Diagnosis of hematological malignancies depends on accurate identification of white blood cells in peripheral blood smears. Deep learning techniques are emerging as a viable solution to scale and optimize this process by automatic identification of cells in laboratories. However, these techniques face several challenges such as limited generalizability, sensitivity to domain shifts and lack of explainability. Here, we are introducing a novel approach based on neural cellular automata (NCA) for white blood cell classification. We test our approach on three datasets of white blood cell images and show that we achieve competitive performance compared to conventional methods. Our NCA-based method is significantly smaller in terms of parameters and exhibits robustness to domain shifts. Furthermore, the architecture is inherently explainable, providing insights into the decision process for each classification, helping experts understand and validate model predictions. Results demonstrate that NCA not only can be used for image classification, but also address key challenges of conventional methods, indicating a high potential for applicability in clinical practice.
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Continuous photoplethysmography (PPG)-based blood pressure monitoring is necessary for healthcare and fitness applications. In Artificial Intelligence (AI), signal classification levels with the machine and deep learning arrangements need to be explored further. Techniques based on time-frequency spectra, such as Short-time Fourier Transform (STFT), have been used to address the challenges of motion artifact correction. Therefore, the proposed study works with PPG signals of more than 200 patients (650+ signal samples) with hypertension, using STFT with various Neural Networks (Convolution Neural Network (CNN), Long Short-Term Memory (LSTM), Bidirectional Long Short-Term Memory (Bi-LSTM), followed by machine learning classifiers, such as, Support Vector Machine (SVM) and Random Forest (RF). The classification has been done for two categories: Prehypertension (normal levels) and Hypertension (includes Stage I and Stage II). Various performance metrics have been obtained with two batch sizes of 3 and 16 for the fusion of the neural networks. With precision and specificity of 100% and recall of 82.1%, the LSTM model provides the best results among all combinations of Neural Networks. However, the maximum accuracy of 71.9% is achieved by the LSTM-CNN model. Further stacked Ensemble method has been used to achieve 100% accuracy for Meta-LSTM-RF, Meta- LSTM-CNN-RF and Meta- STFT-CNN-SVM.
Drug response prediction (DRP) is a crucial phase in drug discovery, and the most important metric for its evaluation is the IC50 score. DRP results are heavily dependent on the quality of the generated molecules. Existing molecule generation methods typically employ classifier-based guidance, enabling sampling within the IC50 classification range. However, these methods fail to ensure the sampling space range's effectiveness, generating numerous ineffective molecules. Through experimental and theoretical study, we hypothesize that conditional generation based on the target IC50 score can obtain a more effective sampling space. As a result, we introduce regressor-free guidance molecule generation to ensure sampling within a more effective space and support DRP. Regressor-free guidance combines a diffusion model's score estimation with a regression controller model's gradient based on number labels. To effectively map regression labels between drugs and cell lines, we design a common-sense numerical knowledge graph that constrains the order of text representations. Experimental results on the real-world dataset for the DRP task demonstrate our method's effectiveness in drug discovery. The code is available at://anonymous.4open.science/r/RMCD-DBD1.
In the medical domain, numerous scenarios necessitate the long-form generation ability of large language models (LLMs). Specifically, when addressing patients' questions, it is essential that the model's response conveys factual claims, highlighting the need for an automated method to evaluate those claims. Thus, we introduce MedLFQA, a benchmark dataset reconstructed using long-form question-answering datasets related to the biomedical domain. We use MedLFQA to facilitate the automatic evaluations of factuality. We also propose OLAPH, a simple and novel framework that enables the improvement of factuality through automatic evaluations. The OLAPH framework iteratively trains LLMs to mitigate hallucinations using sampling predictions and preference optimization. In other words, we iteratively set the highest-scoring response as a preferred response derived from sampling predictions and train LLMs to align with the preferred response that improves factuality. We highlight that, even on evaluation metrics not used during training, LLMs trained with our OLAPH framework demonstrate significant performance improvement in factuality. Our findings reveal that a 7B LLM trained with our OLAPH framework can provide long answers comparable to the medical experts' answers in terms of factuality. We believe that our work could shed light on gauging the long-text generation ability of LLMs in the medical domain. Our code and datasets are available at //github.com/dmis-lab/OLAPH}{//github.com/dmis-lab/OLAPH.
Multi-modal magnetic resonance imaging (MRI) plays a crucial role in comprehensive disease diagnosis in clinical medicine. However, acquiring certain modalities, such as T2-weighted images (T2WIs), is time-consuming and prone to be with motion artifacts. It negatively impacts subsequent multi-modal image analysis. To address this issue, we propose an end-to-end deep learning framework that utilizes T1-weighted images (T1WIs) as auxiliary modalities to expedite T2WIs' acquisitions. While image pre-processing is capable of mitigating misalignment, improper parameter selection leads to adverse pre-processing effects, requiring iterative experimentation and adjustment. To overcome this shortage, we employ Optimal Transport (OT) to synthesize T2WIs by aligning T1WIs and performing cross-modal synthesis, effectively mitigating spatial misalignment effects. Furthermore, we adopt an alternating iteration framework between the reconstruction task and the cross-modal synthesis task to optimize the final results. Then, we prove that the reconstructed T2WIs and the synthetic T2WIs become closer on the T2 image manifold with iterations increasing, and further illustrate that the improved reconstruction result enhances the synthesis process, whereas the enhanced synthesis result improves the reconstruction process. Finally, experimental results from FastMRI and internal datasets confirm the effectiveness of our method, demonstrating significant improvements in image reconstruction quality even at low sampling rates.
In the last two decades, single-arm trials (SATs) have been effectively used to study anticancer therapies in well-defined patient populations using durable response rates as an objective and interpretable clinical endpoints. With a growing trend of regulatory accelerated approval (AA) requiring randomized controlled trials (RCTs), some confusions have arisen about the roles of SATs in AA. This paper is intended to elucidate conditions under which an SAT may be considered reasonable for AA. Specifically, the paper describes (1) two necessary conditions for designing an SAT, (2) three sufficient conditions that help either optimize the study design or interpret the study results, (3) four conditions that demonstrate substantial evidence of clinical benefits of the drug, and (4) a plan of a confirmatory RCT to verify the clinical benefits. Some further considerations are discussed to help design a scientifically sound SAT and communicate with regulatory agencies. Conditions presented in this paper may serve as a set of references for sponsors using SATs for regulatory decision.
We present an index structure, called the color-index, to boost the evaluation of acyclic conjunctive queries (ACQs) over binary schemas. The color-index is based on the color refinement algorithm, a widely used subroutine for graph isomorphism testing algorithms. Given a database $D$, we use a suitable version of the color refinement algorithm to produce a stable coloring of $D$, an assignment from the active domain of $D$ to a set of colors $C_D$. The main ingredient of the color-index is a particular database $D_c$ whose active domain is $C_D$ and whose size is at most $|D|$. Using the color-index, we can evaluate any free-connex ACQ $Q$ over $D$ with preprocessing time $O(|Q| \cdot |D_c|)$ and constant delay enumeration. Furthermore, we can also count the number of results of $Q$ over $D$ in time $O(|Q| \cdot |D_c|)$. Given that $|D_c|$ could be much smaller than $|D|$ (even constant-size for some families of databases), the color-index is the first index structure for evaluating free-connex ACQs that allows efficient enumeration and counting with performance that may be strictly smaller than the database size.
The spread of false and misleading information is receiving significant attention from legislative and regulatory bodies. Consumers place trust in specific sources of information, so a scalable, interoperable method for determining the provenance and authenticity of information is needed. In this paper we analyze the posting of broadcast news content to a social media platform, the role of open standards, the interplay of cryptographic metadata and watermarks when validating provenance, and likely success and failure scenarios. We conclude that the open standards for cryptographically authenticated metadata developed by the Coalition for Provenance and Authenticity (C2PA) and for audio and video watermarking developed by the Advanced Television Systems Committee (ATSC) are well suited to address broadcast provenance. We suggest methods for using these standards for optimal success.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
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