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 Knowledge Engineering


Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data Fan Zhang

Neural Information Processing Systems

Knowledge transfer between multi-omic single-cell data aims to effectively transfer cell types from scRNA-seq data to unannotated scATAC-seq data. Several approaches aim to reduce the heterogeneity of multi-omic data while maintaining the discriminability of cell types with extensive annotated data. However, in reality, the cost of collecting both a large amount of labeled scRNA-seq data and scATAC-seq data is expensive. Therefore, this paper explores a practical yet underexplored problem of knowledge transfer across multi-omic single-cell data under cell type scarcity. To address this problem, we propose a semi-supervised knowledge transfer framework named Dual label scArcity elimiNation with Cross-omic multi-samplE Mixup (DANCE). To overcome the label scarcity in scRNA-seq data, we generate pseudo-labels based on optimal transport and merge them into the labeled scRNAseq data.


On Giant's Shoulders: Effortless Weakto Strong by Dynamic Logits Fusion

Neural Information Processing Systems

Efficient fine-tuning of large language models for task-specific applications is imperative, yet the vast number of parameters in these models makes their training increasingly challenging. Despite numerous proposals for effective methods, a substantial memory overhead remains for gradient computations during updates. Can we fine-tune a series of task-specific small models and transfer their knowledge directly to a much larger model without additional training? In this paper, we explore weak-to-strong specialization using logit arithmetic, facilitating a direct answer to this question. Existing weak-to-strong methods often employ a static knowledge transfer ratio and a single small model for transferring complex knowledge, which leads to suboptimal performance.


Disentangling and mitigating the impact of task similarity for continual learning

Neural Information Processing Systems

Continual learning of partially similar tasks poses a challenge for artificial neural networks, as task similarity presents both an opportunity for knowledge transfer and a risk of interference and catastrophic forgetting. However, it remains unclear how task similarity in input features and readout patterns influences knowledge transfer and forgetting, as well as how they interact with common algorithms for continual learning. Here, we develop a linear teacher-student model with latent structure and show analytically that high input feature similarity coupled with low readout similarity is catastrophic for both knowledge transfer and retention. Conversely, the opposite scenario is relatively benign. Our analysis further reveals that taskdependent activity gating improves knowledge retention at the expense of transfer, while task-dependent plasticity gating does not affect either retention or transfer performance at the over-parameterized limit. In contrast, weight regularization based on the Fisher information metric significantly improves retention, regardless of task similarity, without compromising transfer performance. Nevertheless, its diagonal approximation and regularization in the Euclidean space are much less robust against task similarity. We demonstrate consistent results in a permuted MNIST task with latent variables. Overall, this work provides insights into when continual learning is difficult and how to mitigate it.



Supplementary Material: Knowledge-based in silico models and dataset for the comparative evaluation of mammography AI for a range of breast characteristics, lesion conspicuities and doses

Neural Information Processing Systems

M-SYNTH and code for processing can be found in https://github.com/DIDSR/ Please following the instructions on Github to dowload files from Huggingface. M-SYNTH is organized into a directory structure that indicates the parameters. Each folder contains mammogram data that can be read from.raw Note that only examples with odd PHANTOM_FILEID contain lesions, others do not.



On Giant's Shoulders: Effortless Weakto Strong by Dynamic Logits Fusion

Neural Information Processing Systems

Efficient fine-tuning of large language models for task-specific applications is imperative, yet the vast number of parameters in these models makes their training increasingly challenging. Despite numerous proposals for effective methods, a substantial memory overhead remains for gradient computations during updates. Can we fine-tune a series of task-specific small models and transfer their knowledge directly to a much larger model without additional training? In this paper, we explore weak-to-strong specialization using logit arithmetic, facilitating a direct answer to this question. Existing weak-to-strong methods often employ a static knowledge transfer ratio and a single small model for transferring complex knowledge, which leads to suboptimal performance.


K-L ITE: Learning Transferable Visual Models with External Knowledge

Neural Information Processing Systems

The new generation of state-of-the-art computer vision systems are trained from natural language supervision, ranging from simple object category names to descriptive captions. This form of supervision ensures high generality and usability of the learned visual models, due to the broad concept coverage achieved via largescale data collection process. Alternatively, we argue that learning with external knowledge is a promising way which leverages a much more structured source of supervision and offers sample efficiency.


Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data Fan Zhang

Neural Information Processing Systems

Knowledge transfer between multi-omic single-cell data aims to effectively transfer cell types from scRNA-seq data to unannotated scATAC-seq data. Several approaches aim to reduce the heterogeneity of multi-omic data while maintaining the discriminability of cell types with extensive annotated data. However, in reality, the cost of collecting both a large amount of labeled scRNA-seq data and scATAC-seq data is expensive. Therefore, this paper explores a practical yet underexplored problem of knowledge transfer across multi-omic single-cell data under cell type scarcity. To address this problem, we propose a semi-supervised knowledge transfer framework named Dual label scArcity elimiNation with Cross-omic multi-samplE Mixup (DANCE). To overcome the label scarcity in scRNA-seq data, we generate pseudo-labels based on optimal transport and merge them into the labeled scRNAseq data.


Disentangling and mitigating the impact of task similarity for continual learning

Neural Information Processing Systems

Continual learning of partially similar tasks poses a challenge for artificial neural networks, as task similarity presents both an opportunity for knowledge transfer and a risk of interference and catastrophic forgetting. However, it remains unclear how task similarity in input features and readout patterns influences knowledge transfer and forgetting, as well as how they interact with common algorithms for continual learning. Here, we develop a linear teacher-student model with latent structure and show analytically that high input feature similarity coupled with low readout similarity is catastrophic for both knowledge transfer and retention. Conversely, the opposite scenario is relatively benign. Our analysis further reveals that taskdependent activity gating improves knowledge retention at the expense of transfer, while task-dependent plasticity gating does not affect either retention or transfer performance at the over-parameterized limit. In contrast, weight regularization based on the Fisher information metric significantly improves retention, regardless of task similarity, without compromising transfer performance. Nevertheless, its diagonal approximation and regularization in the Euclidean space are much less robust against task similarity. We demonstrate consistent results in a permuted MNIST task with latent variables. Overall, this work provides insights into when continual learning is difficult and how to mitigate it.