Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.
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Engineering
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Learning
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大語言模型
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語言模型化
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The recent explosion in popularity of large language models (LLMs) has inspired learning engineers to incorporate them into adaptive educational tools that automatically score summary writing. Understanding and evaluating LLMs is vital before deploying them in critical learning environments, yet their unprecedented size and expanding number of parameters inhibits transparency and impedes trust when they underperform. Through a collaborative user-centered design process with several learning engineers building and deploying summary scoring LLMs, we characterized fundamental design challenges and goals around interpreting their models, including aggregating large text inputs, tracking score provenance, and scaling LLM interpretability methods. To address their concerns, we developed iScore, an interactive visual analytics tool for learning engineers to upload, score, and compare multiple summaries simultaneously. Tightly integrated views allow users to iteratively revise the language in summaries, track changes in the resulting LLM scores, and visualize model weights at multiple levels of abstraction. To validate our approach, we deployed iScore with three learning engineers over the course of a month. We present a case study where interacting with iScore led a learning engineer to improve their LLM's score accuracy by three percentage points. Finally, we conducted qualitative interviews with the learning engineers that revealed how iScore enabled them to understand, evaluate, and build trust in their LLMs during deployment.
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of large homo-oligomeric assemblies exhibit internal symmetry, posing a major challenge in structure determination. The performances of existing deep learning methods are limited since the symmetrical protein assembly usually has a long sequence, making structural computation infeasible. In addition, multiple identical subunits in symmetrical protein complex cause the issue of supervision ambiguity in label assignment, requiring a consistent structure modeling for the training. To tackle these problems, we propose a protein folding framework called SGNet to model protein-protein interactions in symmetrical assemblies. SGNet conducts feature extraction on a single subunit and generates the whole assembly using our proposed symmetry module, which largely mitigates computational problems caused by sequence length. Thanks to the elaborate design of modeling symmetry consistently, we can model all global symmetry types in quaternary protein structure prediction. Extensive experimental results on a benchmark of symmetrical protein complexes further demonstrate the effectiveness of our method.
We introduce AnyGPT, an any-to-any multimodal language model that utilizes discrete representations for the unified processing of various modalities, including speech, text, images, and music. AnyGPT can be trained stably without any alterations to the current large language model (LLM) architecture or training paradigms. Instead, it relies exclusively on data-level preprocessing, facilitating the seamless integration of new modalities into LLMs, akin to the incorporation of new languages. We build a multimodal text-centric dataset for multimodal alignment pre-training. Utilizing generative models, we synthesize the first large-scale any-to-any multimodal instruction dataset. It consists of 108k samples of multi-turn conversations that intricately interweave various modalities, thus equipping the model to handle arbitrary combinations of multimodal inputs and outputs. Experimental results demonstrate that AnyGPT is capable of facilitating any-to-any multimodal conversation while achieving performance comparable to specialized models across all modalities, proving that discrete representations can effectively and conveniently unify multiple modalities within a language model. Demos are shown in //junzhan2000.github.io/AnyGPT.github.io/
The field of pharmaceutical development and therapeutic application both face substantial challenges. Therapeutic domain calls for more treatment alternatives while numerous promising pre-clinical drugs fail in clinical trails. One of the reasons is the inadequacy of Cross-drug Response Evaluation (CRE) during the late stage of drug development. Although in-silico CRE models offer a solution to this problem, existing methodologies are either limited to early development stages or lack the capacity for a comprehensive CRE analysis. Herein, we introduce a novel computational model named DeepCRE and present the potential of DeepCRE in advancing therapeutic discovery and development. DeepCRE outperforms the existing best models by achieving an average performance improvement of 17.7\% in patient-level CRE, and a 5-fold increase in indication-level CRE. Furthermore, DeepCRE has identified six drug candidates that show significantly greater effectiveness than a comparator set of two approved drug in 5/8 colorectal cancer (CRC) organoids. This highlights DeepCRE's ability to identify a collection of drug candidates with superior therapeutic effects, underscoring its potential to revolutionize the field of therapeutic development.
Despite the vast repository of global medical knowledge predominantly being in English, local languages are crucial for delivering tailored healthcare services, particularly in areas with limited medical resources. To extend the reach of medical AI advancements to a broader population, we aim to develop medical LLMs across the six most widely spoken languages, encompassing a global population of 6.1 billion. This effort culminates in the creation of the ApolloCorpora multilingual medical dataset and the XMedBench benchmark. In the multilingual medical benchmark, the released Apollo models, at various relatively-small sizes (i.e., 0.5B, 1.8B, 2B, 6B, and 7B), achieve the best performance among models of equivalent size. Especially, Apollo-7B is the state-of-the-art multilingual medical LLMs up to 70B. Additionally, these lite models could be used to improve the multi-lingual medical capabilities of larger models without fine-tuning in a proxy-tuning fashion. We will open-source training corpora, code, model weights and evaluation benchmark.
Fine-grained control over large language models (LLMs) remains a significant challenge, hindering their adaptability to diverse user needs. While Reinforcement Learning from Human Feedback (RLHF) shows promise in aligning LLMs, its reliance on scalar rewards often limits its ability to capture diverse user preferences in real-world applications. To address this limitation, we introduce the Directional Preference Alignment (DPA) framework. Unlike the scalar-reward RLHF, DPA incorporates multi-objective reward modeling to represent diverse preference profiles. Additionally, DPA models user preferences as directions (i.e., unit vectors) in the reward space to achieve user-dependent preference control. Our method involves training a multi-objective reward model and then fine-tuning the LLM with a preference-conditioned variant of Rejection Sampling Finetuning (RSF), an RLHF method adopted by Llama 2. This method enjoys a better performance trade-off across various reward objectives. In comparison with the scalar-reward RLHF, DPA offers users intuitive control over LLM generation: they can arithmetically specify their desired trade-offs (e.g., more helpfulness with less verbosity). We also validate the effectiveness of DPA with real-world alignment experiments on Mistral-7B. Our method provides straightforward arithmetic control over the trade-off between helpfulness and verbosity while maintaining competitive performance with strong baselines such as Direct Preference Optimization (DPO).
In the rapidly evolving landscape of artificial intelligence (AI), generative large language models (LLMs) stand at the forefront, revolutionizing how we interact with our data. However, the computational intensity and memory consumption of deploying these models present substantial challenges in terms of serving efficiency, particularly in scenarios demanding low latency and high throughput. This survey addresses the imperative need for efficient LLM serving methodologies from a machine learning system (MLSys) research perspective, standing at the crux of advanced AI innovations and practical system optimizations. We provide in-depth analysis, covering a spectrum of solutions, ranging from cutting-edge algorithmic modifications to groundbreaking changes in system designs. The survey aims to provide a comprehensive understanding of the current state and future directions in efficient LLM serving, offering valuable insights for researchers and practitioners in overcoming the barriers of effective LLM deployment, thereby reshaping the future of AI.
Language model pre-training, such as BERT, has significantly improved the performances of many natural language processing tasks. However, pre-trained language models are usually computationally expensive and memory intensive, so it is difficult to effectively execute them on some resource-restricted devices. To accelerate inference and reduce model size while maintaining accuracy, we firstly propose a novel transformer distillation method that is a specially designed knowledge distillation (KD) method for transformer-based models. By leveraging this new KD method, the plenty of knowledge encoded in a large teacher BERT can be well transferred to a small student TinyBERT. Moreover, we introduce a new two-stage learning framework for TinyBERT, which performs transformer distillation at both the pre-training and task-specific learning stages. This framework ensures that TinyBERT can capture both the general-domain and task-specific knowledge of the teacher BERT. TinyBERT is empirically effective and achieves comparable results with BERT in GLUE datasets, while being 7.5x smaller and 9.4x faster on inference. TinyBERT is also significantly better than state-of-the-art baselines, even with only about 28% parameters and 31% inference time of baselines.
Pre-trained language representation models, such as BERT, capture a general language representation from large-scale corpora, but lack domain-specific knowledge. When reading a domain text, experts make inferences with relevant knowledge. For machines to achieve this capability, we propose a knowledge-enabled language representation model (K-BERT) with knowledge graphs (KGs), in which triples are injected into the sentences as domain knowledge. However, too much knowledge incorporation may divert the sentence from its correct meaning, which is called knowledge noise (KN) issue. To overcome KN, K-BERT introduces soft-position and visible matrix to limit the impact of knowledge. K-BERT can easily inject domain knowledge into the models by equipped with a KG without pre-training by-self because it is capable of loading model parameters from the pre-trained BERT. Our investigation reveals promising results in twelve NLP tasks. Especially in domain-specific tasks (including finance, law, and medicine), K-BERT significantly outperforms BERT, which demonstrates that K-BERT is an excellent choice for solving the knowledge-driven problems that require experts.
In order to answer natural language questions over knowledge graphs, most processing pipelines involve entity and relation linking. Traditionally, entity linking and relation linking has been performed either as dependent sequential tasks or independent parallel tasks. In this paper, we propose a framework called "EARL", which performs entity linking and relation linking as a joint single task. EARL uses a graph connection based solution to the problem. We model the linking task as an instance of the Generalised Travelling Salesman Problem (GTSP) and use GTSP approximate algorithm solutions. We later develop EARL which uses a pair-wise graph-distance based solution to the problem.The system determines the best semantic connection between all keywords of the question by referring to a knowledge graph. This is achieved by exploiting the "connection density" between entity candidates and relation candidates. The "connection density" based solution performs at par with the approximate GTSP solution.We have empirically evaluated the framework on a dataset with 5000 questions. Our system surpasses state-of-the-art scores for entity linking task by reporting an accuracy of 0.65 to 0.40 from the next best entity linker.
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