AGMDT: Virtual Staining of Renal Histology Images with Adjacency-Guided Multi-Domain Transfer

Renal pathology, as the gold standard of kidney disease diagnosis, requires doctors to analyze a series of tissue slices stained by H&E staining and special staining like Masson, PASM, and PAS, respectively. These special staining methods are costly, time-consuming, and hard to standardize for wide use especially in primary hospitals. Advances of supervised learning methods have enabled the virtually conversion of H&E images into special staining images, but achieving pixel-to-pixel alignment for training remains challenging. In contrast, unsupervised learning methods regarding different stains as different style transfer domains can utilize unpaired data, but they ignore the spatial inter-domain correlations and thus decrease the trustworthiness of structural details for diagnosis. In this paper, we propose a novel virtual staining framework AGMDT to translate images into other domains by avoiding pixel-level alignment and meanwhile utilizing the correlations among adjacent tissue slices. We first build a high-quality multi-domain renal histological dataset where each specimen case comprises a series of slices stained in various ways. Based on it, the proposed framework AGMDT discovers patch-level aligned pairs across the serial slices of multi-domains through glomerulus detection and bipartite graph matching, and utilizes such correlations to supervise the end-to-end model for multi-domain staining transformation. Experimental results show that the proposed AGMDT achieves a good balance between the precise pixel-level alignment and unpaired domain transfer by exploiting correlations across multi-domain serial pathological slices, and outperforms the state-of-the-art methods in both quantitative measure and morphological details.

Enhancing Quantised End-to-End ASR Models via Personalisation

Recent end-to-end automatic speech recognition (ASR) models have become increasingly larger, making them particularly challenging to be deployed on resource-constrained devices. Model quantisation is an effective solution that sometimes causes the word error rate (WER) to increase. In this paper, a novel strategy of personalisation for a quantised model (PQM) is proposed, which combines speaker adaptive training (SAT) with model quantisation to improve the performance of heavily compressed models. Specifically, PQM uses a 4-bit NormalFloat Quantisation (NF4) approach for model quantisation and low-rank adaptation (LoRA) for SAT. Experiments have been performed on the LibriSpeech and the TED-LIUM 3 corpora. Remarkably, with a 7x reduction in model size and 1% additional speaker-specific parameters, 15.1% and 23.3% relative WER reductions were achieved on quantised Whisper and Conformer-based attention-based encoder-decoder ASR models respectively, comparing to the original full precision models.

A Multi-In and Multi-Out Dendritic Neuron Model and its Optimization

Artificial neural networks (ANNs), inspired by the interconnection of real neurons, have achieved unprecedented success in various fields such as computer vision and natural language processing. Recently, a novel mathematical ANN model, known as the dendritic neuron model (DNM), has been proposed to address nonlinear problems by more accurately reflecting the structure of real neurons. However, the single-output design limits its capability to handle multi-output tasks, significantly lowering its applications. In this paper, we propose a novel multi-in and multi-out dendritic neuron model (MODN) to tackle multi-output tasks. Our core idea is to introduce a filtering matrix to the soma layer to adaptively select the desired dendrites to regress each output. Because such a matrix is designed to be learnable, MODN can explore the relationship between each dendrite and output to provide a better solution to downstream tasks. We also model a telodendron layer into MODN to simulate better the real neuron behavior. Importantly, MODN is a more general and unified framework that can be naturally specialized as the DNM by customizing the filtering matrix. To explore the optimization of MODN, we investigate both heuristic and gradient-based optimizers and introduce a 2-step training method for MODN. Extensive experimental results performed on 11 datasets on both binary and multi-class classification tasks demonstrate the effectiveness of MODN, with respect to accuracy, convergence, and generality.

RAIN: Your Language Models Can Align Themselves without Finetuning

Large language models (LLMs) often demonstrate inconsistencies with human preferences. Previous research gathered human preference data and then aligned the pre-trained models using reinforcement learning or instruction tuning, the so-called finetuning step. In contrast, aligning frozen LLMs without any extra data is more appealing. This work explores the potential of the latter setting. We discover that by integrating self-evaluation and rewind mechanisms, unaligned LLMs can directly produce responses consistent with human preferences via self-boosting. We introduce a novel inference method, Rewindable Auto-regressive INference (RAIN), that allows pre-trained LLMs to evaluate their own generation and use the evaluation results to guide backward rewind and forward generation for AI safety. Notably, RAIN operates without the need of extra data for model alignment and abstains from any training, gradient computation, or parameter updates; during the self-evaluation phase, the model receives guidance on which human preference to align with through a fixed-template prompt, eliminating the need to modify the initial prompt. Experimental results evaluated by GPT-4 and humans demonstrate the effectiveness of RAIN: on the HH dataset, RAIN improves the harmlessness rate of LLaMA 30B over vanilla inference from 82% to 97%, while maintaining the helpfulness rate. Under the leading adversarial attack llm-attacks on Vicuna 33B, RAIN establishes a new defense baseline by reducing the attack success rate from 94% to 19%.

Can Whisper perform speech-based in-context learning

This paper investigates the in-context learning abilities of the Whisper automatic speech recognition (ASR) models released by OpenAI. A novel speech-based in-context learning (SICL) approach is proposed for test-time adaptation, which can reduce the word error rates (WERs) with only a small number of labelled speech samples without gradient descent. Language-level adaptation experiments using Chinese dialects showed that when applying SICL to isolated word ASR, consistent and considerable relative WER reductions can be achieved using Whisper models of any size on two dialects, which is on average 32.3%. A k-nearest-neighbours-based in-context example selection technique can be applied to further improve the efficiency of SICL, which can increase the average relative WER reduction to 36.4%. The findings are verified using speaker adaptation or continuous speech recognition tasks, and both achieved considerable relative WER reductions. Detailed quantitative analyses are also provided to shed light on SICL's adaptability to phonological variances and dialect-specific lexical nuances.

Cross-Utterance Conditioned VAE for Speech Generation

Speech synthesis systems powered by neural networks hold promise for multimedia production, but frequently face issues with producing expressive speech and seamless editing. In response, we present the Cross-Utterance Conditioned Variational Autoencoder speech synthesis (CUC-VAE S2) framework to enhance prosody and ensure natural speech generation. This framework leverages the powerful representational capabilities of pre-trained language models and the re-expression abilities of variational autoencoders (VAEs). The core component of the CUC-VAE S2 framework is the cross-utterance CVAE, which extracts acoustic, speaker, and textual features from surrounding sentences to generate context-sensitive prosodic features, more accurately emulating human prosody generation. We further propose two practical algorithms tailored for distinct speech synthesis applications: CUC-VAE TTS for text-to-speech and CUC-VAE SE for speech editing. The CUC-VAE TTS is a direct application of the framework, designed to generate audio with contextual prosody derived from surrounding texts. On the other hand, the CUC-VAE SE algorithm leverages real mel spectrogram sampling conditioned on contextual information, producing audio that closely mirrors real sound and thereby facilitating flexible speech editing based on text such as deletion, insertion, and replacement. Experimental results on the LibriTTS datasets demonstrate that our proposed models significantly enhance speech synthesis and editing, producing more natural and expressive speech.

PolyGET: Accelerating Polymer Simulations by Accurate and Generalizable Forcefield with Equivariant Transformer

Polymer simulation with both accuracy and efficiency is a challenging task. Machine learning (ML) forcefields have been developed to achieve both the accuracy of ab initio methods and the efficiency of empirical force fields. However, existing ML force fields are usually limited to single-molecule settings, and their simulations are not robust enough. In this paper, we present PolyGET, a new framework for Polymer Forcefields with Generalizable Equivariant Transformers. PolyGET is designed to capture complex quantum interactions between atoms and generalize across various polymer families, using a deep learning model called Equivariant Transformers. We propose a new training paradigm that focuses exclusively on optimizing forces, which is different from existing methods that jointly optimize forces and energy. This simple force-centric objective function avoids competing objectives between energy and forces, thereby allowing for learning a unified forcefield ML model over different polymer families. We evaluated PolyGET on a large-scale dataset of 24 distinct polymer types and demonstrated state-of-the-art performance in force accuracy and robust MD simulations. Furthermore, PolyGET can simulate large polymers with high fidelity to the reference ab initio DFT method while being able to generalize to unseen polymers.

Situated Natural Language Explanations

Natural language is among the most accessible tools for explaining decisions to humans, and large pretrained language models (PLMs) have demonstrated impressive abilities to generate coherent natural language explanations (NLE). The existing NLE research perspectives do not take the audience into account. An NLE can have high textual quality, but it might not accommodate audiences' needs and preference. To address this limitation, we propose an alternative perspective, situated NLE, including a situated generation framework and a situated evaluation framework. On the generation side, we propose simple prompt engineering methods that adapt the NLEs to situations. In human studies, the annotators preferred the situated NLEs. On the evaluation side, we set up automated evaluation scores in lexical, semantic, and pragmatic categories. The scores can be used to select the most suitable prompts to generate NLEs. Situated NLE provides a perspective to conduct further research on automatic NLE generations.

kTrans: Knowledge-Aware Transformer for Binary Code Embedding

Binary Code Embedding (BCE) has important applications in various reverse engineering tasks such as binary code similarity detection, type recovery, control-flow recovery and data-flow analysis. Recent studies have shown that the Transformer model can comprehend the semantics of binary code to support downstream tasks. However, existing models overlooked the prior knowledge of assembly language. In this paper, we propose a novel Transformer-based approach, namely kTrans, to generate knowledge-aware binary code embedding. By feeding explicit knowledge as additional inputs to the Transformer, and fusing implicit knowledge with a novel pre-training task, kTrans provides a new perspective to incorporating domain knowledge into a Transformer framework. We inspect the generated embeddings with outlier detection and visualization, and also apply kTrans to 3 downstream tasks: Binary Code Similarity Detection (BCSD), Function Type Recovery (FTR) and Indirect Call Recognition (ICR). Evaluation results show that kTrans can generate high-quality binary code embeddings, and outperforms state-of-the-art (SOTA) approaches on downstream tasks by 5.2%, 6.8%, and 12.6% respectively. kTrans is publicly available at: https://github.com/Learner0x5a/kTrans-release