Deep learning is dramatically transforming the field of medical imaging and radiology, enabling the identification of pathologies in medical images, including computed tomography (CT) and X-ray scans. However, the performance of deep learning models, particularly in segmentation tasks, is often limited by the need for extensive annotated datasets. To address this challenge, the capabilities of weakly supervised semantic segmentation are explored through the lens of Explainable AI and the generation of counterfactual explanations. The scope of this research is development of a novel counterfactual inpainting approach (COIN) that flips the predicted classification label from abnormal to normal by using a generative model. For instance, if the classifier deems an input medical image X as abnormal, indicating the presence of a pathology, the generative model aims to inpaint the abnormal region, thus reversing the classifier's original prediction label. The approach enables us to produce precise segmentations for pathologies without depending on pre-existing segmentation masks. Crucially, image-level labels are utilized, which are substantially easier to acquire than creating detailed segmentation masks. The effectiveness of the method is demonstrated by segmenting synthetic targets and actual kidney tumors from CT images acquired from Tartu University Hospital in Estonia. The findings indicate that COIN greatly surpasses established attribution methods, such as RISE, ScoreCAM, and LayerCAM, as well as an alternative counterfactual explanation method introduced by Singla et al. This evidence suggests that COIN is a promising approach for semantic segmentation of tumors in CT images, and presents a step forward in making deep learning applications more accessible and effective in healthcare, where annotated data is scarce.
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In the realm of advanced steganography, the scale of the model typically correlates directly with the resolution of the fundamental grid, necessitating the training of a distinct neural network for message extraction. This paper proposes an image steganography based on generative implicit neural representation. This approach transcends the constraints of image resolution by portraying data as continuous functional expressions. Notably, this method permits the utilization of a diverse array of multimedia data as cover images, thereby broadening the spectrum of potential carriers. Additionally, by fixing a neural network as the message extractor, we effectively redirect the training burden to the image itself, resulting in both a reduction in computational overhead and an enhancement in steganographic speed. This approach also circumvents potential transmission challenges associated with the message extractor. Experimental findings reveal that this methodology achieves a commendable optimization efficiency, achieving a completion time of just 3 seconds for 64x64 dimensional images, while concealing only 1 bpp of information. Furthermore, the accuracy of message extraction attains an impressive mark of 100%.
Spiking neural networks play an important role in brain-like neuromorphic computations and in studying working mechanisms of neural circuits. One drawback of training a large scale spiking neural network is that updating all weights is quite expensive. Furthermore, after training, all information related to the computational task is hidden into the weight matrix, prohibiting us from a transparent understanding of circuit mechanisms. Therefore, in this work, we address these challenges by proposing a spiking mode-based training protocol, where the recurrent weight matrix is explained as a Hopfield-like multiplication of three matrices: input, output modes and a score matrix. The first advantage is that the weight is interpreted by input and output modes and their associated scores characterizing the importance of each decomposition term. The number of modes is thus adjustable, allowing more degrees of freedom for modeling the experimental data. This significantly reduces the training cost because of significantly reduced space complexity for learning. Training spiking networks is thus carried out in the mode-score space. The second advantage is that one can project the high dimensional neural activity (filtered spike train) in the state space onto the mode space which is typically of a low dimension, e.g., a few modes are sufficient to capture the shape of the underlying neural manifolds. We successfully apply our framework in two computational tasks -- digit classification and selective sensory integration tasks. Our method accelerate the training of spiking neural networks by a Hopfield-like decomposition, and moreover this training leads to low-dimensional attractor structures of high-dimensional neural dynamics.
Recurrent neural networks (RNNs) notoriously struggle to learn long-term memories, primarily due to vanishing and exploding gradients. The recent success of state-space models (SSMs), a subclass of RNNs, to overcome such difficulties challenges our theoretical understanding. In this paper, we delve into the optimization challenges of RNNs and discover that, as the memory of a network increases, changes in its parameters result in increasingly large output variations, making gradient-based learning highly sensitive, even without exploding gradients. Our analysis further reveals the importance of the element-wise recurrence design pattern combined with careful parametrizations in mitigating this effect. This feature is present in SSMs, as well as in other architectures, such as LSTMs. Overall, our insights provide a new explanation for some of the difficulties in gradient-based learning of RNNs and why some architectures perform better than others.
Ptychography is a powerful imaging technique that is used in a variety of fields, including materials science, biology, and nanotechnology. However, the accuracy of the reconstructed ptychography image is highly dependent on the accuracy of the recorded probe positions which often contain errors. These errors are typically corrected jointly with phase retrieval through numerical optimization approaches. When the error accumulates along the scan path or when the error magnitude is large, these approaches may not converge with satisfactory result. We propose a fundamentally new approach for ptychography probe position prediction for data with large position errors, where a neural network is used to make single-shot phase retrieval on individual diffraction patterns, yielding the object image at each scan point. The pairwise offsets among these images are then found using a robust image registration method, and the results are combined to yield the complete scan path by constructing and solving a linear equation. We show that our method can achieve good position prediction accuracy for data with large and accumulating errors on the order of $10^2$ pixels, a magnitude that often makes optimization-based algorithms fail to converge. For ptychography instruments without sophisticated position control equipment such as interferometers, our method is of significant practical potential.
Accurate prediction of antibody structure is a central task in the design and development of monoclonal antibodies, notably to understand both their developability and their binding properties. In this article, we introduce ABodyBuilder3, an improved and scalable antibody structure prediction model based on ImmuneBuilder. We achieve a new state-of-the-art accuracy in the modelling of CDR loops by leveraging language model embeddings, and show how predicted structures can be further improved through careful relaxation strategies. Finally, we incorporate a predicted Local Distance Difference Test into the model output to allow for a more accurate estimation of uncertainties.
Background: The aim of this study was to investigate the role of clinical, dosimetric and pretherapeutic magnetic resonance imaging (MRI) features for lesion-specific outcome prediction of stereotactic radiotherapy (SRT) in patients with brain metastases from malignant melanoma (MBM). Methods: In this multicenter, retrospective analysis, we reviewed 517 MBM from 130 patients treated with SRT (single fraction or hypofractionated). For each gross tumor volume (GTV) 1576 radiomic features (RF) were calculated (788 each for the GTV and for a 3 mm margin around the GTV). Clinical parameters, radiation dose and RF from pretherapeutic contrast-enhanced T1-weighted MRI from different institutions were evaluated with a feature processing and elimination pipeline in a nested cross-validation scheme. Results: Seventy-two (72) of 517 lesions (13.9%) showed a local failure (LF) after SRT. The processing pipeline showed clinical, dosimetric and radiomic features providing information for LF prediction. The most prominent ones were the correlation of the gray level co-occurrence matrix of the margin (hazard ratio (HR): 0.37, confidence interval (CI): 0.23-0.58) and systemic therapy before SRT (HR: 0.55, CI: 0.42-0.70). The majority of RF associated with LF was calculated in the margin around the GTV. Conclusions: Pretherapeutic MRI based RF connected with lesion-specific outcome after SRT could be identified, despite multicentric data and minor differences in imaging protocols. Image data analysis of the surrounding metastatic environment may provide therapy-relevant information with the potential to further individualize radiotherapy strategies.
The iterated learning model is an agent-based model of language change in which language is transmitted from a tutor to a pupil which itself becomes a tutor to a new pupil, and so on. Languages that are stable, expressive, and compositional arise spontaneously as a consequence of a language transmission bottleneck. Previous models have implemented an agent's mapping from signals to meanings using an artificial neural network decoder, but have relied on an unrealistic and computationally expensive process of obversion to implement the associated encoder, mapping from meanings to signals. Here, a new model is presented in which both decoder and encoder are neural networks, trained separately through supervised learning, and trained together through unsupervised learning in the form of an autoencoder. This avoids the substantial computational burden entailed in obversion and introduces a mixture of supervised and unsupervised learning as observed during human development.
Diagnosing and managing a patient is a complex, sequential decision making process that requires physicians to obtain information -- such as which tests to perform -- and to act upon it. Recent advances in artificial intelligence (AI) and large language models (LLMs) promise to profoundly impact clinical care. However, current evaluation schemes overrely on static medical question-answering benchmarks, falling short on interactive decision-making that is required in real-life clinical work. Here, we present AgentClinic: a multimodal benchmark to evaluate LLMs in their ability to operate as agents in simulated clinical environments. In our benchmark, the doctor agent must uncover the patient's diagnosis through dialogue and active data collection. We present two open medical agent benchmarks: a multimodal image and dialogue environment, AgentClinic-NEJM, and a dialogue-only environment, AgentClinic-MedQA. We embed cognitive and implicit biases both in patient and doctor agents to emulate realistic interactions between biased agents. We find that introducing bias leads to large reductions in diagnostic accuracy of the doctor agents, as well as reduced compliance, confidence, and follow-up consultation willingness in patient agents. Evaluating a suite of state-of-the-art LLMs, we find that several models that excel in benchmarks like MedQA are performing poorly in AgentClinic-MedQA. We find that the LLM used in the patient agent is an important factor for performance in the AgentClinic benchmark. We show that both having limited interactions as well as too many interaction reduces diagnostic accuracy in doctor agents. The code and data for this work is publicly available at //AgentClinic.github.io.
Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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