In-Context Learning with Many Demonstration Examples

Large pre-training language models (PLMs) have shown promising in-context learning abilities. However, due to the backbone transformer architecture, existing PLMs are bottlenecked by the memory and computational cost when scaling up to a large context size, leaving instruction tuning and in-context learning of many demonstration examples, as well as long-range language modeling under-explored. In this study, we propose a long-range language model EVALM based on an efficient transformer mechanism. EVALM is trained with 8k tokens per batch line and can test up to 256k-lengthed contexts with extrapolation, 128 times to the limit of existing PLMs (e.g. GPT3). Based on EVALM, we scale up the size of examples efficiently in both instruction tuning and in-context learning to explore the boundary of the benefits from more annotated data. Experimental results on a diverse set of tasks show that EVALM achieves 4.1% higher accuracy on average, and the average length of achieving the best accuracy score over tasks is around 12k. We find that in-context learning can achieve higher performance with more demonstrations under many-shot instruction tuning (8k), and further extending the length of instructions (16k) can further improve the upper bound of scaling in-context learning.

LDMIC: Learning-based Distributed Multi-view Image Coding

Multi-view image compression plays a critical role in 3D-related applications. Existing methods adopt a predictive coding architecture, which requires joint encoding to compress the corresponding disparity as well as residual information. This demands collaboration among cameras and enforces the epipolar geometric constraint between different views, which makes it challenging to deploy these methods in distributed camera systems with randomly overlapping fields of view. Meanwhile, distributed source coding theory indicates that efficient data compression of correlated sources can be achieved by independent encoding and joint decoding, which motivates us to design a learning-based distributed multi-view image coding (LDMIC) framework. With independent encoders, LDMIC introduces a simple yet effective joint context transfer module based on the cross-attention mechanism at the decoder to effectively capture the global inter-view correlations, which is insensitive to the geometric relationships between images. Experimental results show that LDMIC significantly outperforms both traditional and learning-based MIC methods while enjoying fast encoding speed. Code will be released at https://github.com/Xinjie-Q/LDMIC.

Artificial intelligence for diagnosing and predicting survival of patients with renal cell carcinoma: Retrospective multi-center study

Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a weakly-supervised deep learning strategy using conventional histology of 1752 whole slide images from multiple centers. Our study was demonstrated through internal cross-validation and external validations for the deep learning-based models. Results: Automatic diagnosis for ccRCC through intelligent subtyping of renal cell carcinoma was proved in this study. Our graderisk achieved aera the curve (AUC) of 0.840 (95% confidence interval: 0.805-0.871) in the TCGA cohort, 0.840 (0.805-0.871) in the General cohort, and 0.840 (0.805-0.871) in the CPTAC cohort for the recognition of high-grade tumor. The OSrisk for the prediction of 5-year survival status achieved AUC of 0.784 (0.746-0.819) in the TCGA cohort, which was further verified in the independent General cohort and the CPTAC cohort, with AUC of 0.774 (0.723-0.820) and 0.702 (0.632-0.765), respectively. Cox regression analysis indicated that graderisk, OSrisk, tumor grade, and tumor stage were found to be independent prognostic factors, which were further incorporated into the competing-risk nomogram (CRN). Kaplan-Meier survival analyses further illustrated that our CRN could significantly distinguish patients with high survival risk, with hazard ratio of 5.664 (3.893-8.239, p < 0.0001) in the TCGA cohort, 35.740 (5.889-216.900, p < 0.0001) in the General cohort and 6.107 (1.815 to 20.540, p < 0.0001) in the CPTAC cohort. Comparison analyses conformed that our CRN outperformed current prognosis indicators in the prediction of survival status, with higher concordance index for clinical prognosis.

Machine Learning for Large-Scale Optimization in 6G Wireless Networks

The sixth generation (6G) wireless systems are envisioned to enable the paradigm shift from "connected things" to "connected intelligence", featured by ultra high density, large-scale, dynamic heterogeneity, diversified functional requirements and machine learning capabilities, which leads to a growing need for highly efficient intelligent algorithms. The classic optimization-based algorithms usually require highly precise mathematical model of data links and suffer from poor performance with high computational cost in realistic 6G applications. Based on domain knowledge (e.g., optimization models and theoretical tools), machine learning (ML) stands out as a promising and viable methodology for many complex large-scale optimization problems in 6G, due to its superior performance, generalizability, computational efficiency and robustness. In this paper, we systematically review the most representative "learning to optimize" techniques in diverse domains of 6G wireless networks by identifying the inherent feature of the underlying optimization problem and investigating the specifically designed ML frameworks from the perspective of optimization. In particular, we will cover algorithm unrolling, learning to branch-and-bound, graph neural network for structured optimization, deep reinforcement learning for stochastic optimization, end-to-end learning for semantic optimization, as well as federated learning for distributed optimization, for solving challenging large-scale optimization problems arising from various important wireless applications. Through the in-depth discussion, we shed light on the excellent performance of ML-based optimization algorithms with respect to the classical methods, and provide insightful guidance to develop advanced ML techniques in 6G networks.

Large-scale single-photon imaging

Benefiting from its single-photon sensitivity, single-photon avalanche diode (SPAD) array has been widely applied in various fields such as fluorescence lifetime imaging and quantum computing. However, large-scale high-fidelity single-photon imaging remains a big challenge, due to the complex hardware manufacture craft and heavy noise disturbance of SPAD arrays. In this work, we introduce deep learning into SPAD, enabling super-resolution single-photon imaging over an order of magnitude, with significant enhancement of bit depth and imaging quality. We first studied the complex photon flow model of SPAD electronics to accurately characterize multiple physical noise sources, and collected a real SPAD image dataset (64 $\times$ 32 pixels, 90 scenes, 10 different bit depth, 3 different illumination flux, 2790 images in total) to calibrate noise model parameters. With this real-world physical noise model, we for the first time synthesized a large-scale realistic single-photon image dataset (image pairs of 5 different resolutions with maximum megapixels, 17250 scenes, 10 different bit depth, 3 different illumination flux, 2.6 million images in total) for subsequent network training. To tackle the severe super-resolution challenge of SPAD inputs with low bit depth, low resolution, and heavy noise, we further built a deep transformer network with a content-adaptive self-attention mechanism and gated fusion modules, which can dig global contextual features to remove multi-source noise and extract full-frequency details. We applied the technique on a series of experiments including macroscopic and microscopic imaging, microfluidic inspection, and Fourier ptychography. The experiments validate the technique's state-of-the-art super-resolution SPAD imaging performance, with more than 5 dB superiority on PSNR compared to the existing methods.

RLogist: Fast Observation Strategy on Whole-slide Images with Deep Reinforcement Learning

Whole-slide images (WSI) in computational pathology have high resolution with gigapixel size, but are generally with sparse regions of interest, which leads to weak diagnostic relevance and data inefficiency for each area in the slide. Most of the existing methods rely on a multiple instance learning framework that requires densely sampling local patches at high magnification. The limitation is evident in the application stage as the heavy computation for extracting patch-level features is inevitable. In this paper, we develop RLogist, a benchmarking deep reinforcement learning (DRL) method for fast observation strategy on WSIs. Imitating the diagnostic logic of human pathologists, our RL agent learns how to find regions of observation value and obtain representative features across multiple resolution levels, without having to analyze each part of the WSI at the high magnification. We benchmark our method on two whole-slide level classification tasks, including detection of metastases in WSIs of lymph node sections, and subtyping of lung cancer. Experimental results demonstrate that RLogist achieves competitive classification performance compared to typical multiple instance learning algorithms, while having a significantly short observation path. In addition, the observation path given by RLogist provides good decision-making interpretability, and its ability of reading path navigation can potentially be used by pathologists for educational/assistive purposes. Our code is available at: \url{https://github.com/tencent-ailab/RLogist}.

iEnhancer-ELM: Improve Enhancer Identification by Extracting Multi-scale Contextual Information based on Enhancer Language Models

Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many state-of-the-art computational methods have been proposed in order to efficiently identify enhancers, learning globally contextual features is still one of the challenges for computational methods. Regarding the similarities between biological sequences and natural language sentences, the novel BERT-based language techniques have been applied to extracting complex contextual features in various computational biology tasks such as protein function/structure prediction. To speed up the research on enhancer identification, it is urgent to construct a BERT-based enhancer language model. Results: In this paper, we propose a multi-scale enhancer identification method (iEnhancer-ELM) based on enhancer language models, which treat enhancer sequences as natural language sentences that are composed of k-mer nucleotides. iEnhancer-ELM can extract contextual information of multi-scale k-mers with positions from raw enhancer sequences. Benefiting from the complementary information of k-mers in multi-scale, we ensemble four iEnhancer-ELM models for improving enhancer identification. The benchmark comparisons show that our model outperforms state-of-the-art methods. By the interpretable attention mechanism, we finds 30 biological patterns, where 40% (12/30) are verified by a widely used motif tool (STREME) and a popular dataset (JASPAR), demonstrating our model has a potential ability to reveal the biological mechanism of enhancer. Availability: The source code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn and junjie.chen.hit@gmail.com; Supplementary information: Supplementary data are available at Bioinformatics online.

A Self-adaptive Neuroevolution Approach to Constructing Deep Neural Network Architectures Across Different Types

Neuroevolution has greatly promoted Deep Neural Network (DNN) architecture design and its applications, while there is a lack of methods available across different DNN types concerning both their scale and performance. In this study, we propose a self-adaptive neuroevolution (SANE) approach to automatically construct various lightweight DNN architectures for different tasks. One of the key settings in SANE is the search space defined by cells and organs self-adapted to different DNN types. Based on this search space, a constructive evolution strategy with uniform evolution settings and operations is designed to grow DNN architectures gradually. SANE is able to self-adaptively adjust evolution exploration and exploitation to improve search efficiency. Moreover, a speciation scheme is developed to protect evolution from early convergence by restricting selection competition within species. To evaluate SANE, we carry out neuroevolution experiments to generate different DNN architectures including convolutional neural network, generative adversarial network and long short-term memory. The results illustrate that the obtained DNN architectures could have smaller scale with similar performance compared to existing DNN architectures. Our proposed SANE provides an efficient approach to self-adaptively search DNN architectures across different types.

An Adaptive and Robust Deep Learning Framework for THz Ultra-Massive MIMO Channel Estimation

Terahertz ultra-massive MIMO (THz UM-MIMO) is envisioned as one of the key enablers of 6G wireless networks, for which channel estimation is highly challenging. Traditional analytical estimation methods are no longer effective, as the enlarged array aperture and the small wavelength result in a mixture of far-field and near-field paths, constituting a hybrid-field channel. Deep learning (DL)-based methods, despite the competitive performance, generally lack theoretical guarantees and scale poorly with the size of the array. In this paper, we propose a general DL framework for THz UM-MIMO channel estimation, which leverages existing iterative channel estimators and is with provable guarantees. Each iteration is implemented by a fixed point network (FPN), consisting of a closed-form linear estimator and a DL-based non-linear estimator. The proposed method perfectly matches the THz UM-MIMO channel estimation due to several unique advantages. First, the complexity is low and adaptive. It enjoys provable linear convergence with a low per-iteration cost and monotonically increasing accuracy, which enables an adaptive accuracy-complexity tradeoff. Second, it is robust to practical distribution shifts and can directly generalize to a variety of heavily out-of-distribution scenarios with almost no performance loss, which is suitable for the complicated THz channel conditions. Theoretical analysis and extensive simulation results are provided to illustrate the advantages over the state-of-the-art methods in estimation accuracy, convergence rate, complexity, and robustness.