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Modelling in biology must adapt to increasingly complex and massive data. The efficiency of the inference algorithms used to estimate model parameters is therefore questioned. Many of these are based on stochastic optimization processes that require significant computing time. We introduce the Fixed Landscape Inference MethOd (flimo), a new likelihood-free inference method for continuous state-space stochastic models. It applies deterministic gradient-based optimization algorithms to obtain a point estimate of the parameters, minimizing the difference between the data and some simulations according to some prescribed summary statistics. In this sense, it is analogous to Approximate Bayesian Computation (ABC). Like ABC, it can also provide an approximation of the distribution of the parameters. Three applications are proposed: a usual theoretical example, namely the inference of the parameters of g-and-k distributions; a population genetics problem, not so simple as it seems, namely the inference of a selective value from time series in a Wright-Fisher model; and simulations from a Ricker model, representing chaotic population dynamics. In the two first applications, the results show a drastic reduction of the computational time needed for the inference phase compared to the other methods, despite an equivalent accuracy. Even when likelihood-based methods are applicable, the simplicity and efficiency of flimo make it a compelling alternative. Implementations in Julia and in R are available on //metabarcoding.org/flimo. To run flimo, the user must simply be able to simulate data according to the chosen model.

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Distributional reinforcement learning algorithms have attempted to utilize estimated uncertainty for exploration, such as optimism in the face of uncertainty. However, using the estimated variance for optimistic exploration may cause biased data collection and hinder convergence or performance. In this paper, we present a novel distributional reinforcement learning algorithm that selects actions by randomizing risk criterion to avoid one-sided tendency on risk. We provide a perturbed distributional Bellman optimality operator by distorting the risk measure and prove the convergence and optimality of the proposed method with the weaker contraction property. Our theoretical results support that the proposed method does not fall into biased exploration and is guaranteed to converge to an optimal return. Finally, we empirically show that our method outperforms other existing distribution-based algorithms in various environments including Atari 55 games.

Consciousness, a central element of human cognition, has been studied with multiple scientific approaches spanning neuroscience, psychology, artificial intelligence and robotics. Unfortunately, poor integration between these fields limits a full and clear understanding of consciousness. Here we contribute to improving this integration by proposing, within a neurocomputational framework, the `Goal-Aligning Representations Internal Manipulation' (GARIM) theory of consciousness. The central idea of the GARIM theory is that consciousness supports the active manipulation of goal-relevant internal representations (e.g., world states, objects, and action sequences), making them more aligned with the goals pursued. These manipulations allow the conscious agent to internally produce the knowledge it lacks to cope with novel conditions and goals, increasing the flexibility of goal-directed behaviour. The manipulation of representations is supported by four neuro-functional macro-systems (hierarchical perceptual working memories, abstract working memory, internal manipulator, motivational systems) that operate through a set of computational manipulation operations (abstraction, specification, decomposition, composition). The theory also presents the concept of `GARIM agency', proposing that subjective conscious experience derives from the ability of agents to generate and control a vivid internally simulated reality. Furthermore, the theory highlights the criticalities of the experimental investigation of consciousness, suggesting a new approach to testing consciousness in biological and artificial agents. Finally, the GARIM theory can benefit technological fields such as machine learning and autonomous robotics (e.g., the manipulation processes proposed by the theory could be linked to the operations performed by systems based on transformers).

Although large language models (LLMs) have apparently acquired a certain level of grammatical knowledge and the ability to make generalizations, they fail to interpret negation, a crucial step in Natural Language Processing. We try to clarify the reasons for the sub-optimal performance of LLMs understanding negation. We introduce a large semi-automatically generated dataset of circa 400,000 descriptive sentences about commonsense knowledge that can be true or false in which negation is present in about 2/3 of the corpus in different forms. We have used our dataset with the largest available open LLMs in a zero-shot approach to grasp their generalization and inference capability and we have also fine-tuned some of the models to assess whether the understanding of negation can be trained. Our findings show that, while LLMs are proficient at classifying affirmative sentences, they struggle with negative sentences and lack a deep understanding of negation, often relying on superficial cues. Although fine-tuning the models on negative sentences improves their performance, the lack of generalization in handling negation is persistent, highlighting the ongoing challenges of LLMs regarding negation understanding and generalization. The dataset and code are publicly available.

A cost-effective alternative to manual data labeling is weak supervision (WS), where data samples are automatically annotated using a predefined set of labeling functions (LFs), rule-based mechanisms that generate artificial labels for the associated classes. In this work, we investigate noise reduction techniques for WS based on the principle of k-fold cross-validation. We introduce a new algorithm ULF for Unsupervised Labeling Function correction, which denoises WS data by leveraging models trained on all but some LFs to identify and correct biases specific to the held-out LFs. Specifically, ULF refines the allocation of LFs to classes by re-estimating this assignment on highly reliable cross-validated samples. Evaluation on multiple datasets confirms ULF's effectiveness in enhancing WS learning without the need for manual labeling.

Classical evolutionary approaches for multiobjective optimization are quite effective but incur a lot of queries to the objectives; this can be prohibitive when objectives are expensive oracles. A sample-efficient approach to solving multiobjective optimization is via Gaussian process (GP) surrogates and Bayesian optimization (BO). Multiobjective Bayesian optimization (MOBO) involves the construction of an acquisition function which is optimized to acquire new observation candidates. This ``inner'' optimization can be hard due to various reasons: acquisition functions being nonconvex, nondifferentiable and/or unavailable in analytical form; the success of MOBO heavily relies on this inner optimization. We do away with this hard acquisition function optimization step and propose a simple, but effective, Thompson sampling based approach ($q\texttt{POTS}$) where new candidate(s) are chosen from the Pareto frontier of random GP posterior sample paths obtained by solving a much cheaper multiobjective optimization problem. To further improve computational tractability in higher dimensions we propose an automated active set of candidates selection combined with a Nystr\"{o}m approximation. Our approach applies to arbitrary GP prior assumptions and demonstrates strong empirical performance over the state of the art, both in terms of accuracy and computational efficiency, on synthetic as well as real-world experiments.

The use of pessimism, when reasoning about datasets lacking exhaustive exploration has recently gained prominence in offline reinforcement learning. Despite the robustness it adds to the algorithm, overly pessimistic reasoning can be equally damaging in precluding the discovery of good policies, which is an issue for the popular bonus-based pessimism. In this paper, we introduce the notion of Bellman-consistent pessimism for general function approximation: instead of calculating a point-wise lower bound for the value function, we implement pessimism at the initial state over the set of functions consistent with the Bellman equations. Our theoretical guarantees only require Bellman closedness as standard in the exploratory setting, in which case bonus-based pessimism fails to provide guarantees. Even in the special case of linear function approximation where stronger expressivity assumptions hold, our result improves upon a recent bonus-based approach by $\mathcal{O}(d)$ in its sample complexity when the action space is finite. Remarkably, our algorithms automatically adapt to the best bias-variance tradeoff in the hindsight, whereas most prior approaches require tuning extra hyperparameters a priori.

Thematic analysis (TA) has been widely used for analyzing qualitative data in many disciplines and fields. To ensure reliable analysis, the same piece of data is typically assigned to at least two human coders. Moreover, to produce meaningful and useful analysis, human coders develop and deepen their data interpretation and coding over multiple iterations, making TA labor-intensive and time-consuming. Recently the emerging field of large language models (LLMs) research has shown that LLMs have the potential replicate human-like behavior in various tasks: in particular, LLMs outperform crowd workers on text-annotation tasks, suggesting an opportunity to leverage LLMs on TA. We propose a human-LLM collaboration framework (i.e., LLM-in-the-loop) to conduct TA with in-context learning (ICL). This framework provides the prompt to frame discussions with a LLM (e.g., GPT-3.5) to generate the final codebook for TA. We demonstrate the utility of this framework using survey datasets on the aspects of the music listening experience and the usage of a password manager. Results of the two case studies show that the proposed framework yields similar coding quality to that of human coders but reduces TA's labor and time demands.

Multi-label text classification is a critical task in the industry. It helps to extract structured information from large amount of textual data. We propose Text to Topic (Text2Topic), which achieves high multi-label classification performance by employing a Bi-Encoder Transformer architecture that utilizes concatenation, subtraction, and multiplication of embeddings on both text and topic. Text2Topic also supports zero-shot predictions, produces domain-specific text embeddings, and enables production-scale batch-inference with high throughput. The final model achieves accurate and comprehensive results compared to state-of-the-art baselines, including large language models (LLMs). In this study, a total of 239 topics are defined, and around 1.6 million text-topic pairs annotations (in which 200K are positive) are collected on approximately 120K texts from 3 main data sources on Booking.com. The data is collected with optimized smart sampling and partial labeling. The final Text2Topic model is deployed on a real-world stream processing platform, and it outperforms other models with 92.9% micro mAP, as well as a 75.8% macro mAP score. We summarize the modeling choices which are extensively tested through ablation studies, and share detailed in-production decision-making steps.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

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