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Adaptive gradient algorithms have been widely adopted in training large-scale deep neural networks, especially large foundation models. Despite their huge success in practice, their theoretical advantages over stochastic gradient descent (SGD) have not been fully understood, especially in the large batch-size setting commonly used in practice. This is because the only theoretical result that can demonstrate the benefit of Adagrad over SGD was obtained in the original paper of Adagrad for nonsmooth objective functions. However, for nonsmooth objective functions, there can be a linear slowdown of convergence when batch size increases, and thus a convergence analysis based on nonsmooth assumption cannot be used for large batch algorithms. In this work, we resolve this gap between theory and practice by providing a new analysis of Adagrad on both convex and nonconvex smooth objectives suitable for the large batch setting. It is shown that under the anisotropic smoothness and noise conditions, increased batch size does not slow down convergence for Adagrad, and thus it can still achieve a faster convergence guarantee over SGD even in the large batch setting. We present detailed comparisons between SGD and Adagrad to provide a better understanding of the benefits of adaptive gradient methods. Experiments in logistic regression and instruction following fine-tuning tasks provide strong evidence to support our theoretical analysis.

In clinical dictation, utterances after automatic speech recognition (ASR) without explicit punctuation marks may lead to the misunderstanding of dictated reports. To give a precise and understandable clinical report with ASR, automatic punctuation restoration is required. Considering a practical scenario, we propose a fast and light pre-trained model for Chinese medical punctuation restoration based on 'pretraining and fine-tuning' paradigm. In this work, we distill pre-trained models by incorporating supervised contrastive learning and a novel auxiliary pre-training task (Punctuation Mark Prediction) to make it well-suited for punctuation restoration. Our experiments on various distilled models reveal that our model can achieve 95% performance while 10% model size relative to state-of-the-art Chinese RoBERTa.

Robotic assistance for experimental manipulation in the life sciences is expected to enable favorable outcomes, regardless of the skill of the scientist. Experimental specimens in the life sciences are subject to individual variability hence require intricate algorithms for successful autonomous robotic control. As a use case, we are studying the creation of cranial windows in mice. This operation requires the removal of an 8-mm-circular patch of the skull, which is approximately 300 um thick, but the shape and thickness of the mouse skull significantly varies depending on the strain of mouse, sex, and age. In this work, we propose an autonomous robotic drilling method with no offline planning, consisting of a trajectory planning block with execution-time feedback with completion level recognition based on image and force information. The force information allows for completion-level resolution to increase 10 fold. We evaluate the proposed method in two ways. First, in an eggshell drilling task and achieved a success rate of 95% and average drilling time of 7.1 min out of 20 trials. Second, in postmortem mice and with a success rate of 70% and average drilling time of 9.3 min out of 20 trials.

In this evolving era of machine learning security, membership inference attacks have emerged as a potent threat to the confidentiality of sensitive data. In this attack, adversaries aim to determine whether a particular point was used during the training of a target model. This paper proposes a new method to gauge a data point's membership in a model's training set. Instead of correlating loss with membership, as is traditionally done, we have leveraged the fact that training examples generally exhibit higher confidence values when classified into their actual class. During training, the model is essentially being 'fit' to the training data and might face particular difficulties in generalization to unseen data. This asymmetry leads to the model achieving higher confidence on the training data as it exploits the specific patterns and noise present in the training data. Our proposed approach leverages the confidence values generated by the machine learning model. These confidence values provide a probabilistic measure of the model's certainty in its predictions and can further be used to infer the membership of a given data point. Additionally, we also introduce another variant of our method that allows us to carry out this attack without knowing the ground truth(true class) of a given data point, thus offering an edge over existing label-dependent attack methods.

Recent strides in automatic speech recognition (ASR) have accelerated their application in the medical domain where their performance on accented medical named entities (NE) such as drug names, diagnoses, and lab results, is largely unknown. We rigorously evaluate multiple ASR models on a clinical English dataset of 93 African accents. Our analysis reveals that despite some models achieving low overall word error rates (WER), errors in clinical entities are higher, potentially posing substantial risks to patient safety. To empirically demonstrate this, we extract clinical entities from transcripts, develop a novel algorithm to align ASR predictions with these entities, and compute medical NE Recall, medical WER, and character error rate. Our results show that fine-tuning on accented clinical speech improves medical WER by a wide margin (25-34 % relative), improving their practical applicability in healthcare environments.

Medicinal synergy prediction is a powerful tool in drug discovery and development that harnesses the principles of combination therapy to enhance therapeutic outcomes by improving efficacy, reducing toxicity, and preventing drug resistance. While a myriad of computational methods has emerged for predicting synergistic drug combinations, a large portion of them may overlook the intricate, yet critical relationships between various entities in drug interaction networks, such as drugs, cell lines, and diseases. These relationships are complex and multidimensional, requiring sophisticated modeling to capture nuanced interplay that can significantly influence therapeutic efficacy. We introduce a salient deep hypergraph learning method, namely, Heterogeneous Entity Representation for MEdicinal Synergy prediction (HERMES), to predict anti-cancer drug synergy. HERMES integrates heterogeneous data sources, encompassing drug, cell line, and disease information, to provide a comprehensive understanding of the interactions involved. By leveraging advanced hypergraph neural networks with gated residual mechanisms, HERMES can effectively learn complex relationships/interactions within the data. Our results show HERMES demonstrates state-of-the-art performance, particularly in forecasting new drug combinations, significantly surpassing previous methods. This advancement underscores the potential of HERMES to facilitate more effective and precise drug combination predictions, thereby enhancing the development of novel therapeutic strategies.

Recent strides in neural speech synthesis technologies, while enjoying widespread applications, have nonetheless introduced a series of challenges, spurring interest in the defence against the threat of misuse and abuse. Notably, source attribution of synthesized speech has value in forensics and intellectual property protection, but prior work in this area has certain limitations in scope. To address the gaps, we present our findings concerning the identification of the sources of synthesized speech in this paper. We investigate the existence of speech synthesis model fingerprints in the generated speech waveforms, with a focus on the acoustic model and the vocoder, and study the influence of each component on the fingerprint in the overall speech waveforms. Our research, conducted using the multi-speaker LibriTTS dataset, demonstrates two key insights: (1) vocoders and acoustic models impart distinct, model-specific fingerprints on the waveforms they generate, and (2) vocoder fingerprints are the more dominant of the two, and may mask the fingerprints from the acoustic model. These findings strongly suggest the existence of model-specific fingerprints for both the acoustic model and the vocoder, highlighting their potential utility in source identification applications.

Estimating the counterfactual outcome of treatment is essential for decision-making in public health and clinical science, among others. Often, treatments are administered in a sequential, time-varying manner, leading to an exponentially increased number of possible counterfactual outcomes. Furthermore, in modern applications, the outcomes are high-dimensional and conventional average treatment effect estimation fails to capture disparities in individuals. To tackle these challenges, we propose a novel conditional generative framework capable of producing counterfactual samples under time-varying treatment, without the need for explicit density estimation. Our method carefully addresses the distribution mismatch between the observed and counterfactual distributions via a loss function based on inverse probability re-weighting, and supports integration with state-of-the-art conditional generative models such as the guided diffusion and conditional variational autoencoder. We present a thorough evaluation of our method using both synthetic and real-world data. Our results demonstrate that our method is capable of generating high-quality counterfactual samples and outperforms the state-of-the-art baselines.

Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.

The amount of publicly available biomedical literature has been growing rapidly in recent years, yet question answering systems still struggle to exploit the full potential of this source of data. In a preliminary processing step, many question answering systems rely on retrieval models for identifying relevant documents and passages. This paper proposes a weighted cosine distance retrieval scheme based on neural network word embeddings. Our experiments are based on publicly available data and tasks from the BioASQ biomedical question answering challenge and demonstrate significant performance gains over a wide range of state-of-the-art models.