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We propose an approach utilizing gamma-distributed random variables, coupled with log-Gaussian modeling, to generate synthetic datasets suitable for training neural networks. This addresses the challenge of limited real observations in various applications. We apply this methodology to both Raman and coherent anti-Stokes Raman scattering (CARS) spectra, using experimental spectra to estimate gamma process parameters. Parameter estimation is performed using Markov chain Monte Carlo methods, yielding a full Bayesian posterior distribution for the model which can be sampled for synthetic data generation. Additionally, we model the additive and multiplicative background functions for Raman and CARS with Gaussian processes. We train two Bayesian neural networks to estimate parameters of the gamma process which can then be used to estimate the underlying Raman spectrum and simultaneously provide uncertainty through the estimation of parameters of a probability distribution. We apply the trained Bayesian neural networks to experimental Raman spectra of phthalocyanine blue, aniline black, naphthol red, and red 264 pigments and also to experimental CARS spectra of adenosine phosphate, fructose, glucose, and sucrose. The results agree with deterministic point estimates for the underlying Raman and CARS spectral signatures.

Surrogate Optimization (SO) algorithms have shown promise for optimizing expensive black-box functions. However, their performance is heavily influenced by hyperparameters related to sampling and surrogate fitting, which poses a challenge to their widespread adoption. We investigate the impact of hyperparameters on various SO algorithms and propose a Hyperparameter Adaptive Search for SO (HASSO) approach. HASSO is not a hyperparameter tuning algorithm, but a generic self-adjusting SO algorithm that dynamically tunes its own hyperparameters while concurrently optimizing the primary objective function, without requiring additional evaluations. The aim is to improve the accessibility, effectiveness, and convergence speed of SO algorithms for practitioners. Our approach identifies and modifies the most influential hyperparameters specific to each problem and SO approach, reducing the need for manual tuning without significantly increasing the computational burden. Experimental results demonstrate the effectiveness of HASSO in enhancing the performance of various SO algorithms across different global optimization test problems.

As scientific literature has grown exponentially, researchers often rely on paper triaging strategies such as browsing abstracts before deciding to delve into a paper's full text. However, when an abstract is insufficient, researchers are required to navigate an informational chasm between 150-word abstracts and 10,000-word papers. To bridge that gap, we introduce the idea of recursively expandable summaries and present Qlarify, an interactive system that allows users to recursively expand an abstract by progressively incorporating additional information from a paper's full text. Starting from an abstract, users can brush over summary text to specify targeted information needs or select AI-suggested entities in the text. Responses are then generated on-demand by an LLM and appear in the form of a fluid, threaded expansion of the existing text. Each generated summary can be efficiently verified through attribution to a relevant source-passage in the paper. Through an interview study (n=9) and a field deployment (n=275) at a research conference, we use Qlarify as a technology probe to elaborate upon the expandable summaries design space, highlight how scholars benefit from Qlarify's expandable abstracts, and identify future opportunities to support low-effort and just-in-time exploration of scientific documents $\unicode{x2013}$ and other information spaces $\unicode{x2013}$ through LLM-powered interactions.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{//github.com/QizhiPei/BioT5}{Github}$.

We introduce Lemur and Lemur-Chat, openly accessible language models optimized for both natural language and coding capabilities to serve as the backbone of versatile language agents. The evolution from language chat models to functional language agents demands that models not only master human interaction, reasoning, and planning but also ensure grounding in the relevant environments. This calls for a harmonious blend of language and coding capabilities in the models. Lemur and Lemur-Chat are proposed to address this necessity, demonstrating balanced proficiencies in both domains, unlike existing open-source models that tend to specialize in either. Through meticulous pre-training using a code-intensive corpus and instruction fine-tuning on text and code data, our models achieve state-of-the-art averaged performance across diverse text and coding benchmarks among open-source models. Comprehensive experiments demonstrate Lemur's superiority over existing open-source models and its proficiency across various agent tasks involving human communication, tool usage, and interaction under fully- and partially- observable environments. The harmonization between natural and programming languages enables Lemur-Chat to significantly narrow the gap with proprietary models on agent abilities, providing key insights into developing advanced open-source agents adept at reasoning, planning, and operating seamlessly across environments. //github.com/OpenLemur/Lemur

Surrogate-assisted evolutionary algorithms have been widely developed to solve complex and computationally expensive multi-objective optimization problems in recent years. However, when dealing with high-dimensional optimization problems, the performance of these surrogate-assisted multi-objective evolutionary algorithms deteriorate drastically. In this work, a novel Classifier-assisted rank-based learning and Local Model based multi-objective Evolutionary Algorithm (CLMEA) is proposed for high-dimensional expensive multi-objective optimization problems. The proposed algorithm consists of three parts: classifier-assisted rank-based learning, hypervolume-based non-dominated search, and local search in the relatively sparse objective space. Specifically, a probabilistic neural network is built as classifier to divide the offspring into a number of ranks. The offspring in different ranks uses rank-based learning strategy to generate more promising and informative candidates for real function evaluations. Then, radial basis function networks are built as surrogates to approximate the objective functions. After searching non-dominated solutions assisted by the surrogate model, the candidates with higher hypervolume improvement are selected for real evaluations. Subsequently, in order to maintain the diversity of solutions, the most uncertain sample point from the non-dominated solutions measured by the crowding distance is selected as the guided parent to further infill in the uncertain region of the front. The experimental results of benchmark problems and a real-world application on geothermal reservoir heat extraction optimization demonstrate that the proposed algorithm shows superior performance compared with the state-of-the-art surrogate-assisted multi-objective evolutionary algorithms. The source code for this work is available at //github.com/JellyChen7/CLMEA.

Many recent works in simulation-based inference (SBI) rely on deep generative models to approximate complex, high-dimensional posterior distributions. However, evaluating whether or not these approximations can be trusted remains a challenge. Most approaches evaluate the posterior estimator only in expectation over the observation space. This limits their interpretability and is not sufficient to identify for which observations the approximation can be trusted or should be improved. Building upon the well-known classifier two-sample test (C2ST), we introduce L-C2ST, a new method that allows for a local evaluation of the posterior estimator at any given observation. It offers theoretically grounded and easy to interpret -- e.g. graphical -- diagnostics, and unlike C2ST, does not require access to samples from the true posterior. In the case of normalizing flow-based posterior estimators, L-C2ST can be specialized to offer better statistical power, while being computationally more efficient. On standard SBI benchmarks, L-C2ST provides comparable results to C2ST and outperforms alternative local approaches such as coverage tests based on highest predictive density (HPD). We further highlight the importance of local evaluation and the benefit of interpretability of L-C2ST on a challenging application from computational neuroscience.

The emergence of large language models (LLMs) has substantially influenced natural language processing, demonstrating exceptional results across various tasks. In this study, we employ ``Introspective Tips" to facilitate LLMs in self-optimizing their decision-making. By introspectively examining trajectories, LLM refines its policy by generating succinct and valuable tips. Our method enhances the agent's performance in both few-shot and zero-shot learning situations by considering three essential scenarios: learning from the agent's past experiences, integrating expert demonstrations, and generalizing across diverse games. Importantly, we accomplish these improvements without fine-tuning the LLM parameters; rather, we adjust the prompt to generalize insights from the three aforementioned situations. Our framework not only supports but also emphasizes the advantage of employing LLM in in-contxt decision-making. Experiments involving over 100 games in TextWorld illustrate the superior performance of our approach.

Causal Machine Learning (CausalML) is an umbrella term for machine learning methods that formalize the data-generation process as a structural causal model (SCM). This allows one to reason about the effects of changes to this process (i.e., interventions) and what would have happened in hindsight (i.e., counterfactuals). We categorize work in \causalml into five groups according to the problems they tackle: (1) causal supervised learning, (2) causal generative modeling, (3) causal explanations, (4) causal fairness, (5) causal reinforcement learning. For each category, we systematically compare its methods and point out open problems. Further, we review modality-specific applications in computer vision, natural language processing, and graph representation learning. Finally, we provide an overview of causal benchmarks and a critical discussion of the state of this nascent field, including recommendations for future work.

Meta-reinforcement learning algorithms can enable robots to acquire new skills much more quickly, by leveraging prior experience to learn how to learn. However, much of the current research on meta-reinforcement learning focuses on task distributions that are very narrow. For example, a commonly used meta-reinforcement learning benchmark uses different running velocities for a simulated robot as different tasks. When policies are meta-trained on such narrow task distributions, they cannot possibly generalize to more quickly acquire entirely new tasks. Therefore, if the aim of these methods is to enable faster acquisition of entirely new behaviors, we must evaluate them on task distributions that are sufficiently broad to enable generalization to new behaviors. In this paper, we propose an open-source simulated benchmark for meta-reinforcement learning and multi-task learning consisting of 50 distinct robotic manipulation tasks. Our aim is to make it possible to develop algorithms that generalize to accelerate the acquisition of entirely new, held-out tasks. We evaluate 6 state-of-the-art meta-reinforcement learning and multi-task learning algorithms on these tasks. Surprisingly, while each task and its variations (e.g., with different object positions) can be learned with reasonable success, these algorithms struggle to learn with multiple tasks at the same time, even with as few as ten distinct training tasks. Our analysis and open-source environments pave the way for future research in multi-task learning and meta-learning that can enable meaningful generalization, thereby unlocking the full potential of these methods.