain Injury Phenotyping

Self-supervised learning approaches provide a promising direction for clustering multivariate time-series data. However, real-world time-series data often include missing values, and the existing approaches require imputing missing values before clustering, which may cause extensive computations and noise and result in invalid interpretations. To address these challenges, we present a Self-supervised Learning-based Approach to Clustering multivariate Time-series data with missing values (SLAC-Time). SLAC-Time is a Transformer-based clustering method that uses time-series forecasting as a proxy task for leveraging unlabeled data and learning more robust time-series representations. This method jointly learns the neural network parameters and the cluster assignments of the learned representations. It iteratively clusters the learned representations with the K-means method and then utilizes the subsequent cluster assignments as pseudo-labels to update the model parameters. To evaluate our proposed approach, we applied it to clustering and phenotyping Traumatic Brain Injury (TBI) patients in the TRACK-TBI dataset. Our experiments demonstrate that SLAC-Time outperforms the baseline K-means clustering algorithm in terms of silhouette coefficient, Calinski Harabasz index, Dunn index, and Davies Bouldin index. We identified three TBI phenotypes that are distinct from one another in terms of clinically significant variables as well as clinical outcomes, including the Extended Glasgow Outcome Scale (GOSE) score, Intensive Care Unit (ICU) length of stay, and mortality rate. The experiments show that the TBI phenotypes identified by SLAC-Time can be potentially used for developing targeted clinical trials and therapeutic strategies.

Execution-based Code Generation using Deep Reinforcement Learning

The utilization of programming language (PL) models, pretrained on large-scale code corpora, as a means of automating software engineering processes has demonstrated considerable potential in streamlining various code generation tasks such as code completion, code translation, and program synthesis. However, current approaches mainly rely on supervised fine-tuning objectives borrowed from text generation, neglecting specific sequence-level features of code, including but not limited to compilability as well as syntactic and functional correctness. To address this limitation, we propose PPOCoder, a new framework for code generation that combines pretrained PL models with Proximal Policy Optimization (PPO) deep reinforcement learning and employs execution feedback as the external source of knowledge into the model optimization. PPOCoder is transferable across different code generation tasks and PLs. Extensive experiments on three code generation tasks demonstrate the effectiveness of our proposed approach compared to SOTA methods, improving the success rate of compilation and functional correctness over different PLs. Our code can be found at https://github.com/reddy-lab-code-research/PPOCoder .

Transformer-based Models for Long-Form Document Matching: Challenges and Empirical Analysis

Recent advances in the area of long document matching have primarily focused on using transformer-based models for long document encoding and matching. There are two primary challenges associated with these models. Firstly, the performance gain provided by transformer-based models comes at a steep cost - both in terms of the required training time and the resource (memory and energy) consumption. The second major limitation is their inability to handle more than a pre-defined input token length at a time. In this work, we empirically demonstrate the effectiveness of simple neural models (such as feed-forward networks, and CNNs) and simple embeddings (like GloVe, and Paragraph Vector) over transformer-based models on the task of document matching. We show that simple models outperform the more complex BERT-based models while taking significantly less training time, energy, and memory. The simple models are also more robust to variations in document length and text perturbations.

An Empirical Comparison of Explainable Artificial Intelligence Methods for Clinical Data: A Case Study on Traumatic Brain Injury

A longstanding challenge surrounding deep learning algorithms is unpacking and understanding how they make their decisions. Explainable Artificial Intelligence (XAI) offers methods to provide explanations of internal functions of algorithms and reasons behind their decisions in ways that are interpretable and understandable to human users. . Numerous XAI approaches have been developed thus far, and a comparative analysis of these strategies seems necessary to discern their relevance to clinical prediction models. To this end, we first implemented two prediction models for short- and long-term outcomes of traumatic brain injury (TBI) utilizing structured tabular as well as time-series physiologic data, respectively. Six different interpretation techniques were used to describe both prediction models at the local and global levels. We then performed a critical analysis of merits and drawbacks of each strategy, highlighting the implications for researchers who are interested in applying these methodologies. The implemented methods were compared to one another in terms of several XAI characteristics such as understandability, fidelity, and stability. Our findings show that SHAP is the most stable with the highest fidelity but falls short of understandability. Anchors, on the other hand, is the most understandable approach, but it is only applicable to tabular data and not time series data.

Text Enriched Sparse Hyperbolic Graph Convolutional Networks

Heterogeneous networks, which connect informative nodes containing text with different edge types, are routinely used to store and process information in various real-world applications. Graph Neural Networks (GNNs) and their hyperbolic variants provide a promising approach to encode such networks in a low-dimensional latent space through neighborhood aggregation and hierarchical feature extraction, respectively. However, these approaches typically ignore metapath structures and the available semantic information. Furthermore, these approaches are sensitive to the noise present in the training data. To tackle these limitations, in this paper, we propose Text Enriched Sparse Hyperbolic Graph Convolution Network (TESH-GCN) to capture the graph's metapath structures using semantic signals and further improve prediction in large heterogeneous graphs. In TESH-GCN, we extract semantic node information, which successively acts as a connection signal to extract relevant nodes' local neighborhood and graph-level metapath features from the sparse adjacency tensor in a reformulated hyperbolic graph convolution layer. These extracted features in conjunction with semantic features from the language model (for robustness) are used for the final downstream task. Experiments on various heterogeneous graph datasets show that our model outperforms the current state-of-the-art approaches by a large margin on the task of link prediction. We also report a reduction in both the training time and model parameters compared to the existing hyperbolic approaches through a reformulated hyperbolic graph convolution. Furthermore, we illustrate the robustness of our model by experimenting with different levels of simulated noise in both the graph structure and text, and also, present a mechanism to explain TESH-GCN's prediction by analyzing the extracted metapaths.

XLCoST: A Benchmark Dataset for Cross-lingual Code Intelligence

Recent advances in machine learning have significantly improved the understanding of source code data and achieved good performance on a number of downstream tasks. Open source repositories like GitHub enable this process with rich unlabeled code data. However, the lack of high quality labeled data has largely hindered the progress of several code related tasks, such as program translation, summarization, synthesis, and code search. This paper introduces XLCoST, Cross-Lingual Code SnippeT dataset, a new benchmark dataset for cross-lingual code intelligence. Our dataset contains fine-grained parallel data from 8 languages (7 commonly used programming languages and English), and supports 10 cross-lingual code tasks. To the best of our knowledge, it is the largest parallel dataset for source code both in terms of size and the number of languages. We also provide the performance of several state-of-the-art baseline models for each task. We believe this new dataset can be a valuable asset for the research community and facilitate the development and validation of new methods for cross-lingual code intelligence.