Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

The recent prevalence of publicly accessible, large medical imaging datasets has led to a proliferation of artificial intelligence (AI) models for cardiovascular image classification and analysis. At the same time, the potentially significant impacts of these models have motivated the development of a range of explainable AI (XAI) methods that aim to explain model predictions given certain image inputs. However, many of these methods are not developed or evaluated with domain experts, and explanations are not contextualized in terms of medical expertise or domain knowledge. In this paper, we propose a novel framework and python library, MiMICRI, that provides domain-centered counterfactual explanations of cardiovascular image classification models. MiMICRI helps users interactively select and replace segments of medical images that correspond to morphological structures. From the counterfactuals generated, users can then assess the influence of each segment on model predictions, and validate the model against known medical facts. We evaluate this library with two medical experts. Our evaluation demonstrates that a domain-centered XAI approach can enhance the interpretability of model explanations, and help experts reason about models in terms of relevant domain knowledge. However, concerns were also surfaced about the clinical plausibility of the counterfactuals generated. We conclude with a discussion on the generalizability and trustworthiness of the MiMICRI framework, as well as the implications of our findings on the development of domain-centered XAI methods for model interpretability in healthcare contexts.

We present a diachronic acoustic analysis of the voice of 1023 speakers from French media archives. The speakers are spread across 32 categories based on four periods (years 1955/56, 1975/76, 1995/96, 2015/16), four age groups (20-35; 36-50; 51-65, >65), and two genders. The fundamental frequency ($F_0$) and the first four formants (F1-4) were estimated. Procedures used to ensure the quality of these estimations on heterogeneous data are described. From each speaker's $F_0$ distribution, the base-$F_0$ value was calculated to estimate the register. Average vocal tract length was estimated from formant frequencies. Base-$F_0$ and vocal tract length were fit by linear mixed models to evaluate how they may have changed across time periods and genders, corrected for age effects. Results show an effect of the period with a tendency to lower voices, independently of gender. A lowering of pitch is observed with age for female but not male speakers.

Embedding models play a pivot role in modern NLP applications such as IR and RAG. While the context limit of LLMs has been pushed beyond 1 million tokens, embedding models are still confined to a narrow context window not exceeding 8k tokens, refrained from application scenarios requiring long inputs such as legal contracts. This paper explores context window extension of existing embedding models, pushing the limit to 32k without requiring additional training. First, we examine the performance of current embedding models for long context retrieval on our newly constructed LongEmbed benchmark. LongEmbed comprises two synthetic tasks and four carefully chosen real-world tasks, featuring documents of varying length and dispersed target information. Benchmarking results underscore huge room for improvement in these models. Based on this, comprehensive experiments show that training-free context window extension strategies like position interpolation can effectively extend the context window of existing embedding models by several folds, regardless of their original context being 512 or beyond 4k. Furthermore, for models employing absolute position encoding (APE), we show the possibility of further fine-tuning to harvest notable performance gains while strictly preserving original behavior for short inputs. For models using rotary position embedding (RoPE), significant enhancements are observed when employing RoPE-specific methods, such as NTK and SelfExtend, indicating RoPE's superiority over APE for context window extension. To facilitate future research, we release E5-Base-4k and E5-RoPE-Base, along with the LongEmbed benchmark.

Deep learning methods are increasingly becoming instrumental as modeling tools in computational neuroscience, employing optimality principles to build bridges between neural responses and perception or behavior. Developing models that adequately represent uncertainty is however challenging for deep learning methods, which often suffer from calibration problems. This constitutes a difficulty in particular when modeling cortical circuits in terms of Bayesian inference, beyond single point estimates such as the posterior mean or the maximum a posteriori. In this work we systematically studied uncertainty representations in latent representations of variational auto-encoders (VAEs), both in a perceptual task from natural images and in two other canonical tasks of computer vision, finding a poor alignment between uncertainty and informativeness or ambiguities in the images. We next showed how a novel approach which we call explaining-away variational auto-encoders (EA-VAEs), fixes these issues, producing meaningful reports of uncertainty in a variety of scenarios, including interpolation, image corruption, and even out-of-distribution detection. We show EA-VAEs may prove useful both as models of perception in computational neuroscience and as inference tools in computer vision.

Automated program repair (APR) has achieved promising results, especially using neural networks. Yet, the overwhelming majority of patches produced by APR tools are confined to one single location. When looking at the patches produced with neural repair, most of them fail to compile, while a few uncompilable ones go in the right direction. In both cases, the fundamental problem is to ignore the potential of partial patches. In this paper, we propose an iterative program repair paradigm called ITER founded on the concept of improving partial patches until they become plausible and correct. First, ITER iteratively improves partial single-location patches by fixing compilation errors and further refining the previously generated code. Second, ITER iteratively improves partial patches to construct multi-location patches, with fault localization re-execution. ITER is implemented for Java based on battle-proven deep neural networks and code representation. ITER is evaluated on 476 bugs from 10 open-source projects in Defects4J 2.0. ITER succeeds in repairing 15.5% of them, including 9 uniquely repaired multi-location bugs.

Deep neural networks are largely used for complex prediction tasks. There is plenty of empirical evidence of their successful end-to-end training for a diversity of tasks. Success is often measured based solely on the final performance of the trained network, and explanations on when, why and how they work are less emphasized. In this paper we study encoder-decoder recurrent neural networks with attention mechanisms for the task of reading handwritten chess scoresheets. Rather than prediction performance, our concern is to better understand how learning occurs in these type of networks. We characterize the task in terms of three subtasks, namely input-output alignment, sequential pattern recognition, and handwriting recognition, and experimentally investigate which factors affect their learning. We identify competition, collaboration and dependence relations between the subtasks, and argue that such knowledge might help one to better balance factors to properly train a network.

In recent times, there has been a growing interest in utilizing personalized large models on low-spec devices, such as mobile and CPU-only devices. However, utilizing a personalized large model in the on-device is inefficient, and sometimes limited due to computational cost. To tackle the problem, this paper presents the weights separation method to minimize on-device model weights using parameter-efficient fine-tuning methods. Moreover, some people speak multiple languages in an utterance, as known as code-switching, the personalized ASR model is necessary to address such cases. However, current multilingual speech recognition models are limited to recognizing a single language within each utterance. To tackle this problem, we propose code-switching speech recognition models that incorporate fine-tuned monolingual and multilingual speech recognition models. Additionally, we introduce a gated low-rank adaptation(GLoRA) for parameter-efficient fine-tuning with minimal performance degradation. Our experiments, conducted on Korean-English code-switching datasets, demonstrate that fine-tuning speech recognition models for code-switching surpasses the performance of traditional code-switching speech recognition models trained from scratch. Furthermore, GLoRA enhances parameter-efficient fine-tuning performance compared to conventional LoRA.

A graph is a fundamental data model to represent various entities and their complex relationships in society and nature, such as social networks, transportation networks, financial networks, and biomedical systems. Recently, large language models (LLMs) have showcased a strong generalization ability to handle various NLP and multi-mode tasks to answer users' arbitrary questions and specific-domain content generation. Compared with graph learning models, LLMs enjoy superior advantages in addressing the challenges of generalizing graph tasks by eliminating the need for training graph learning models and reducing the cost of manual annotation. In this survey, we conduct a comprehensive investigation of existing LLM studies on graph data, which summarizes the relevant graph analytics tasks solved by advanced LLM models and points out the existing remaining challenges and future directions. Specifically, we study the key problems of LLM-based generative graph analytics (LLM-GGA) with three categories: LLM-based graph query processing (LLM-GQP), LLM-based graph inference and learning (LLM-GIL), and graph-LLM-based applications. LLM-GQP focuses on an integration of graph analytics techniques and LLM prompts, including graph understanding and knowledge graph (KG) based augmented retrieval, while LLM-GIL focuses on learning and reasoning over graphs, including graph learning, graph-formed reasoning and graph representation. We summarize the useful prompts incorporated into LLM to handle different graph downstream tasks. Moreover, we give a summary of LLM model evaluation, benchmark datasets/tasks, and a deep pro and cons analysis of LLM models. We also explore open problems and future directions in this exciting interdisciplinary research area of LLMs and graph analytics.

This paper presents a software allowing to describe voices using a continuous Voice Femininity Percentage (VFP). This system is intended for transgender speakers during their voice transition and for voice therapists supporting them in this process. A corpus of 41 French cis- and transgender speakers was recorded. A perceptual evaluation allowed 57 participants to estimate the VFP for each voice. Binary gender classification models were trained on external gender-balanced data and used on overlapping windows to obtain average gender prediction estimates, which were calibrated to predict VFP and obtained higher accuracy than $F_0$ or vocal track length-based models. Training data speaking style and DNN architecture were shown to impact VFP estimation. Accuracy of the models was affected by speakers' age. This highlights the importance of style, age, and the conception of gender as binary or not, to build adequate statistical representations of cultural concepts.