Enhancing Audiovisual Speech Recognition through Bifocal Preference Optimization

Audiovisual Automatic Speech Recognition (AV-ASR) aims to improve speech recognition accuracy by leveraging visual signals. It is particularly challenging in unconstrained real-world scenarios across various domains due to noisy acoustic environments, spontaneous speech, and the uncertain use of visual information. Most previous works fine-tune audio-only ASR models on audiovisual datasets, optimizing them for conventional ASR objectives. However, they often neglect visual features and common errors in unconstrained video scenarios. In this paper, we propose using a preference optimization strategy to improve speech recognition accuracy for real-world videos. First, we create preference data via simulating common errors that occurred in AV-ASR from two focals: manipulating the audio or vision input and rewriting the output transcript. Second, we propose BPO-AVASR, a Bifocal Preference Optimization method to improve AV-ASR models by leveraging both input-side and output-side preference. Extensive experiments demonstrate that our approach significantly improves speech recognition accuracy across various domains, outperforming previous state-of-the-art models on real-world video speech recognition.

Semi-Supervised Learning from Small Annotated Data and Large Unlabeled Data for Fine-grained PICO Entity Recognition

Objective: Extracting PICO elements -- Participants, Intervention, Comparison, and Outcomes -- from clinical trial literature is essential for clinical evidence retrieval, appraisal, and synthesis. Existing approaches do not distinguish the attributes of PICO entities. This study aims to develop a named entity recognition (NER) model to extract PICO entities with fine granularities. Materials and Methods: Using a corpus of 2,511 abstracts with PICO mentions from 4 public datasets, we developed a semi-supervised method to facilitate the training of a NER model, FinePICO, by combining limited annotated data of PICO entities and abundant unlabeled data. For evaluation, we divided the entire dataset into two subsets: a smaller group with annotations and a larger group without annotations. We then established the theoretical lower and upper performance bounds based on the performance of supervised learning models trained solely on the small, annotated subset and on the entire set with complete annotations, respectively. Finally, we evaluated FinePICO on both the smaller annotated subset and the larger, initially unannotated subset. We measured the performance of FinePICO using precision, recall, and F1. Results: Our method achieved precision/recall/F1 of 0.567/0.636/0.60, respectively, using a small set of annotated samples, outperforming the baseline model (F1: 0.437) by more than 16\%. The model demonstrates generalizability to a different PICO framework and to another corpus, which consistently outperforms the benchmark in diverse experimental settings (p-value \textless0.001). Conclusion: This study contributes a generalizable and effective semi-supervised approach to named entity recognition leveraging large unlabeled data together with small, annotated data. It also initially supports fine-grained PICO extraction.

KunServe: Elastic and Efficient Large Language Model Serving with Parameter-centric Memory Management

The stateful nature of large language model (LLM) servingcan easily throttle precious GPU memory under load burstor long-generation requests like chain-of-thought reasoning,causing latency spikes due to queuing incoming requests. However, state-of-the-art KVCache centric approaches handleload spikes by dropping, migrating, or swapping KVCache,which faces an essential tradeoff between the performance ofongoing vs. incoming requests and thus still severely violatesSLO.This paper makes a key observation such that model param-eters are independent of the requests and are replicated acrossGPUs, and thus proposes a parameter-centric approach byselectively dropping replicated parameters to leave preciousmemory for requests. However, LLM requires KVCache tobe saved in bound with model parameters and thus droppingparameters can cause either huge computation waste or longnetwork delay, affecting all ongoing requests. Based on the ob-servation that attention operators can be decoupled from otheroperators, this paper further proposes a novel remote attentionmechanism through pipeline parallelism so as to serve up-coming requests with the additional memory borrowed fromparameters on remote GPUs. This paper further addresses sev-eral other challenges including lively exchanging KVCachewith incomplete parameters, generating an appropriate planthat balances memory requirements with cooperative exe-cution overhead, and seamlessly restoring parameters whenthe throttling has gone. Evaluations show thatKUNSERVEreduces the tail TTFT of requests under throttling by up to 27.3x compared to the state-of-the-art.

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models

While holding great promise for improving and facilitating healthcare, large language models (LLMs) struggle to produce up-to-date responses on evolving topics due to outdated knowledge or hallucination. Retrieval-augmented generation (RAG) is a pivotal innovation that improves the accuracy and relevance of LLM responses by integrating LLMs with a search engine and external sources of knowledge. However, the quality of RAG responses can be largely impacted by the rank and density of key information in the retrieval results, such as the "lost-in-the-middle" problem. In this work, we aim to improve the robustness and reliability of the RAG workflow in the medical domain. Specifically, we propose a map-reduce strategy, BriefContext, to combat the "lost-in-the-middle" issue without modifying the model weights. We demonstrated the advantage of the workflow with various LLM backbones and on multiple QA datasets. This method promises to improve the safety and reliability of LLMs deployed in healthcare domains.

Deciphering genomic codes using advanced NLP techniques: a scoping review

Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large Language Models (LLMs) and transformer architectures, in deciphering genomic codes, focusing on tokenization, transformer models, and regulatory annotation prediction. The goal of this review is to assess data and model accessibility in the most recent literature, gaining a better understanding of the existing capabilities and constraints of these tools in processing genomic sequencing data. Methods: Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, our scoping review was conducted across PubMed, Medline, Scopus, Web of Science, Embase, and ACM Digital Library. Studies were included if they focused on NLP methodologies applied to genomic sequencing data analysis, without restrictions on publication date or article type. Results: A total of 26 studies published between 2021 and April 2024 were selected for review. The review highlights that tokenization and transformer models enhance the processing and understanding of genomic data, with applications in predicting regulatory annotations like transcription-factor binding sites and chromatin accessibility. Discussion: The application of NLP and LLMs to genomic sequencing data interpretation is a promising field that can help streamline the processing of large-scale genomic data while also providing a better understanding of its complex structures. It has the potential to drive advancements in personalized medicine by offering more efficient and scalable solutions for genomic analysis. Further research is also needed to discuss and overcome current limitations, enhancing model transparency and applicability.

Suicide Risk Assessment on Social Media with Semi-Supervised Learning

With social media communities increasingly becoming places where suicidal individuals post and congregate, natural language processing presents an exciting avenue for the development of automated suicide risk assessment systems. However, past efforts suffer from a lack of labeled data and class imbalances within the available labeled data. To accommodate this task's imperfect data landscape, we propose a semi-supervised framework that leverages labeled (n=500) and unlabeled (n=1,500) data and expands upon the self-training algorithm with a novel pseudo-label acquisition process designed to handle imbalanced datasets. To further ensure pseudo-label quality, we manually verify a subset of the pseudo-labeled data that was not predicted unanimously across multiple trials of pseudo-label generation. We test various models to serve as the backbone for this framework, ultimately deciding that RoBERTa performs the best. Ultimately, by leveraging partially validated pseudo-labeled data in addition to ground-truth labeled data, we substantially improve our model's ability to assess suicide risk from social media posts.

Demystifying Large Language Models for Medicine: A Primer

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

VoiceTextBlender: Augmenting Large Language Models with Speech Capabilities via Single-Stage Joint Speech-Text Supervised Fine-Tuning

Recent studies have augmented large language models (LLMs) with speech capabilities, leading to the development of speech language models (SpeechLMs). Earlier SpeechLMs focused on single-turn speech-based question answering (QA), where user input comprised a speech context and a text question. More recent studies have extended this to multi-turn conversations, though they often require complex, multi-stage supervised fine-tuning (SFT) with diverse data. Another critical challenge with SpeechLMs is catastrophic forgetting-where models optimized for speech tasks suffer significant degradation in text-only performance. To mitigate these issues, we propose a novel single-stage joint speech-text SFT approach on the low-rank adaptation (LoRA) of the LLM backbone. Our joint SFT combines text-only SFT data with three types of speech-related data: speech recognition and translation, speech-based QA, and mixed-modal SFT. Compared to previous SpeechLMs with 7B or 13B parameters, our 3B model demonstrates superior performance across various speech benchmarks while preserving the original capabilities on text-only tasks. Furthermore, our model shows emergent abilities of effectively handling previously unseen prompts and tasks, including multi-turn, mixed-modal inputs.

DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization

Sharing protected health information (PHI) is critical for furthering biomedical research. Before data can be distributed, practitioners often perform deidentification to remove any PHI contained in the text. Contemporary deidentification methods are evaluated on highly saturated datasets (tools achieve near-perfect accuracy) which may not reflect the full variability or complexity of real-world clinical text and annotating them is resource intensive, which is a barrier to real-world applications. To address this gap, we developed an adversarial approach using a large language model (LLM) to re-identify the patient corresponding to a redacted clinical note and evaluated the performance with a novel De-Identification/Re-Identification (DIRI) method. Our method uses a large language model to reidentify the patient corresponding to a redacted clinical note. We demonstrate our method on medical data from Weill Cornell Medicine anonymized with three deidentification tools: rule-based Philter and two deep-learning-based models, BiLSTM-CRF and ClinicalBERT. Although ClinicalBERT was the most effective, masking all identified PII, our tool still reidentified 9% of clinical notes Our study highlights significant weaknesses in current deidentification technologies while providing a tool for iterative development and improvement.

Enhancing disease detection in radiology reports through fine-tuning lightweight LLM on weak labels

Despite significant progress in applying large language models (LLMs) to the medical domain, several limitations still prevent them from practical applications. Among these are the constraints on model size and the lack of cohort-specific labeled datasets. In this work, we investigated the potential of improving a lightweight LLM, such as Llama 3.1-8B, through fine-tuning with datasets using synthetic labels. Two tasks are jointly trained by combining their respective instruction datasets. When the quality of the task-specific synthetic labels is relatively high (e.g., generated by GPT4- o), Llama 3.1-8B achieves satisfactory performance on the open-ended disease detection task, with a micro F1 score of 0.91. Conversely, when the quality of the task-relevant synthetic labels is relatively low (e.g., from the MIMIC-CXR dataset), fine-tuned Llama 3.1-8B is able to surpass its noisy teacher labels (micro F1 score of 0.67 v.s. 0.63) when calibrated against curated labels, indicating the strong inherent underlying capability of the model. These findings demonstrate the potential of fine-tuning LLMs with synthetic labels, offering a promising direction for future research on LLM specialization in the medical domain.