DEL-Ranking: Ranking-Correction Denoising Framework for Elucidating Molecular Affinities in DNA-Encoded Libraries

DNA-encoded library (DEL) screening has revolutionized the detection of protein-ligand interactions through read counts, enabling rapid exploration of vast chemical spaces. However, noise in read counts, stemming from nonspecific interactions, can mislead this exploration process. We present DEL-Ranking, a novel distribution-correction denoising framework that addresses these challenges. Our approach introduces two key innovations: (1) a novel ranking loss that rectifies relative magnitude relationships between read counts, enabling the learning of causal features determining activity levels, and (2) an iterative algorithm employing self-training and consistency loss to establish model coherence between activity label and read count predictions. Furthermore, we contribute three new DEL screening datasets, the first to comprehensively include multi-dimensional molecular representations, protein-ligand enrichment values, and their activity labels. These datasets mitigate data scarcity issues in AI-driven DEL screening research. Rigorous evaluation on diverse DEL datasets demonstrates DEL-Ranking's superior performance across multiple correlation metrics, with significant improvements in binding affinity prediction accuracy. Our model exhibits zero-shot generalization ability across different protein targets and successfully identifies potential motifs determining compound binding affinity. This work advances DEL screening analysis and provides valuable resources for future research in this area.

SurgPETL: Parameter-Efficient Image-to-Surgical-Video Transfer Learning for Surgical Phase Recognition

Capitalizing on image-level pre-trained models for various downstream tasks has recently emerged with promising performance. However, the paradigm of "image pre-training followed by video fine-tuning" for high-dimensional video data inevitably poses significant performance bottlenecks. Furthermore, in the medical domain, many surgical video tasks encounter additional challenges posed by the limited availability of video data and the necessity for comprehensive spatial-temporal modeling. Recently, Parameter-Efficient Image-to-Video Transfer Learning has emerged as an efficient and effective paradigm for video action recognition tasks, which employs image-level pre-trained models with promising feature transferability and involves cross-modality temporal modeling with minimal fine-tuning. Nevertheless, the effectiveness and generalizability of this paradigm within intricate surgical domain remain unexplored. In this paper, we delve into a novel problem of efficiently adapting image-level pre-trained models to specialize in fine-grained surgical phase recognition, termed as Parameter-Efficient Image-to-Surgical-Video Transfer Learning. Firstly, we develop a parameter-efficient transfer learning benchmark SurgPETL for surgical phase recognition, and conduct extensive experiments with three advanced methods based on ViTs of two distinct scales pre-trained on five large-scale natural and medical datasets. Then, we introduce the Spatial-Temporal Adaptation module, integrating a standard spatial adapter with a novel temporal adapter to capture detailed spatial features and establish connections across temporal sequences for robust spatial-temporal modeling. Extensive experiments on three challenging datasets spanning various surgical procedures demonstrate the effectiveness of SurgPETL with STA.

CODIS: Benchmarking Context-Dependent Visual Comprehension for Multimodal Large Language Models

Multimodal large language models (MLLMs) have demonstrated promising results in a variety of tasks that combine vision and language. As these models become more integral to research and applications, conducting comprehensive evaluations of their capabilities has grown increasingly important. However, most existing benchmarks fail to consider that, in certain situations, images need to be interpreted within a broader context. In this work, we introduce a new benchmark, named as CODIS, designed to assess the ability of models to use context provided in free-form text to enhance visual comprehension. Our findings indicate that MLLMs consistently fall short of human performance on this benchmark. Further analysis confirms that these models struggle to effectively extract and utilize contextual information to improve their understanding of images. This underscores the pressing need to enhance the ability of MLLMs to comprehend visuals in a context-dependent manner. View our project website at https://thunlp-mt.github.io/CODIS.

Partition Speeds Up Learning Implicit Neural Representations Based on Exponential-Increase Hypothesis

$\textit{Implicit neural representations}$ (INRs) aim to learn a $\textit{continuous function}$ (i.e., a neural network) to represent an image, where the input and output of the function are pixel coordinates and RGB/Gray values, respectively. However, images tend to consist of many objects whose colors are not perfectly consistent, resulting in the challenge that image is actually a $\textit{discontinuous piecewise function}$ and cannot be well estimated by a continuous function. In this paper, we empirically investigate that if a neural network is enforced to fit a discontinuous piecewise function to reach a fixed small error, the time costs will increase exponentially with respect to the boundaries in the spatial domain of the target signal. We name this phenomenon the $\textit{exponential-increase}$ hypothesis. Under the $\textit{exponential-increase}$ hypothesis, learning INRs for images with many objects will converge very slowly. To address this issue, we first prove that partitioning a complex signal into several sub-regions and utilizing piecewise INRs to fit that signal can significantly speed up the convergence. Based on this fact, we introduce a simple partition mechanism to boost the performance of two INR methods for image reconstruction: one for learning INRs, and the other for learning-to-learn INRs. In both cases, we partition an image into different sub-regions and dedicate smaller networks for each part. In addition, we further propose two partition rules based on regular grids and semantic segmentation maps, respectively. Extensive experiments validate the effectiveness of the proposed partitioning methods in terms of learning INR for a single image (ordinary learning framework) and the learning-to-learn framework.

Intelligibility prediction with a pretrained noise-robust automatic speech recognition model

This paper describes two intelligibility prediction systems derived from a pretrained noise-robust automatic speech recognition (ASR) model for the second Clarity Prediction Challenge (CPC2). One system is intrusive and leverages the hidden representations of the ASR model. The other system is non-intrusive and makes predictions with derived ASR uncertainty. The ASR model is only pretrained with a simulated noisy speech corpus and does not take advantage of the CPC2 data. For that reason, the intelligibility prediction systems are robust to unseen scenarios given the accurate prediction performance on the CPC2 evaluation.

Homophily-enhanced Structure Learning for Graph Clustering

Graph clustering is a fundamental task in graph analysis, and recent advances in utilizing graph neural networks (GNNs) have shown impressive results. Despite the success of existing GNN-based graph clustering methods, they often overlook the quality of graph structure, which is inherent in real-world graphs due to their sparse and multifarious nature, leading to subpar performance. Graph structure learning allows refining the input graph by adding missing links and removing spurious connections. However, previous endeavors in graph structure learning have predominantly centered around supervised settings, and cannot be directly applied to our specific clustering tasks due to the absence of ground-truth labels. To bridge the gap, we propose a novel method called \textbf{ho}mophily-enhanced structure \textbf{le}arning for graph clustering (HoLe). Our motivation stems from the observation that subtly enhancing the degree of homophily within the graph structure can significantly improve GNNs and clustering outcomes. To realize this objective, we develop two clustering-oriented structure learning modules, i.e., hierarchical correlation estimation and cluster-aware sparsification. The former module enables a more accurate estimation of pairwise node relationships by leveraging guidance from latent and clustering spaces, while the latter one generates a sparsified structure based on the similarity matrix and clustering assignments. Additionally, we devise a joint optimization approach alternating between training the homophily-enhanced structure learning and GNN-based clustering, thereby enforcing their reciprocal effects. Extensive experiments on seven benchmark datasets of various types and scales, across a range of clustering metrics, demonstrate the superiority of HoLe against state-of-the-art baselines.

Multi-source adversarial transfer learning for ultrasound image segmentation with limited similarity

Lesion segmentation of ultrasound medical images based on deep learning techniques is a widely used method for diagnosing diseases. Although there is a large amount of ultrasound image data in medical centers and other places, labeled ultrasound datasets are a scarce resource, and it is likely that no datasets are available for new tissues/organs. Transfer learning provides the possibility to solve this problem, but there are too many features in natural images that are not related to the target domain. As a source domain, redundant features that are not conducive to the task will be extracted. Migration between ultrasound images can avoid this problem, but there are few types of public datasets, and it is difficult to find sufficiently similar source domains. Compared with natural images, ultrasound images have less information, and there are fewer transferable features between different ultrasound images, which may cause negative transfer. To this end, a multi-source adversarial transfer learning network for ultrasound image segmentation is proposed. Specifically, to address the lack of annotations, the idea of adversarial transfer learning is used to adaptively extract common features between a certain pair of source and target domains, which provides the possibility to utilize unlabeled ultrasound data. To alleviate the lack of knowledge in a single source domain, multi-source transfer learning is adopted to fuse knowledge from multiple source domains. In order to ensure the effectiveness of the fusion and maximize the use of precious data, a multi-source domain independent strategy is also proposed to improve the estimation of the target domain data distribution, which further increases the learning ability of the multi-source adversarial migration learning network in multiple domains.

Unsupervised Uncertainty Measures of Automatic Speech Recognition for Non-intrusive Speech Intelligibility Prediction

Non-intrusive intelligibility prediction is important for its application in realistic scenarios, where a clean reference signal is difficult to access. The construction of many non-intrusive predictors require either ground truth intelligibility labels or clean reference signals for supervised learning. In this work, we leverage an unsupervised uncertainty estimation method for predicting speech intelligibility, which does not require intelligibility labels or reference signals to train the predictor. Our experiments demonstrate that the uncertainty from state-of-the-art end-to-end automatic speech recognition (ASR) models is highly correlated with speech intelligibility. The proposed method is evaluated on two databases and the results show that the unsupervised uncertainty measures of ASR models are more correlated with speech intelligibility from listening results than the predictions made by widely used intrusive methods.

Exploiting Hidden Representations from a DNN-based Speech Recogniser for Speech Intelligibility Prediction in Hearing-impaired Listeners

An accurate objective speech intelligibility prediction algorithms is of great interest for many applications such as speech enhancement for hearing aids. Most algorithms measures the signal-to-noise ratios or correlations between the acoustic features of clean reference signals and degraded signals. However, these hand-picked acoustic features are usually not explicitly correlated with recognition. Meanwhile, deep neural network (DNN) based automatic speech recogniser (ASR) is approaching human performance in some speech recognition tasks. This work leverages the hidden representations from DNN-based ASR as features for speech intelligibility prediction in hearing-impaired listeners. The experiments based on a hearing aid intelligibility database show that the proposed method could make better prediction than a widely used short-time objective intelligibility (STOI) based binaural measure.

Auditory-Based Data Augmentation for End-to-End Automatic Speech Recognition

End-to-end models have achieved significant improvement on automatic speech recognition. One common method to improve performance of these models is expanding the data-space through data augmentation. Meanwhile, human auditory inspired front-ends have also demonstrated improvement for automatic speech recognisers. In this work, a well-verified auditory-based model, which can simulate various hearing abilities, is investigated for the purpose of data augmentation for end-to-end speech recognition. By introducing the auditory model into the data augmentation process, end-to-end systems are encouraged to ignore variation from the signal that cannot be heard and thereby focus on robust features for speech recognition. Two mechanisms in the auditory model, spectral smearing and loudness recruitment, are studied on the LibriSpeech dataset with a transformer-based end-to-end model. The results show that the proposed augmentation methods can bring statistically significant improvement on the performance of the state-of-the-art SpecAugment.