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Objective: To report imaging protocol and scheduling variance in routine care of glioblastoma patients in order to demonstrate challenges of integrating deep-learning models in glioblastoma care pathways. Additionally, to understand the most common imaging studies and image contrasts to inform the development of potentially robust deep-learning models. Methods: MR imaging data were analysed from a random sample of five patients from the prospective cohort across five participating sites of the ZGBM consortium. Reported clinical and treatment data alongside DICOM header information were analysed to understand treatment pathway imaging schedules. Results: All sites perform all structural imaging at every stage in the pathway except for the presurgical study, where in some sites only contrast-enhanced T1-weighted imaging is performed. Diffusion MRI is the most common non-structural imaging type, performed at every site. Conclusion: The imaging protocol and scheduling varies across the UK, making it challenging to develop machine-learning models that could perform robustly at other centres. Structural imaging is performed most consistently across all centres. Advances in knowledge: Successful translation of deep-learning models will likely be based on structural post-treatment imaging unless there is significant effort made to standardise non-structural or peri-operative imaging protocols and schedules.

Learning to predict masked tokens in a sequence has been shown to be a helpful pretraining objective for powerful language models such as PaLM2. After training, such masked language models (MLMs) can provide distributions of tokens in the masked positions in a sequence. However, this paper shows that distributions corresponding to different masking patterns can demonstrate considerable inconsistencies, i.e., they cannot be derived from a coherent joint distribution when considered together. This fundamental flaw in MLMs can lead to self-contradictory behaviors during inference. On various benchmark datasets including MMLU, MLMs can give different predictions to the same input question. From BERT-base to UL2-20B, we show that such inconsistencies exist ubiquitously in MLMs of diverse sizes and configurations. In light of our observations, we further propose an inference-time strategy for MLMs called Ensemble of Conditionals. It jointly considers a selected range of inconsistent conditionals directly produced by the MLM for the final prediction, which often leads to considerable accuracy improvement.

The goal of building dialogue agents that can converse with humans naturally has been a long-standing dream of researchers since the early days of artificial intelligence. The well-known Turing Test proposed to judge the ultimate validity of an artificial intelligence agent on the indistinguishability of its dialogues from humans'. It should come as no surprise that human-level dialogue systems are very challenging to build. But, while early effort on rule-based systems found limited success, the emergence of deep learning enabled great advance on this topic. In this thesis, we focus on methods that address the numerous issues that have been imposing the gap between artificial conversational agents and human-level interlocutors. These methods were proposed and experimented with in ways that were inspired by general state-of-the-art AI methodologies. But they also targeted the characteristics that dialogue systems possess., Comment: PhD thesis

The goal of building intelligent dialogue systems has largely been separately pursued under two paradigms: task-oriented dialogue (TOD) systems, which perform goal-oriented functions, and open-domain dialogue (ODD) systems, which focus on non-goal-oriented chitchat. The two dialogue modes can potentially be intertwined together seamlessly in the same conversation, as easily done by a friendly human assistant. Such ability is desirable in conversational agents, as the integration makes them more accessible and useful. Our paper addresses this problem of fusing TODs and ODDs in multi-turn dialogues. Based on the popular TOD dataset MultiWOZ, we build a new dataset FusedChat, by rewriting the existing TOD turns and adding new ODD turns. This procedure constructs conversation sessions containing exchanges from both dialogue modes. It features inter-mode contextual dependency, i.e., the dialogue turns from the two modes depend on each other. Rich dependency patterns including co-reference and ellipsis are features. The new dataset, with 60k new human-written ODD turns and 5k re-written TOD turns, offers a benchmark to test a dialogue model's ability to perform inter-mode conversations. This is a more challenging task since the model has to determine the appropriate dialogue mode and generate the response based on the inter-mode context. But such models would better mimic human-level conversation capabilities. We evaluate baseline models on this task, including classification-based two-stage models and two-in-one fused models. We publicly release FusedChat and the baselines to propel future work on inter-mode dialogue systems https://github.com/tomyoung903/FusedChat.

Dialogue systems are a popular natural language processing (NLP) task as it is promising in real-life applications. It is also a complicated task since many NLP tasks deserving study are involved. As a result, a multitude of novel works on this task are carried out, and most of them are deep learning based due to the outstanding performance. In this survey, we mainly focus on the deep learning based dialogue systems. We comprehensively review state-of-the-art research outcomes in dialogue systems and analyze them from two angles: model type and system type. Specifically, from the angle of model type, we discuss the principles, characteristics, and applications of different models that are widely used in dialogue systems. This will help researchers acquaint these models and see how they are applied in state-of-the-art frameworks, which is rather helpful when designing a new dialogue system. From the angle of system type, we discuss task-oriented and open-domain dialogue systems as two streams of research, providing insight into the hot topics related. Furthermore, we comprehensively review the evaluation methods and datasets for dialogue systems to pave the way for future research. Finally, some possible research trends are identified based on the recent research outcomes. To the best of our knowledge, this survey is the most comprehensive and up-to-date one at present for deep learning based dialogue systems, extensively covering the popular techniques. We speculate that this work is a good starting point for academics who are new to the dialogue systems or those who want to quickly grasp up-to-date techniques in this area., Comment: 80 pages, 17 figures

Building dialog agents that can converse naturally with humans is a challenging yet intriguing problem of artificial intelligence. In open-domain human-computer conversation, where the conversational agent is expected to respond to human responses in an interesting and engaging way, commonsense knowledge has to be integrated into the model effectively. In this paper, we investigate the impact of providing commonsense knowledge about the concepts covered in the dialog. Our model represents the first attempt to integrating a large commonsense knowledge base into end-to-end conversational models. In the retrieval-based scenario, we propose the Tri-LSTM model to jointly take into account message and commonsense for selecting an appropriate response. Our experiments suggest that the knowledge-augmented models are superior to their knowledge-free counterparts in automatic evaluation.

Deep learning methods employ multiple processing layers to learn hierarchical representations of data and have produced state-of-the-art results in many domains. Recently, a variety of model designs and methods have blossomed in the context of natural language processing (NLP). In this paper, we review significant deep learning related models and methods that have been employed for numerous NLP tasks and provide a walk-through of their evolution. We also summarize, compare and contrast the various models and put forward a detailed understanding of the past, present and future of deep learning in NLP., Comment: Added BERT, ELMo, Transformer

Changes in hydration are central to the phenomenon of biomolecular recognition, but it has been difficult to properly frame and answer questions about their precise thermodynamic role. We address this problem by introducing Grid Inhomogeneous Solvation Theory (GIST), which discretizes the equations of Inhomogeneous Solvation Theory on a 3D grid in a volume of interest. Here, the solvent volume is divided into small grid boxes and localized thermodynamic entropies, energies and free energies are defined for each grid box. Thermodynamic solvation quantities are defined in such a manner that summing the quantities over all the grid boxes yields the desired total quantity for the system. This approach smoothly accounts for the thermodynamics of not only highly occupied water sites but also partly occupied and water depleted regions of the solvent, without the need for ad hoc terms drawn from other theories. The GIST method has the further advantage of allowing a rigorous end-states analysis that, for example in the problem of molecular recognition, can account for not only the thermodynamics of displacing water from the surface but also for the thermodynamics of solvent reorganization around the bound complex. As a preliminary application, we present GIST calculations at the 1-body level for the host cucurbit[7]uril, a low molecular weight receptor molecule which represents a tractable model for biomolecular recognition. One of the most striking results is the observation of a toroidal region of water density, at the center of the host's nonpolar cavity, which is significantly disfavored entropically, and hence may contribute to the ability of this small receptor to bind guest molecules with unusually high affinities., Comment: 16 pages, 5 figures