Da Ma

Liangtai Sun, Yang Han, Zihan Zhao et al.

Recently, there has been growing interest in using Large Language Models (LLMs) for scientific research. Numerous benchmarks have been proposed to evaluate the ability of LLMs for scientific research. However, current benchmarks are mostly based on pre-collected objective questions. This design suffers from data leakage problem and lacks the evaluation of subjective Q/A ability. In this paper, we propose SciEval, a comprehensive and multi-disciplinary evaluation benchmark to address these issues. Based on Bloom's taxonomy, SciEval covers four dimensions to systematically evaluate scientific research ability. In particular, we design a "dynamic" subset based on scientific principles to prevent evaluation from potential data leakage. Both objective and subjective questions are included in SciEval. These characteristics make SciEval a more effective benchmark for scientific research ability evaluation of LLMs. Comprehensive experiments on most advanced LLMs show that, although GPT-4 achieves SOTA performance compared to other LLMs, there is still substantial room for improvement, especially for dynamic questions. The codes and data are publicly available on https://github.com/OpenDFM/SciEval.

Ghazal Mirabnahrazam, Da Ma, Cédric Beaulac et al.

Dementia of Alzheimer's Type (DAT) is a complex disorder influenced by numerous factors, but it is unclear how each factor contributes to disease progression. An in-depth examination of these factors may yield an accurate estimate of time-to-conversion to DAT for patients at various disease stages. We used 401 subjects with 63 features from MRI, genetic, and CDC (Cognitive tests, Demographic, and CSF) data modalities in the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We used a deep learning-based survival analysis model that extends the classic Cox regression model to predict time-to-conversion to DAT. Our findings showed that genetic features contributed the least to survival analysis, while CDC features contributed the most. Combining MRI and genetic features improved survival prediction over using either modality alone, but adding CDC to any combination of features only worked as well as using only CDC features. Consequently, our study demonstrated that using the current clinical procedure, which includes gathering cognitive test results, can outperform survival analysis results produced using costly genetic or CSF data.

Ghazal Mirabnahrazam, Da Ma, Sieun Lee et al.

Background: The increasing availability of databases containing both magnetic resonance imaging (MRI) and genetic data allows researchers to utilize multimodal data to better understand the characteristics of dementia of Alzheimer's type (DAT). Objective: The goal of this study was to develop and analyze novel biomarkers that can help predict the development and progression of DAT. Methods: We used feature selection and ensemble learning classifier to develop an image/genotype-based DAT score that represents a subject's likelihood of developing DAT in the future. Three feature types were used: MRI only, genetic only, and combined multimodal data. We used a novel data stratification method to better represent different stages of DAT. Using a pre-defined 0.5 threshold on DAT scores, we predicted whether or not a subject would develop DAT in the future. Results: Our results on Alzheimer's Disease Neuroimaging Initiative (ADNI) database showed that dementia scores using genetic data could better predict future DAT progression for currently normal control subjects (Accuracy=0.857) compared to MRI (Accuracy=0.143), while MRI can better characterize subjects with stable mild cognitive impairment (Accuracy=0.614) compared to genetics (Accuracy=0.356). Combining MRI and genetic data showed improved classification performance in the remaining stratified groups. Conclusion: MRI and genetic data can contribute to DAT prediction in different ways. MRI data reflects anatomical changes in the brain, while genetic data can detect the risk of DAT progression prior to the symptomatic onset. Combining information from multimodal data in the right way can improve prediction performance.

Liangtai Sun, Danyu Luo, Da Ma et al.

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as chemical molecules and amino acid sequences. To bridge these gaps, we introduce SciDFM, a mixture-of-experts LLM, which is trained from scratch and is able to conduct college-level scientific reasoning and understand molecules and amino acid sequences. We collect a large-scale training corpus containing numerous scientific papers and books from different disciplines as well as data from domain-specific databases. We further fine-tune the pre-trained model on lots of instruction data to improve performances on downstream benchmarks. From experiment results, we show that SciDFM achieves strong performance on general scientific benchmarks such as SciEval and SciQ, and it reaches a SOTA performance on domain-specific benchmarks among models of similar size. We further analyze the expert layers and show that the results of expert selection vary with data from different disciplines. To benefit the broader research community, we open-source SciDFM at https://huggingface.co/OpenDFM/SciDFM-MoE-A5.6B-v1.0.

Shuo Chen, Da Ma, Sieun Lee et al.

Optical Coherence Tomography(OCT) is a non-invasive technique capturing cross-sectional area of the retina in micro-meter resolutions. It has been widely used as a auxiliary imaging reference to detect eye-related pathology and predict longitudinal progression of the disease characteristics. Retina layer segmentation is one of the crucial feature extraction techniques, where the variations of retinal layer thicknesses and the retinal layer deformation due to the presence of the fluid are highly correlated with multiple epidemic eye diseases like Diabetic Retinopathy(DR) and Age-related Macular Degeneration (AMD). However, these images are acquired from different devices, which have different intensity distribution, or in other words, belong to different imaging domains. This paper proposes a segmentation-guided domain-adaptation method to adapt images from multiple devices into single image domain, where the state-of-art pre-trained segmentation model is available. It avoids the time consumption of manual labelling for the upcoming new dataset and the re-training of the existing network. The semantic consistency and global feature consistency of the network will minimize the hallucination effect that many researchers reported regarding Cycle-Consistent Generative Adversarial Networks(CycleGAN) architecture.

Zhi Chen, Jijia Bao, Lu Chen et al.

Building a universal conversational agent has been a long-standing goal of the dialogue research community. Most previous works only focus on a small set of dialogue tasks. In this work, we aim to build a unified dialogue foundation model (DFM) which can be used to solve massive diverse dialogue tasks. To achieve this goal, a large-scale well-annotated dialogue dataset with rich task diversity (DialogZoo) is collected. We introduce a framework to unify all dialogue tasks and propose novel auxiliary self-supervised tasks to achieve stable training of DFM on the highly diverse large scale DialogZoo corpus. Experiments show that, compared with models of the same size, DFM can achieve state-of-the-art or competitive performance on very rich cross-domain downstream dialogue tasks. This demonstrates that DFM largely extends the ability of unified dialogue pre-trained model.

Ziyue Yang, Da Ma, Hanqi Li et al.

As scientific literature grows rapidly, automated survey generation has become a key capability for AI scientists and human researchers. However, existing systems suffer from limited analytical depth due to reliance on abstracts and isolated paper processing, and unreliable citations from imprecise retrieval and post-hoc grounding, producing superficial surveys and may mislead researchers. We present DeepSurvey, an agentic system that addresses both. To enhance depth, DeepSurvey extracts structured keynotes from full-text papers, models cross-paper relationships through clustering and comparative analysis, and integrates code-repository analysis to recover implementation-level details. To fortify reliability, it combines citation-graph expansion with hybrid filtering for topic-focussed retrieval, enforces evidence-constrained citation assignment, and deploys multi-granularity agentic refinement to validate citation-claim alignment. Experiments show that DeepSurvey achieves the highest content score (8.644/10) and citation quality (12.3% and 9.3% recall and precision gains over the strongest baseline), generalizes more robustly across domains (0.14 vs 0.22 to 0.69 CS-to-non-CS drop), and is preferred over human-written surveys by domain experts (83.3% overall quality, 100% content depth).

Timothy T. Yu, Da Ma, Jayden Cole et al.

Optical coherence tomography (OCT) captures cross-sectional data and is used for the screening, monitoring, and treatment planning of retinal diseases. Technological developments to increase the speed of acquisition often results in systems with a narrower spectral bandwidth, and hence a lower axial resolution. Traditionally, image-processing-based techniques have been utilized to reconstruct subsampled OCT data and more recently, deep-learning-based methods have been explored. In this study, we simulate reduced axial scan (A-scan) resolution by Gaussian windowing in the spectral domain and investigate the use of a learning-based approach for image feature reconstruction. In anticipation of the reduced resolution that accompanies wide-field OCT systems, we build upon super-resolution techniques to explore methods to better aid clinicians in their decision-making to improve patient outcomes, by reconstructing lost features using a pixel-to-pixel approach with an altered super-resolution generative adversarial network (SRGAN) architecture.

Ruisheng Cao, Hanchong Zhang, Hongshen Xu et al.

Text-to-SQL aims to generate an executable SQL program given the user utterance and the corresponding database schema. To ensure the well-formedness of output SQLs, one prominent approach adopts a grammar-based recurrent decoder to produce the equivalent SQL abstract syntax tree (AST). However, previous methods mainly utilize an RNN-series decoder, which 1) is time-consuming and inefficient and 2) introduces very few structure priors. In this work, we propose an AST structure-aware Transformer decoder (ASTormer) to replace traditional RNN cells. The structural knowledge, such as node types and positions in the tree, is seamlessly incorporated into the decoder via both absolute and relative position embeddings. Besides, the proposed framework is compatible with different traversing orders even considering adaptive node selection. Extensive experiments on five text-to-SQL benchmarks demonstrate the effectiveness and efficiency of our structured decoder compared to competitive baselines.

Hongshen Xu, Lu Chen, Zihan Zhao et al.

The growing prevalence of visually rich documents, such as webpages and scanned/digital-born documents (images, PDFs, etc.), has led to increased interest in automatic document understanding and information extraction across academia and industry. Although various document modalities, including image, text, layout, and structure, facilitate human information retrieval, the interconnected nature of these modalities presents challenges for neural networks. In this paper, we introduce WebLM, a multimodal pre-training network designed to address the limitations of solely modeling text and structure modalities of HTML in webpages. Instead of processing document images as unified natural images, WebLM integrates the hierarchical structure of document images to enhance the understanding of markup-language-based documents. Additionally, we propose several pre-training tasks to model the interaction among text, structure, and image modalities effectively. Empirical results demonstrate that the pre-trained WebLM significantly surpasses previous state-of-the-art pre-trained models across several webpage understanding tasks. The pre-trained models and code are available at https://github.com/X-LANCE/weblm.

Hanqi Li, Lu Chen, Da Ma et al.

Large language models have ushered in a new era of artificial intelligence research. However, their substantial training costs hinder further development and widespread adoption. In this paper, inspired by the redundancy in the parameters of large language models, we propose a novel training paradigm: Evolving Subnetwork Training (EST). EST samples subnetworks from the layers of the large language model and from commonly used modules within each layer, Multi-Head Attention (MHA) and Multi-Layer Perceptron (MLP). By gradually increasing the size of the subnetworks during the training process, EST can save the cost of training. We apply EST to train GPT2 model and TinyLlama model, resulting in 26.7\% FLOPs saving for GPT2 and 25.0\% for TinyLlama without an increase in loss on the pre-training dataset. Moreover, EST leads to performance improvements in downstream tasks, indicating that it benefits generalization. Additionally, we provide intuitive theoretical studies based on training dynamics and Dropout theory to ensure the feasibility of EST. Our code is available at https://github.com/OpenDFM/EST.

Da Ma, Lu Chen, Pengyu Wang et al.

Large language models (LLMs) have demonstrated proficiency across various natural language processing (NLP) tasks but often require additional training, such as continual pre-training and supervised fine-tuning. However, the costs associated with this, primarily due to their large parameter count, remain high. This paper proposes leveraging \emph{sparsity} in pre-trained LLMs to expedite this training process. By observing sparsity in activated neurons during forward iterations, we identify the potential for computational speed-ups by excluding inactive neurons. We address associated challenges by extending existing neuron importance evaluation metrics and introducing a ladder omission rate scheduler. Our experiments on Llama-2 demonstrate that Sparsity-Accelerated Training (SAT) achieves comparable or superior performance to standard training while significantly accelerating the process. Specifically, SAT achieves a $45\%$ throughput improvement in continual pre-training and saves $38\%$ training time in supervised fine-tuning in practice. It offers a simple, hardware-agnostic, and easily deployable framework for additional LLM training. Our code is available at https://github.com/OpenDFM/SAT.

Zihan Zhao, Da Ma, Lu Chen et al.

Artificial intelligence (AI) has played an increasingly important role in chemical research. However, most models currently used in chemistry are specialist models that require training and tuning for specific tasks. A more generic and efficient solution would be an AI model that could address many tasks and support free-form dialogue in the broad field of chemistry. In its utmost form, such a generalist AI chemist could be referred to as Chemical General Intelligence. Large language models (LLMs) have recently logged tremendous success in the general domain of natural language processing, showing emerging task generalization and free-form dialogue capabilities. However, domain knowledge of chemistry is largely missing when training general-domain LLMs. The lack of such knowledge greatly hinders the performance of generalist LLMs in the field of chemistry. To this end, we develop ChemDFM, a pioneering LLM for chemistry trained on 34B tokens from chemical literature and textbooks, and fine-tuned using 2.7M instructions. As a result, it can understand and reason with chemical knowledge in free-form dialogue. Quantitative evaluations show that ChemDFM significantly surpasses most representative open-source LLMs. It outperforms GPT-4 on a great portion of chemical tasks, despite the substantial size difference. We have open-sourced the inference codes, evaluation datasets, and model weights of ChemDFM on Huggingface (https://huggingface.co/OpenDFM/ChemDFM-v1.0-13B).

Ricky Chen, Timothy T. Yu, Gavin Xu et al.

With the FDA approval of Artificial Intelligence (AI) for point-of-care clinical diagnoses, model generalizability is of the utmost importance as clinical decision-making must be domain-agnostic. A method of tackling the problem is to increase the dataset to include images from a multitude of domains; while this technique is ideal, the security requirements of medical data is a major limitation. Additionally, researchers with developed tools benefit from the addition of open-sourced data, but are limited by the difference in domains. Herewith, we investigated the implementation of a Cycle-Consistent Generative Adversarial Networks (CycleGAN) for the domain adaptation of Optical Coherence Tomography (OCT) volumes. This study was done in collaboration with the Biomedical Optics Research Group and Functional & Anatomical Imaging & Shape Analysis Lab at Simon Fraser University. In this study, we investigated a learning-based approach of adapting the domain of a publicly available dataset, UK Biobank dataset (UKB). To evaluate the performance of domain adaptation, we utilized pre-existing retinal layer segmentation tools developed on a different set of RETOUCH OCT data. This study provides insight on state-of-the-art tools for domain adaptation compared to traditional processing techniques as well as a pipeline for adapting publicly available retinal data to the domains previously used by our collaborators.

Hongshen Xu, Zichen Zhu, Situo Zhang et al.

Large Language Models (LLMs) often generate erroneous outputs, known as hallucinations, due to their limitations in discerning questions beyond their knowledge scope. While addressing hallucination has been a focal point in research, previous efforts primarily concentrate on enhancing correctness without giving due consideration to the significance of rejection mechanisms. In this paper, we conduct a comprehensive examination of the role of rejection, introducing the notion of model reliability along with corresponding metrics. These metrics measure the model's ability to provide accurate responses while adeptly rejecting questions exceeding its knowledge boundaries, thereby minimizing hallucinations. To improve the inherent reliability of LLMs, we present a novel alignment framework called Reinforcement Learning from Knowledge Feedback (RLKF). RLKF leverages knowledge feedback to dynamically determine the model's knowledge boundary and trains a reliable reward model to encourage the refusal of out-of-knowledge questions. Experimental results on mathematical questions affirm the substantial efficacy of RLKF in significantly enhancing LLM reliability.

Hongshen Xu, Zichen Zhu, Lei Pan et al.

Large Language Models (LLMs) have expanded their capabilities beyond language generation to interact with external tools, enabling automation and real-world applications. However, tool hallucinations, where models either select inappropriate tools or misuse them, pose significant challenges, leading to erroneous task execution, increased computational costs, and reduced system reliability. To systematically address this issue, we define and categorize tool hallucinations into two main types, tool selection hallucination and tool usage hallucination. To evaluate and mitigate these issues, we introduce RelyToolBench, which integrates specialized test cases and novel metrics to assess hallucination-aware task success and efficiency. Finally, we propose Relign, a reliability alignment framework that expands the tool-use action space to include indecisive actions, allowing LLMs to defer tool use, seek clarification, or adjust tool selection dynamically. Through extensive experiments, we demonstrate that Relign significantly reduces tool hallucinations, improves task reliability, and enhances the efficiency of LLM tool interactions.

Da Ma, Lu Chen, Situo Zhang et al.

The rapid expansion of context window sizes in Large Language Models~(LLMs) has enabled them to tackle increasingly complex tasks involving lengthy documents. However, this progress comes at the cost of a substantial increase in memory usage during inference, primarily due to the linear growth of the key-value~(KV) cache. Existing KV cache compression methods often discard less relevant tokens, which can lead to significant performance degradation when critical information is lost. In this paper, we propose \textsc{PoD}~(Proximal tokens over Distant tokens), a novel KV cache compression framework that allocates memory according to token importance, retaining less important tokens in a more compact, shared form rather than discarding them entirely. Our approach is motivated by two key observations: (1) proximal tokens -- those at the beginning and end of the context -- are significantly more important for next-token prediction, and (2) attention scores for distant tokens are highly redundant across consecutive layers. Leveraging these insights, \textsc{PoD} preserves the full KV cache for proximal tokens, while for distant tokens, it shares key states across layers. Since attention scores are determined by both queries and keys, sharing key states enables multiple layers to reuse a single set of keys for distant tokens, substantially reducing KV cache memory without discarding essential context. We further introduce a lightweight post-training adaptation to enable the model to adjust to this new attention-sharing structure. Extensive experiments on both synthetic~(Needle in a Haystack) and real-world long-context benchmarks demonstrate that \textsc{PoD} reduces KV cache memory usage by up to 35\% without compromising performance. Our method is orthogonal to existing token-selection-based techniques and can be combined with them for further KV cache compression.

Situo Zhang, Hankun Wang, Da Ma et al.

Speculative Decoding (SD) is a popular lossless technique for accelerating the inference of Large Language Models (LLMs). We show that the decoding speed of SD frameworks with static draft structures can be significantly improved by incorporating context-aware adaptive draft structures. However, current studies on adaptive draft structures are limited by their performance, modeling approaches, and applicability. In this paper, we introduce AdaEAGLE, the first SD framework that explicitly models adaptive draft structures. AdaEAGLE leverages the Lightweight Draft Length Predictor (LDLP) module to explicitly predict the optimal number of draft tokens during inference to guide the draft model. It achieves comparable speedup results without manual thresholds and allows for deeper, more specialized optimizations. Moreover, together with threshold-based strategies, AdaEAGLE achieves a $1.62\times$ speedup over the vanilla AR decoding and outperforms fixed-length SotA baseline while maintaining output quality.

Situo Zhang, Yifan Zhang, Zichen Zhu et al.

Charts are ubiquitous in scientific and financial literature for presenting structured data. However, chart reasoning remains challenging for multimodal large language models (MLLMs) due to the lack of high-quality training data, as well as the need for fine-grained visual grounding and precise numerical computation. To address these challenges, we first propose DuoChart, a scalable dual-source data pipeline that combines synthesized charts with real-world charts to construct diverse, high-quality chart training data. We then introduce CharTool, which equips MLLMs with external tools, including image cropping for localized visual perception and code-based computation for accurate numerical reasoning. Through agentic reinforcement learning on DuoChart, CharTool learns tool-integrated reasoning grounded in chart content. Extensive experiments on six chart benchmarks show that our method consistently improves over strong MLLM baselines across model scales. Notably, CharTool-7B outperforms the base model by **+8.0%** on CharXiv (Reasoning) and **+9.78%** on ChartQAPro, while achieving competitive performance with substantially larger or proprietary models. Moreover, CharTool demonstrates positive generalization to out-of-domain visual math reasoning benchmarks.

Zihan Zhao, Bo Chen, Ziping Wan et al.

While large language models (LLMs) have achieved impressive progress, their application in scientific domains such as chemistry remains hindered by shallow domain understanding and limited reasoning capabilities. In this work, we focus on the specific field of chemistry and develop a Chemical Reasoner LLM, ChemDFM-R. We first construct a comprehensive dataset of atomized knowledge points to enhance the model's understanding of the fundamental principles and logical structure of chemistry. Then, we propose a mix-sourced distillation strategy that integrates expert-curated knowledge with general-domain reasoning skills, followed by domain-specific reinforcement learning to enhance chemical reasoning. Experiments on diverse chemical benchmarks demonstrate that ChemDFM-R achieves cutting-edge performance while providing interpretable, rationale-driven outputs. Further case studies illustrate how explicit reasoning chains significantly improve the reliability, transparency, and practical utility of the model in real-world human-AI collaboration scenarios.

Zijian Wang, Tiancheng Huang, Hanqi Li et al.

The accelerating growth of the scientific literature makes it increasingly difficult for researchers to track new advances through manual reading alone. Recent progress in large language models (LLMs) has therefore spurred interest in autonomous agents that can read scientific papers and extract task-relevant information. However, most existing approaches rely either on heavily engineered prompting or on a conventional SFT-RL training pipeline, both of which often lead to excessive and low-yield exploration. Drawing inspiration from cognitive science, we propose PaperCompass, a framework that mitigates these issues by separating high-level planning from fine-grained execution. PaperCompass first drafts an explicit plan that outlines the intended sequence of actions, and then performs detailed reasoning to instantiate each step by selecting the parameters for the corresponding function calls. To train such behavior, we introduce Draft-and-Follow Policy Optimization (DFPO), a tailored RL method that jointly optimizes both the draft plan and the final solution. DFPO can be viewed as a lightweight form of hierarchical reinforcement learning, aimed at narrowing the `knowing-doing' gap in LLMs. We provide a theoretical analysis that establishes DFPO's favorable optimization properties, supporting a stable and reliable training process. Experiments on paper-based question answering (Paper-QA) benchmarks show that PaperCompass improves efficiency over strong baselines without sacrificing performance, achieving results comparable to much larger models.

Situo Zhang, Yifan Zhang, Zichen Zhu et al.

Speculative decoding (SD) is a powerful technique for accelerating the inference process of large language models (LLMs) without sacrificing accuracy. Typically, SD employs a small draft model to generate a fixed number of draft tokens, which are then verified in parallel by the target model. However, our experiments reveal that the optimal draft length varies significantly across different decoding steps. This variation suggests that using a fixed draft length limits the potential for further improvements in decoding speed. To address this challenge, we propose Pacer, a novel approach that dynamically controls draft length using a lightweight, trainable pre-verification layer. This layer pre-verifies draft tokens blockwise before they are sent to the target model, allowing the draft model to stop token generation if the blockwise pre-verification fails. We implement Pacer on multiple SD model pairs and evaluate its performance across various benchmarks. Our results demonstrate that Pacer achieves up to 2.66x Speedup over autoregressive decoding and consistently outperforms standard speculative decoding. Furthermore, when integrated with Ouroboros, Pacer attains up to 3.09x Speedup.

Da Ma, Gonghu Shang, Zhi Chen et al.

Instruction tuning improves the ability of large language models (LLMs) to follow diverse human instructions, but achieving strong performance on specific target tasks remains challenging. A critical bottleneck is selecting the most relevant data to maximize task-specific performance. Existing data selection approaches include unstable influence-based methods and more stable distribution alignment methods, the latter of which critically rely on the underlying sample representation. In practice, most distribution alignment methods, from shallow features (e.g., BM25) to neural embeddings (e.g., BGE, LLM2Vec), may fail to capture how the model internally processes samples. To bridge this gap, we adopt a model-centric strategy in which each sample is represented by its neuronal activation pattern in the model, directly reflecting internal computation. However, directly using raw neuron activations leads to spurious similarity between unrelated samples due to neuron polysemanticity, where a single neuron may respond to multiple, unrelated concepts. To address this, we employ sparse autoencoders to disentangle polysemantic activations into sparse, monosemantic representations, and introduce a dedicated similarity metric for this space to better identify task-relevant data. Comprehensive experiments across multiple instruction datasets, models, tasks, and selection ratios show that our approach consistently outperforms existing data selection baselines in both stability and task-specific performance.

Da Ma, Donghuan Lu, Karteek Popuri et al.

Frontotemporal dementia and Alzheimer's disease are two common forms of dementia and are easily misdiagnosed as each other due to their similar pattern of clinical symptoms. Differentiating between the two dementia types is crucial for determining disease-specific intervention and treatment. Recent development of Deep-learning-based approaches in the field of medical image computing are delivering some of the best performance for many binary classification tasks, although its application in differential diagnosis, such as neuroimage-based differentiation for multiple types of dementia, has not been explored. In this study, a novel framework was proposed by using the Generative Adversarial Network technique to distinguish FTD, AD and normal control subjects, using volumetric features extracted at coarse-to-fine structural scales from Magnetic Resonance Imaging scans. Experiments of 10-folds cross-validation on 1,954 images achieved high accuracy. With the proposed framework, we have demonstrated that the combination of multi-scale structural features and synthetic data augmentation based on generative adversarial network can improve the performance of challenging tasks such as differentiating Dementia sub-types.

Zhi Chen, Lu Chen, Hanqi Li et al.

Recently, Text-to-SQL for multi-turn dialogue has attracted great interest. Here, the user input of the current turn is parsed into the corresponding SQL query of the appropriate database, given all previous dialogue history. Current approaches mostly employ end-to-end models and consequently face two challenges. First, dialogue history modeling and Text-to-SQL parsing are implicitly combined, hence it is hard to carry out interpretable analysis and obtain targeted improvement. Second, SQL annotation of multi-turn dialogue is very expensive, leading to training data sparsity. In this paper, we propose a novel decoupled multi-turn Text-to-SQL framework, where an utterance rewrite model first explicitly solves completion of dialogue context, and then a single-turn Text-to-SQL parser follows. A dual learning approach is also proposed for the utterance rewrite model to address the data sparsity problem. Compared with end-to-end approaches, the proposed decoupled method can achieve excellent performance without any annotated in-domain data. With just a few annotated rewrite cases, the decoupled method outperforms the released state-of-the-art end-to-end models on both SParC and CoSQL datasets.

Da Ma, Vincent Chow, Karteek Popuri et al.

The latest advances in computer-assisted precision medicine are making it feasible to move from population-wide models that are useful to discover aggregate patterns that hold for group-based analysis to patient-specific models that can drive patient-specific decisions with regard to treatment choices, and predictions of outcomes of treatment. Body Composition is recognized as an important driver and risk factor for a wide variety of diseases, as well as a predictor of individual patient-specific clinical outcomes to treatment choices or surgical interventions. 3D CT images are routinely acquired in the oncological worklows and deliver accurate rendering of internal anatomy and therefore can be used opportunistically to assess the amount of skeletal muscle and adipose tissue compartments. Powerful tools of artificial intelligence such as deep learning are making it feasible now to segment the entire 3D image and generate accurate measurements of all internal anatomy. These will enable the overcoming of the severe bottleneck that existed previously, namely, the need for manual segmentation, which was prohibitive to scale to the hundreds of 2D axial slices that made up a 3D volumetric image. Automated tools such as presented here will now enable harvesting whole-body measurements from 3D CT or MRI images, leading to a new era of discovery of the drivers of various diseases based on individual tissue, organ volume, shape, and functional status. These measurements were hitherto unavailable thereby limiting the field to a very small and limited subset. These discoveries and the potential to perform individual image segmentation with high speed and accuracy are likely to lead to the incorporation of these 3D measures into individual specific treatment planning models related to nutrition, aging, chemotoxicity, surgery and survival after the onset of a major disease such as cancer.

Donghuan Lu, Morgan Heisler, Da Ma et al.

Optical coherence tomography (OCT) is a non-invasive imaging technology which can provide micrometer-resolution cross-sectional images of the inner structures of the eye. It is widely used for the diagnosis of ophthalmic diseases with retinal alteration, such as layer deformation and fluid accumulation. In this paper, a novel framework was proposed to segment retinal layers with fluid presence. The main contribution of this study is two folds: 1) we developed a cascaded network framework to incorporate the prior structural knowledge; 2) we proposed a novel deep neural network based on U-Net and fully convolutional network, termed LF-UNet. Cross validation experiments proved that the proposed LF-UNet has superior performance comparing with the state-of-the-art methods, and incorporating the relative distance map structural prior information could further improve the performance regardless the network.

Da Ma, Manuel J. Cardoso, Maria A. Zuluaga et al.

The cerebellar grey matter morphology is an important feature to study neurodegenerative diseases such as Alzheimer's disease or Down's syndrome. Its volume or thickness is commonly used as a surrogate imaging biomarker for such diseases. Most studies about grey matter thickness estimation focused on the cortex, and little attention has been drawn on the morphology of the cerebellum. Using ex vivo high-resolution MRI, it is now possible to visualise the different cell layers in the mouse cerebellum. In this work, we introduce a framework to extract the Purkinje layer within the grey matter, enabling the estimation of the thickness of the cerebellar grey matter, the granular layer and molecular layer from gadolinium-enhanced ex vivo mouse brain MRI. Application to mouse model of Down's syndrome found reduced cortical and layer thicknesses in the transchromosomic group.