Fine-tuned large language models (LLMs) often exhibit overconfidence, particularly when trained on small datasets, resulting in poor calibration and inaccurate uncertainty estimates. Evidential Deep Learning (EDL), an uncertainty-aware approach, enables uncertainty estimation in a single forward pass, making it a promising method for calibrating fine-tuned LLMs. However, despite its computational efficiency, EDL is prone to overfitting, as its training objective can result in overly concentrated probability distributions. To mitigate this, we propose regularizing EDL by incorporating an information bottleneck (IB). Our approach IB-EDL suppresses spurious information in the evidence generated by the model and encourages truly predictive information to influence both the predictions and uncertainty estimates. Extensive experiments across various fine-tuned LLMs and tasks demonstrate that IB-EDL outperforms both existing EDL and non-EDL approaches. By improving the trustworthiness of LLMs, IB-EDL facilitates their broader adoption in domains requiring high levels of confidence calibration.

Self-supervised learning (SSL) has gained prominence due to the increasing availability of unlabeled data and advances in computational efficiency, leading to revolutionized natural language processing with pre-trained language models like BERT and GPT. Representation learning, a core concept in SSL, aims to reduce data dimensionality while preserving meaningful aspects. Conventional SSL methods typically embed data in Euclidean space. However, recent research has revealed that alternative geometries can hold even richer representations, unlocking more meaningful insights from the data. Motivated by this, we propose two novel methods for integrating Hilbert geometry into self-supervised learning for efficient document embedding. First, we present a method directly incorporating Hilbert geometry into the standard Euclidean contrastive learning framework. Additionally, we propose a multi-view hyperbolic contrastive learning framework contrasting both documents and paragraphs. Our findings demonstrate that contrasting only paragraphs, rather than entire documents, can lead to superior efficiency and effectiveness.

% Self-supervised learning methods have shown promising results across a wide range of tasks in computer vision, natural language processing, and multimodal analysis. However, self-supervised approaches come with a notable limitation, dimensional collapse, where a model doesn't fully utilize its capacity to encode information optimally. Motivated by this, we propose ProSMin, a novel probabilistic self-supervised learning approach that leverages the power of probabilistic models to enhance representation quality and mitigate collapsing representations. Our proposed approach involves two neural networks, the online network and the target network, which collaborate and learn the diverse distribution of representations from each other through probabilistic knowledge distillation. The two networks are trained via our new loss function based on proper scoring rules. We provide a theoretical justification for ProSMin and demonstrate its modified scoring rule. This insight validates the method's optimization process and contributes to its robustness and effectiveness in improving representation quality. We evaluate our probabilistic model on various downstream tasks, such as in-distribution generalization, out-of-distribution detection, dataset corruption, low-shot learning, and transfer learning. Our method achieves superior accuracy and calibration, outperforming the self-supervised baseline in a variety of experiments on large datasets such as ImageNet-O and ImageNet-C. ProSMin thus demonstrates its scalability and real-world applicability. Our code is publicly available: https://github.com/amirvhd/SSL-sore-rule.

Deep learning has enabled outstanding progress on bioinformatics datasets and a variety of tasks, such as protein structure prediction, identification of regulatory regions, genome annotation, and interpretation of the noncoding genome. The layout and configuration of neural networks used for these tasks have mostly been developed manually by human experts, which is a time-consuming and error-prone process. Therefore, there is growing interest in automated neural architecture search (NAS) methods in bioinformatics. In this paper, we present a novel search space for NAS algorithms that operate on genome data, thus creating extensions for existing NAS algorithms for sequence data that we name Genome-DARTS, Genome-P-DARTS, Genome-BONAS, Genome-SH, and Genome-RS. Moreover, we introduce two novel NAS algorithms, CWP-DARTS and EDPDARTS, that build on and extend the idea of P-DARTS. We evaluate the presented methods and compare them to manually designed neural architectures on a widely used genome sequence machine learning task to show that NAS methods can be adapted well for bioinformatics sequence datasets. Our experiments show that architectures optimized by our NAS methods outperform manually developed architectures while having significantly fewer parameters.

The field of computational biology has been enhanced by deep learning models, which hold great promise for revolutionizing domains such as protein folding and drug discovery. Recent studies have underscored the tremendous potential of these models, particularly in the realm of gene regulation and the more profound understanding of the non-coding regions of the genome. On the other hand, this raises significant concerns about the reliability and efficacy of such models, which have their own biases by design, along with those learned from the data. Uncertainty quantification allows us to measure where the system is confident and know when it can be trusted. In this paper, we study several uncertainty quantification methods with respect to a multi-target regression task, specifically predicting regulatory activity profiles using DNA sequence data. Using the Basenji model, we investigate how such methods can improve in-domain generalization, out-of-distribution detection, and provide coverage guarantees on prediction intervals.

The ability to estimate epistemic uncertainty is often crucial when deploying machine learning in the real world, but modern methods often produce overconfident, uncalibrated uncertainty predictions. A common approach to quantify epistemic uncertainty, usable across a wide class of prediction models, is to train a model ensemble. In a naive implementation, the ensemble approach has high computational cost and high memory demand. This challenges in particular modern deep learning, where even a single deep network is already demanding in terms of compute and memory, and has given rise to a number of attempts to emulate the model ensemble without actually instantiating separate ensemble members. We introduce FiLM-Ensemble, a deep, implicit ensemble method based on the concept of Feature-wise Linear Modulation (FiLM). That technique was originally developed for multi-task learning, with the aim of decoupling different tasks. We show that the idea can be extended to uncertainty quantification: by modulating the network activations of a single deep network with FiLM, one obtains a model ensemble with high diversity, and consequently well-calibrated estimates of epistemic uncertainty, with low computational overhead in comparison. Empirically, FiLM-Ensemble outperforms other implicit ensemble methods, and it comes very close to the upper bound of an explicit ensemble of networks (sometimes even beating it), at a fraction of the memory cost.

We propose a new generative adversarial architecture to mitigate imbalance data problem in medical image semantic segmentation where the majority of pixels belongs to a healthy region and few belong to lesion or non-health region. A model trained with imbalanced data tends to bias towards healthy data which is not desired in clinical applications and predicted outputs by these networks have high precision and low sensitivity. We propose a new conditional generative refinement network with three components: a generative, a discriminative, and a refinement networks to mitigate imbalanced data problem through ensemble learning. The generative network learns to the segment at the pixel level by getting feedback from the discriminative network according to the true positive and true negative maps. On the other hand, the refinement network learns to predict the false positive and the false negative masks produced by the generative network that has significant value, especially in medical application. The final semantic segmentation masks are then composed by the output of the three networks. The proposed architecture shows state-of-the-art results on LiTS-2017 for simultaneous liver and lesion segmentation, and MDA231 for microscopic cell segmentation. We have achieved competitive results on BraTS-2017 for brain tumor segmentation.

Automatic tumor segmentation is an important and challenging clinical task because tumors have different sizes, shapes, contrasts, and locations. In this paper, we present an automatic instance semantic segmentation method based on deep neural networks (DNNs). The proposed networks are tailored to picture tumors in magnetic resonance imaging (MRI) and computed tomography (CT) images. We present an end-to-end multitask learning architecture comprising three stages, namely detection, segmentation, and classification. This paper introduces a new technique for tumor detection based on high-level extracted features from convolutional neural networks (CNNs) using the Hough transform technique. The detected tumor(s), are segmented with a set of fully connected (FC) layers, and the segmented mask is classified through FCs. The proposed architecture gives promising results on the popular medical image benchmarks. Our framework is generalized in the sense that it can be used in different types of medical images in varied sizes, such as the Liver Tumor Segmentation (LiTS-2017) challenge, and the Brain Tumor Segmentation (BraTS-2016) benchmark.