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This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: //kimialabmayo.github.io/PathDino-Page/

Tool learning aims to extend the capabilities of large language models (LLMs) with external tools. A major challenge in tool learning is how to support a large number of tools, including unseen tools. To address this challenge, previous studies have proposed retrieving suitable tools for the LLM based on the user query. However, previously proposed methods do not consider the differences between seen and unseen tools, nor do they take the hierarchy of the tool library into account, which may lead to suboptimal performance for tool retrieval. Therefore, to address the aforementioned issues, we propose ToolRerank, an adaptive and hierarchy-aware reranking method for tool retrieval to further refine the retrieval results. Specifically, our proposed ToolRerank includes Adaptive Truncation, which truncates the retrieval results related to seen and unseen tools at different positions, and Hierarchy-Aware Reranking, which makes retrieval results more concentrated for single-tool queries and more diverse for multi-tool queries. Experimental results show that ToolRerank can improve the quality of the retrieval results, leading to better execution results generated by the LLM.

Discourse Entity (DE) recognition is the task of identifying novel and known entities introduced within a text. While previous work has found that large language models have basic, if imperfect, DE recognition abilities (Schuster and Linzen, 2022), it remains largely unassessed which of the fundamental semantic properties that govern the introduction and subsequent reference to DEs they have knowledge of. We propose the Linguistically-Informed Evaluation for Discourse Entity Recognition (LIEDER) dataset that allows for a detailed examination of language models' knowledge of four crucial semantic properties: existence, uniqueness, plurality, and novelty. We find evidence that state-of-the-art large language models exhibit sensitivity to all of these properties except novelty, which demonstrates that they have yet to reach human-level language understanding abilities.

In recent times, a plethora of hardware accelerators have been put forth for graph learning applications such as vertex classification and graph classification. However, previous works have paid little attention to Knowledge Graph Completion (KGC), a task that is well-known for its significantly higher algorithm complexity. The state-of-the-art KGC solutions based on graph convolution neural network (GCN) involve extensive vertex/relation embedding updates and complicated score functions, which are inherently cumbersome for acceleration. As a result, existing accelerator designs are no longer optimal, and a novel algorithm-hardware co-design for KG reasoning is needed. Recently, brain-inspired HyperDimensional Computing (HDC) has been introduced as a promising solution for lightweight machine learning, particularly for graph learning applications. In this paper, we leverage HDC for an intrinsically more efficient and acceleration-friendly KGC algorithm. We also co-design an acceleration framework named HDReason targeting FPGA platforms. On the algorithm level, HDReason achieves a balance between high reasoning accuracy, strong model interpretability, and less computation complexity. In terms of architecture, HDReason offers reconfigurability, high training throughput, and low energy consumption. When compared with NVIDIA RTX 4090 GPU, the proposed accelerator achieves an average 10.6x speedup and 65x energy efficiency improvement. When conducting cross-models and cross-platforms comparison, HDReason yields an average 4.2x higher performance and 3.4x better energy efficiency with similar accuracy versus the state-of-the-art FPGA-based GCN training platform.

Curating high quality datasets that play a key role in the emergence of new AI applications requires considerable time, money, and computational resources. So, effective ownership protection of datasets is becoming critical. Recently, to protect the ownership of an image dataset, imperceptible watermarking techniques are used to store ownership information (i.e., watermark) into the individual image samples. Embedding the entire watermark into all samples leads to significant redundancy in the embedded information which damages the watermarked dataset quality and extraction accuracy. In this paper, a multi-segment encoding-decoding method for dataset watermarking (called AMUSE) is proposed to adaptively map the original watermark into a set of shorter sub-messages and vice versa. Our message encoder is an adaptive method that adjusts the length of the sub-messages according to the protection requirements for the target dataset. Existing image watermarking methods are then employed to embed the sub-messages into the original images in the dataset and also to extract them from the watermarked images. Our decoder is then used to reconstruct the original message from the extracted sub-messages. The proposed encoder and decoder are plug-and-play modules that can easily be added to any watermarking method. To this end, extensive experiments are preformed with multiple watermarking solutions which show that applying AMUSE improves the overall message extraction accuracy upto 28% for the same given dataset quality. Furthermore, the image dataset quality is enhanced by a PSNR of $\approx$2 dB on average, while improving the extraction accuracy for one of the tested image watermarking methods.

Deep learning has achieved remarkable success in graph-related tasks, yet this accomplishment heavily relies on large-scale high-quality annotated datasets. However, acquiring such datasets can be cost-prohibitive, leading to the practical use of labels obtained from economically efficient sources such as web searches and user tags. Unfortunately, these labels often come with noise, compromising the generalization performance of deep networks. To tackle this challenge and enhance the robustness of deep learning models against label noise in graph-based tasks, we propose a method called ERASE (Error-Resilient representation learning on graphs for lAbel noiSe tolerancE). The core idea of ERASE is to learn representations with error tolerance by maximizing coding rate reduction. Particularly, we introduce a decoupled label propagation method for learning representations. Before training, noisy labels are pre-corrected through structural denoising. During training, ERASE combines prototype pseudo-labels with propagated denoised labels and updates representations with error resilience, which significantly improves the generalization performance in node classification. The proposed method allows us to more effectively withstand errors caused by mislabeled nodes, thereby strengthening the robustness of deep networks in handling noisy graph data. Extensive experimental results show that our method can outperform multiple baselines with clear margins in broad noise levels and enjoy great scalability. Codes are released at //github.com/eraseai/erase.

Deep learning has become the dominant approach in coping with various tasks in Natural LanguageProcessing (NLP). Although text inputs are typically represented as a sequence of tokens, there isa rich variety of NLP problems that can be best expressed with a graph structure. As a result, thereis a surge of interests in developing new deep learning techniques on graphs for a large numberof NLP tasks. In this survey, we present a comprehensive overview onGraph Neural Networks(GNNs) for Natural Language Processing. We propose a new taxonomy of GNNs for NLP, whichsystematically organizes existing research of GNNs for NLP along three axes: graph construction,graph representation learning, and graph based encoder-decoder models. We further introducea large number of NLP applications that are exploiting the power of GNNs and summarize thecorresponding benchmark datasets, evaluation metrics, and open-source codes. Finally, we discussvarious outstanding challenges for making the full use of GNNs for NLP as well as future researchdirections. To the best of our knowledge, this is the first comprehensive overview of Graph NeuralNetworks for Natural Language Processing.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{//github.com/IBM/EvolveGCN}.

UMAP (Uniform Manifold Approximation and Projection) is a novel manifold learning technique for dimension reduction. UMAP is constructed from a theoretical framework based in Riemannian geometry and algebraic topology. The result is a practical scalable algorithm that applies to real world data. The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance. Furthermore, UMAP has no computational restrictions on embedding dimension, making it viable as a general purpose dimension reduction technique for machine learning.

We study the problem of learning to reason in large scale knowledge graphs (KGs). More specifically, we describe a novel reinforcement learning framework for learning multi-hop relational paths: we use a policy-based agent with continuous states based on knowledge graph embeddings, which reasons in a KG vector space by sampling the most promising relation to extend its path. In contrast to prior work, our approach includes a reward function that takes the accuracy, diversity, and efficiency into consideration. Experimentally, we show that our proposed method outperforms a path-ranking based algorithm and knowledge graph embedding methods on Freebase and Never-Ending Language Learning datasets.