Training-Free Large Model Priors for Multiple-in-One Image Restoration

Image restoration aims to reconstruct the latent clear images from their degraded versions. Despite the notable achievement, existing methods predominantly focus on handling specific degradation types and thus require specialized models, impeding real-world applications in dynamic degradation scenarios. To address this issue, we propose Large Model Driven Image Restoration framework (LMDIR), a novel multiple-in-one image restoration paradigm that leverages the generic priors from large multi-modal language models (MMLMs) and the pretrained diffusion models. In detail, LMDIR integrates three key prior knowledges: 1) global degradation knowledge from MMLMs, 2) scene-aware contextual descriptions generated by MMLMs, and 3) fine-grained high-quality reference images synthesized by diffusion models guided by MMLM descriptions. Standing on above priors, our architecture comprises a query-based prompt encoder, degradation-aware transformer block injecting global degradation knowledge, content-aware transformer block incorporating scene description, and reference-based transformer block incorporating fine-grained image priors. This design facilitates single-stage training paradigm to address various degradations while supporting both automatic and user-guided restoration. Extensive experiments demonstrate that our designed method outperforms state-of-the-art competitors on multiple evaluation benchmarks.

Du-IN: Discrete units-guided mask modeling for decoding speech from Intracranial Neural signals

Invasive brain-computer interfaces have garnered significant attention due to their high performance. The current intracranial stereoElectroEncephaloGraphy (sEEG) foundation models typically build univariate representations based on a single channel. Some of them further use Transformer to model the relationship among channels. However, due to the locality and specificity of brain computation, their performance on more difficult tasks, e.g., speech decoding, which demands intricate processing in specific brain regions, is yet to be fully investigated. We hypothesize that building multi-variate representations within certain brain regions can better capture the specific neural processing. To explore this hypothesis, we collect a well-annotated Chinese word-reading sEEG dataset, targeting language-related brain networks, over 12 subjects. Leveraging this benchmark dataset, we developed the Du-IN model that can extract contextual embeddings from specific brain regions through discrete codebook-guided mask modeling. Our model achieves SOTA performance on the downstream 61-word classification task, surpassing all baseline models. Model comparison and ablation analysis reveal that our design choices, including (i) multi-variate representation by fusing channels in vSMC and STG regions and (ii) self-supervision by discrete codebook-guided mask modeling, significantly contribute to these performances. Collectively, our approach, inspired by neuroscience findings, capitalizing on multi-variate neural representation from specific brain regions, is suitable for invasive brain modeling. It marks a promising neuro-inspired AI approach in BCI.

Universal Sleep Decoder: Aligning awake and sleep neural representation across subjects

Decoding memory content from brain activity during sleep has long been a goal in neuroscience. While spontaneous reactivation of memories during sleep in rodents is known to support memory consolidation and offline learning, capturing memory replay in humans is challenging due to the absence of well-annotated sleep datasets and the substantial differences in neural patterns between wakefulness and sleep. To address these challenges, we designed a novel cognitive neuroscience experiment and collected a comprehensive, well-annotated electroencephalography (EEG) dataset from 52 subjects during both wakefulness and sleep. Leveraging this benchmark dataset, we developed the Universal Sleep Decoder (USD) to align neural representations between wakefulness and sleep across subjects. Our model achieves up to 16.6% top-1 zero-shot accuracy on unseen subjects, comparable to decoding performances using individual sleep data. Furthermore, fine-tuning USD on test subjects enhances decoding accuracy to 25.9% top-1 accuracy, a substantial improvement over the baseline chance of 6.7%. Model comparison and ablation analyses reveal that our design choices, including the use of (i) an additional contrastive objective to integrate awake and sleep neural signals and (ii) the pretrain-finetune paradigm to incorporate different subjects, significantly contribute to these performances. Collectively, our findings and methodologies represent a significant advancement in the field of sleep decoding.

Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.