Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method \cite{Wei2022ChainOT} can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at \url{//tianchi.aliyun.com/dataset/95414}, and the source codes are open-sourced at \url{//github.com/michael-wzhu/text2dt}.
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Optical coherence tomography (OCT) is a non-invasive, micrometer-scale imaging modality that has become a clinical standard in ophthalmology. By raster-scanning the retina, sequential cross-sectional image slices are acquired to generate volumetric data. In-vivo imaging suffers from discontinuities between slices that show up as motion and illumination artifacts. We present a new illumination model that exploits continuity in orthogonally raster-scanned volume data. Our novel spatiotemporal parametrization adheres to illumination continuity both temporally, along the imaged slices, as well as spatially, in the transverse directions. Yet, our formulation does not make inter-slice assumptions, which could have discontinuities. This is the first optimization of a 3D inverse model in an image reconstruction context in OCT. Evaluation in 68 volumes from eyes with pathology showed reduction of illumination artifacts in 88\% of the data, and only 6\% showed moderate residual illumination artifacts. The method enables the use of forward-warped motion corrected data, which is more accurate, and enables supersampling and advanced 3D image reconstruction in OCT.
Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.
Crowdsourced machine learning on competition platforms such as Kaggle is a popular and often effective method for generating accurate models. Typically, teams vie for the most accurate model, as measured by overall error on a holdout set, and it is common towards the end of such competitions for teams at the top of the leaderboard to ensemble or average their models outside the platform mechanism to get the final, best global model. In arXiv:2201.10408, the authors developed an alternative crowdsourcing framework in the context of fair machine learning, in order to integrate community feedback into models when subgroup unfairness is present and identifiable. There, unlike in classical crowdsourced ML, participants deliberately specialize their efforts by working on subproblems, such as demographic subgroups in the service of fairness. Here, we take a broader perspective on this work: we note that within this framework, participants may both specialize in the service of fairness and simply to cater to their particular expertise (e.g., focusing on identifying bird species in an image classification task). Unlike traditional crowdsourcing, this allows for the diversification of participants' efforts and may provide a participation mechanism to a larger range of individuals (e.g. a machine learning novice who has insight into a specific fairness concern). We present the first medium-scale experimental evaluation of this framework, with 46 participating teams attempting to generate models to predict income from American Community Survey data. We provide an empirical analysis of teams' approaches, and discuss the novel system architecture we developed. From here, we give concrete guidance for how best to deploy such a framework.
In pursuit of fairness and balanced development, recommender systems (RS) often prioritize group fairness, ensuring that specific groups maintain a minimum level of exposure over a given period. For example, RS platforms aim to ensure adequate exposure for new providers or specific categories of items according to their needs. Modern industry RS usually adopts a two-stage pipeline: stage-1 (retrieval stage) retrieves hundreds of candidates from millions of items distributed across various servers, and stage-2 (ranking stage) focuses on presenting a small-size but accurate selection from items chosen in stage-1. Existing efforts for ensuring amortized group exposures focus on stage-2, however, stage-1 is also critical for the task. Without a high-quality set of candidates, the stage-2 ranker cannot ensure the required exposure of groups. Previous fairness-aware works designed for stage-2 typically require accessing and traversing all items. In stage-1, however, millions of items are distributively stored in servers, making it infeasible to traverse all of them. How to ensure group exposures in the distributed retrieval process is a challenging question. To address this issue, we introduce a model named FairSync, which transforms the problem into a constrained distributed optimization problem. Specifically, FairSync resolves the issue by moving it to the dual space, where a central node aggregates historical fairness data into a vector and distributes it to all servers. To trade off the efficiency and accuracy, the gradient descent technique is used to periodically update the parameter of the dual vector. The experiment results on two public recommender retrieval datasets showcased that FairSync outperformed all the baselines, achieving the desired minimum level of exposures while maintaining a high level of retrieval accuracy.
Stickers, while widely recognized for enhancing empathetic communication in online interactions, remain underexplored in current empathetic dialogue research, notably due to the challenge of a lack of comprehensive datasets. In this paper, we introduce the Agent for STICKERCONV (Agent4SC), which uses collaborative agent interactions to realistically simulate human behavior with sticker usage, thereby enhancing multimodal empathetic communication. Building on this foundation, we develop a multimodal empathetic dialogue dataset, STICKERCONV, comprising 12.9K dialogue sessions, 5.8K unique stickers, and 2K diverse conversational scenarios. This dataset serves as a benchmark for multimodal empathetic generation. To advance further, we propose PErceive and Generate Stickers (PEGS), a multimodal empathetic response generation framework, complemented by a comprehensive set of empathy evaluation metrics based on LLM. Our experiments demonstrate PEGS's effectiveness in generating contextually relevant and emotionally resonant multimodal empathetic responses, contributing to the advancement of more nuanced and engaging empathetic dialogue systems.
Malaria is a major health issue worldwide, and its diagnosis requires scalable solutions that can work effectively with low-cost microscopes (LCM). Deep learning-based methods have shown success in computer-aided diagnosis from microscopic images. However, these methods need annotated images that show cells affected by malaria parasites and their life stages. Annotating images from LCM significantly increases the burden on medical experts compared to annotating images from high-cost microscopes (HCM). For this reason, a practical solution would be trained on HCM images which should generalize well on LCM images during testing. While earlier methods adopted a multi-stage learning process, they did not offer an end-to-end approach. In this work, we present an end-to-end learning framework, named CodaMal (Contrastive Domain Adpation for Malaria). In order to bridge the gap between HCM (training) and LCM (testing), we propose a domain adaptive contrastive loss. It reduces the domain shift by promoting similarity between the representations of HCM and its corresponding LCM image, without imposing an additional annotation burden. In addition, the training objective includes object detection objectives with carefully designed augmentations, ensuring the accurate detection of malaria parasites. On the publicly available large-scale M5-dataset, our proposed method shows a significant improvement of 16% over the state-of-the-art methods in terms of the mean average precision metric (mAP), provides 21x speed up during inference, and requires only half learnable parameters than the prior methods. Our code is publicly available.
Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending task-specific knowledge, suggesting the potential for ChatGPT-like systems specialized in protein to facilitate basic research. In this work, we introduce ProtChatGPT, which aims at learning and understanding protein structures via natural languages. ProtChatGPT enables users to upload proteins, ask questions, and engage in interactive conversations to produce comprehensive answers. The system comprises protein encoders, a Protein-Language Pertaining Transformer (PLP-former), a projection adapter, and an LLM. The protein first undergoes protein encoders and PLP-former to produce protein embeddings, which are then projected by the adapter to conform with the LLM. The LLM finally combines user questions with projected embeddings to generate informative answers. Experiments show that ProtChatGPT can produce promising responses to proteins and their corresponding questions. We hope that ProtChatGPT could form the basis for further exploration and application in protein research. Code and our pre-trained model will be publicly available.
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.
Exploration-exploitation is a powerful and practical tool in multi-agent learning (MAL), however, its effects are far from understood. To make progress in this direction, we study a smooth analogue of Q-learning. We start by showing that our learning model has strong theoretical justification as an optimal model for studying exploration-exploitation. Specifically, we prove that smooth Q-learning has bounded regret in arbitrary games for a cost model that explicitly captures the balance between game and exploration costs and that it always converges to the set of quantal-response equilibria (QRE), the standard solution concept for games under bounded rationality, in weighted potential games with heterogeneous learning agents. In our main task, we then turn to measure the effect of exploration in collective system performance. We characterize the geometry of the QRE surface in low-dimensional MAL systems and link our findings with catastrophe (bifurcation) theory. In particular, as the exploration hyperparameter evolves over-time, the system undergoes phase transitions where the number and stability of equilibria can change radically given an infinitesimal change to the exploration parameter. Based on this, we provide a formal theoretical treatment of how tuning the exploration parameter can provably lead to equilibrium selection with both positive as well as negative (and potentially unbounded) effects to system performance.
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
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