MeNTi: Bridging Medical Calculator and LLM Agent with Nested Tool Calling

Integrating tools into Large Language Models (LLMs) has facilitated the widespread application. Despite this, in specialized downstream task contexts, reliance solely on tools is insufficient to fully address the complexities of the real world. This particularly restricts the effective deployment of LLMs in fields such as medicine. In this paper, we focus on the downstream tasks of medical calculators, which use standardized tests to assess an individual's health status. We introduce MeNTi, a universal agent architecture for LLMs. MeNTi integrates a specialized medical toolkit and employs meta-tool and nested calling mechanisms to enhance LLM tool utilization. Specifically, it achieves flexible tool selection and nested tool calling to address practical issues faced in intricate medical scenarios, including calculator selection, slot filling, and unit conversion. To assess the capabilities of LLMs for quantitative assessment throughout the clinical process of calculator scenarios, we introduce CalcQA. This benchmark requires LLMs to use medical calculators to perform calculations and assess patient health status. CalcQA is constructed by professional physicians and includes 100 case-calculator pairs, complemented by a toolkit of 281 medical tools. The experimental results demonstrate significant performance improvements with our framework. This research paves new directions for applying LLMs in demanding scenarios of medicine.

DeReStainer: H&E to IHC Pathological Image Translation via Decoupled Staining Channels

Breast cancer is a highly fatal disease among cancers in women, and early detection is crucial for treatment. HER2 status, a valuable diagnostic marker based on Immunohistochemistry (IHC) staining, is instrumental in determining breast cancer status. The high cost of IHC staining and the ubiquity of Hematoxylin and Eosin (H&E) staining make the conversion from H&E to IHC staining essential. In this article, we propose a destain-restain framework for converting H&E staining to IHC staining, leveraging the characteristic that H&E staining and IHC staining of the same tissue sections share the Hematoxylin channel. We further design loss functions specifically for Hematoxylin and Diaminobenzidin (DAB) channels to generate IHC images exploiting insights from separated staining channels. Beyond the benchmark metrics on BCI contest, we have developed semantic information metrics for the HER2 level. The experimental results demonstrated that our method outperforms previous open-sourced methods in terms of image intrinsic property and semantic information.

TBA: Faster Large Language Model Training Using SSD-Based Activation Offloading

The growth rate of the GPU memory capacity has not been able to keep up with that of the size of large language models (LLMs), hindering the model training process. In particular, activations -- the intermediate tensors produced during forward propagation and reused in backward propagation -- dominate the GPU memory use. To address this challenge, we propose TBA to efficiently offload activations to high-capacity NVMe SSDs. This approach reduces GPU memory usage without impacting performance by adaptively overlapping data transfers with computation. TBA is compatible with popular deep learning frameworks like PyTorch, Megatron, and DeepSpeed, and it employs techniques such as tensor deduplication, forwarding, and adaptive offloading to further enhance efficiency. We conduct extensive experiments on GPT, BERT, and T5. Results demonstrate that TBA effectively reduces 47% of the activation peak memory usage. At the same time, TBA perfectly overlaps the I/O with the computation and incurs negligible performance overhead. We introduce the recompute-offload-keep (ROK) curve to compare the TBA offloading with other two tensor placement strategies, keeping activations in memory and layerwise full recomputation. We find that TBA achieves better memory savings than layerwise full recomputation while retaining the performance of keeping the activations in memory.

MedOdyssey: A Medical Domain Benchmark for Long Context Evaluation Up to 200K Tokens

Numerous advanced Large Language Models (LLMs) now support context lengths up to 128K, and some extend to 200K. Some benchmarks in the generic domain have also followed up on evaluating long-context capabilities. In the medical domain, tasks are distinctive due to the unique contexts and need for domain expertise, necessitating further evaluation. However, despite the frequent presence of long texts in medical scenarios, evaluation benchmarks of long-context capabilities for LLMs in this field are still rare. In this paper, we propose MedOdyssey, the first medical long-context benchmark with seven length levels ranging from 4K to 200K tokens. MedOdyssey consists of two primary components: the medical-context "needles in a haystack" task and a series of tasks specific to medical applications, together comprising 10 datasets. The first component includes challenges such as counter-intuitive reasoning and novel (unknown) facts injection to mitigate knowledge leakage and data contamination of LLMs. The second component confronts the challenge of requiring professional medical expertise. Especially, we design the ``Maximum Identical Context'' principle to improve fairness by guaranteeing that different LLMs observe as many identical contexts as possible. Our experiment evaluates advanced proprietary and open-source LLMs tailored for processing long contexts and presents detailed performance analyses. This highlights that LLMs still face challenges and need for further research in this area. Our code and data are released in the repository: \url{https://github.com/JOHNNY-fans/MedOdyssey.}

New Solutions on LLM Acceleration, Optimization, and Application

Large Language Models (LLMs) have become extremely potent instruments with exceptional capacities for comprehending and producing human-like text in a wide range of applications. However, the increasing size and complexity of LLMs present significant challenges in both training and deployment, leading to substantial computational and storage costs as well as heightened energy consumption. In this paper, we provide a review of recent advancements and research directions aimed at addressing these challenges and enhancing the efficiency of LLM-based systems. We begin by discussing algorithm-level acceleration techniques focused on optimizing LLM inference speed and resource utilization. We also explore LLM-hardware co-design strategies with a vision to improve system efficiency by tailoring hardware architectures to LLM requirements. Further, we delve into LLM-to-accelerator compilation approaches, which involve customizing hardware accelerators for efficient LLM deployment. Finally, as a case study to leverage LLMs for assisting circuit design, we examine LLM-aided design methodologies for an important task: High-Level Synthesis (HLS) functional verification, by creating a new dataset that contains a large number of buggy and bug-free codes, which can be essential for training LLMs to specialize on HLS verification and debugging. For each aspect mentioned above, we begin with a detailed background study, followed by the presentation of several novel solutions proposed to overcome specific challenges. We then outline future research directions to drive further advancements. Through these efforts, we aim to pave the way for more efficient and scalable deployment of LLMs across a diverse range of applications.

SyntheT2C: Generating Synthetic Data for Fine-Tuning Large Language Models on the Text2Cypher Task

Integrating Large Language Models (LLMs) with existing Knowledge Graph (KG) databases presents a promising avenue for enhancing LLMs' efficacy and mitigating their "hallucinations". Given that most KGs reside in graph databases accessible solely through specialized query languages (e.g., Cypher), there exists a critical need to bridge the divide between LLMs and KG databases by automating the translation of natural language into Cypher queries (commonly termed the "Text2Cypher" task). Prior efforts tried to bolster LLMs' proficiency in Cypher generation through Supervised Fine-Tuning. However, these explorations are hindered by the lack of annotated datasets of Query-Cypher pairs, resulting from the labor-intensive and domain-specific nature of annotating such datasets. In this study, we propose SyntheT2C, a methodology for constructing a synthetic Query-Cypher pair dataset, comprising two distinct pipelines: (1) LLM-based prompting and (2) template-filling. SyntheT2C facilitates the generation of extensive Query-Cypher pairs with values sampled from an underlying Neo4j graph database. Subsequently, SyntheT2C is applied to two medical databases, culminating in the creation of a synthetic dataset, MedT2C. Comprehensive experiments demonstrate that the MedT2C dataset effectively enhances the performance of backbone LLMs on the Text2Cypher task. Both the SyntheT2C codebase and the MedT2C dataset will be released soon.

CAT: Coordinating Anatomical-Textual Prompts for Multi-Organ and Tumor Segmentation

Existing promptable segmentation methods in the medical imaging field primarily consider either textual or visual prompts to segment relevant objects, yet they often fall short when addressing anomalies in medical images, like tumors, which may vary greatly in shape, size, and appearance. Recognizing the complexity of medical scenarios and the limitations of textual or visual prompts, we propose a novel dual-prompt schema that leverages the complementary strengths of visual and textual prompts for segmenting various organs and tumors. Specifically, we introduce CAT, an innovative model that Coordinates Anatomical prompts derived from 3D cropped images with Textual prompts enriched by medical domain knowledge. The model architecture adopts a general query-based design, where prompt queries facilitate segmentation queries for mask prediction. To synergize two types of prompts within a unified framework, we implement a ShareRefiner, which refines both segmentation and prompt queries while disentangling the two types of prompts. Trained on a consortium of 10 public CT datasets, CAT demonstrates superior performance in multiple segmentation tasks. Further validation on a specialized in-house dataset reveals the remarkable capacity of segmenting tumors across multiple cancer stages. This approach confirms that coordinating multimodal prompts is a promising avenue for addressing complex scenarios in the medical domain.

ShiftAddLLM: Accelerating Pretrained LLMs via Post-Training Multiplication-Less Reparameterization

Large language models (LLMs) have shown impressive performance on language tasks but face challenges when deployed on resource-constrained devices due to their extensive parameters and reliance on dense multiplications, resulting in high memory demands and latency bottlenecks. Shift-and-add reparameterization offers a promising solution by replacing costly multiplications with hardware-friendly primitives in both the attention and multi-layer perceptron (MLP) layers of an LLM. However, current reparameterization techniques require training from scratch or full parameter fine-tuning to restore accuracy, which is resource-intensive for LLMs. To address this, we propose accelerating pretrained LLMs through post-training shift-and-add reparameterization, creating efficient multiplication-free models, dubbed ShiftAddLLM. Specifically, we quantize each weight matrix into binary matrices paired with group-wise scaling factors. The associated multiplications are reparameterized into (1) shifts between activations and scaling factors and (2) queries and adds according to the binary matrices. To reduce accuracy loss, we present a multi-objective optimization method to minimize both weight and output activation reparameterization errors. Additionally, based on varying sensitivity across layers to reparameterization, we develop an automated bit allocation strategy to further reduce memory usage and latency. Experiments on five LLM families and eight tasks consistently validate the effectiveness of ShiftAddLLM, achieving average perplexity improvements of 5.6 and 22.7 points at comparable or lower latency compared to the most competitive quantized LLMs at 3 and 2 bits, respectively, and more than 80% memory and energy reductions over the original LLMs. Codes and models are available at https://github.com/GATECH-EIC/ShiftAddLLM.

Mix-of-Granularity: Optimize the Chunking Granularity for Retrieval-Augmented Generation

Integrating information from different reference data sources is a major challenge for Retrieval-Augmented Generation (RAG) systems because each knowledge source adopts a unique data structure and follows different conventions. Retrieving from multiple knowledge sources with one fixed strategy usually leads to under-exploitation of information. To mitigate this drawback, inspired by Mix-of-Expert, we introduce Mix-of-Granularity (MoG), a method that dynamically determines the optimal granularity of a knowledge database based on input queries using a router. The router is efficiently trained with a newly proposed loss function employing soft labels. We further extend MoG to Mix-of-Granularity-Graph (MoGG), where reference documents are pre-processed into graphs, enabling the retrieval of relevant information from distantly situated chunks. Extensive experiments demonstrate that both MoG and MoGG effectively predict optimal granularity levels, significantly enhancing the performance of the RAG system in downstream tasks. The code of both MoG and MoGG will be made public.

Incorporating Clinical Guidelines through Adapting Multi-modal Large Language Model for Prostate Cancer PI-RADS Scoring

The Prostate Imaging Reporting and Data System (PI-RADS) is pivotal in the diagnosis of clinically significant prostate cancer through MRI imaging. Current deep learning-based PI-RADS scoring methods often lack the incorporation of essential PI-RADS clinical guidelines~(PICG) utilized by radiologists, potentially compromising scoring accuracy. This paper introduces a novel approach that adapts a multi-modal large language model (MLLM) to incorporate PICG into PI-RADS scoring without additional annotations and network parameters. We present a two-stage fine-tuning process aimed at adapting MLLMs originally trained on natural images to the MRI data domain while effectively integrating the PICG. In the first stage, we develop a domain adapter layer specifically tailored for processing 3D MRI image inputs and design the MLLM instructions to differentiate MRI modalities effectively. In the second stage, we translate PICG into guiding instructions for the model to generate PICG-guided image features. Through feature distillation, we align scoring network features with the PICG-guided image feature, enabling the scoring network to effectively incorporate the PICG information. We develop our model on a public dataset and evaluate it in a real-world challenging in-house dataset. Experimental results demonstrate that our approach improves the performance of current scoring networks.