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Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. Here, we develop BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function. Moreover, BioDiscoveryAgent achieves an average of 18% improvement in detecting desired phenotypes across five datasets, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' capabilities.

Large language models (LLMs) have shown impressive capabilities across diverse settings, but still struggle as the length and complexity of the context increases. To address this challenge, we propose Thinking Recursively and Dynamically (ThReaD). THREAD frames model generation as a thread of execution that, based on the context, can run to completion or dynamically spawn new threads. By spawning, threads can offload work (e.g., thinking, retrieving information) to child threads, which only return tokens needed for the parent thread to do its work. In effect, this enables the model to adapt, as needed, the amount of intermediate work used to produce tokens. We apply THREAD in the settings of LLM task solving and question answering, where the dynamic threading allows the model to recursively decompose the given task or question into progressively simpler sub-problems that can be solved by separate child threads. We test THREAD, implemented using a few-shot learning approach, on diverse benchmarks for agent tasks and data-grounded question answering. THREAD achieves state-of-the-art performance with GPT-4 and GPT-3.5 on these benchmarks, including ALFWorld, TextCraft, and WebShop, along with two new benchmarks, DataCommons QA and MIMIC-III ICU QA. In addition, THREAD outperforms existing frameworks by 10% to 50% absolute points with smaller models, including Llama-3-8b and CodeLlama-7b.

3D Gaussian Splatting-based techniques have recently advanced 3D scene reconstruction and novel view synthesis, achieving high-quality real-time rendering. However, these approaches are inherently limited by the underlying pinhole camera assumption in modeling the images and hence only work for All-in-Focus (AiF) sharp image inputs. This severely affects their applicability in real-world scenarios where images often exhibit defocus blur due to the limited depth-of-field (DOF) of imaging devices. Additionally, existing 3D Gaussian Splatting (3DGS) methods also do not support rendering of DOF effects. To address these challenges, we introduce DOF-GS that allows for rendering adjustable DOF effects, removing defocus blur as well as refocusing of 3D scenes, all from multi-view images degraded by defocus blur. To this end, we re-imagine the traditional Gaussian Splatting pipeline by employing a finite aperture camera model coupled with explicit, differentiable defocus rendering guided by the Circle-of-Confusion (CoC). The proposed framework provides for dynamic adjustment of DOF effects by changing the aperture and focal distance of the underlying camera model on-demand. It also enables rendering varying DOF effects of 3D scenes post-optimization, and generating AiF images from defocused training images. Furthermore, we devise a joint optimization strategy to further enhance details in the reconstructed scenes by jointly optimizing rendered defocused and AiF images. Our experimental results indicate that DOF-GS produces high-quality sharp all-in-focus renderings conditioned on inputs compromised by defocus blur, with the training process incurring only a modest increase in GPU memory consumption. We further demonstrate the applications of the proposed method for adjustable defocus rendering and refocusing of the 3D scene from input images degraded by defocus blur.

This paper presents a theoretical extension of the DeTEcT framework proposed by Sadykhov et al., DeTEcT, where a formal analysis framework was introduced for modelling wealth distribution in token economies. DeTEcT is a framework for analysing economic activity, simulating macroeconomic scenarios, and algorithmically setting policies in token economies. This paper proposes four ways of parametrizing the framework, where dynamic vs static parametrization is considered along with the probabilistic vs non-probabilistic. Using these parametrization techniques, we demonstrate that by adding restrictions to the framework it is possible to derive the existing wealth distribution models from DeTEcT. In addition to exploring parametrization techniques, this paper studies how money supply in DeTEcT framework can be transformed to become dynamic, and how this change will affect the dynamics of wealth distribution. The motivation for studying dynamic money supply is that it enables DeTEcT to be applied to modelling token economies without maximum supply (i.e., Ethereum), and it adds constraints to the framework in the form of symmetries.

We consider the problem of multi-objective alignment of foundation models with human preferences, which is a critical step towards helpful and harmless AI systems. However, it is generally costly and unstable to fine-tune large foundation models using reinforcement learning (RL), and the multi-dimensionality, heterogeneity, and conflicting nature of human preferences further complicate the alignment process. In this paper, we introduce Rewards-in-Context (RiC), which conditions the response of a foundation model on multiple rewards in its prompt context and applies supervised fine-tuning for alignment. The salient features of RiC are simplicity and adaptivity, as it only requires supervised fine-tuning of a single foundation model and supports dynamic adjustment for user preferences during inference time. Inspired by the analytical solution of an abstracted convex optimization problem, our dynamic inference-time adjustment method approaches the Pareto-optimal solution for multiple objectives. Empirical evidence demonstrates the efficacy of our method in aligning both Large Language Models (LLMs) and diffusion models to accommodate diverse rewards with only around 10% GPU hours compared with multi-objective RL baseline.

We introduce GECKO, a bilingual large language model (LLM) optimized for Korean and English, along with programming languages. GECKO is pretrained on the balanced, high-quality corpus of Korean and English employing LLaMA architecture. In this report, we share the experiences of several efforts to build a better data pipeline for the corpus and to train our model. GECKO shows great efficiency in token generations for both Korean and English, despite its small size of vocabulary. We measure the performance on the representative benchmarks in terms of Korean, English and Code, and it exhibits great performance on KMMLU (Korean MMLU) and modest performance in English and Code, even with its smaller number of trained tokens compared to English-focused LLMs. GECKO is available to the open-source community under a permissive license. We hope our work offers a research baseline and practical insights for Korean LLM research. The model can be found at: //huggingface.co/kifai/GECKO-7B

Pre-trained language representation models, such as BERT, capture a general language representation from large-scale corpora, but lack domain-specific knowledge. When reading a domain text, experts make inferences with relevant knowledge. For machines to achieve this capability, we propose a knowledge-enabled language representation model (K-BERT) with knowledge graphs (KGs), in which triples are injected into the sentences as domain knowledge. However, too much knowledge incorporation may divert the sentence from its correct meaning, which is called knowledge noise (KN) issue. To overcome KN, K-BERT introduces soft-position and visible matrix to limit the impact of knowledge. K-BERT can easily inject domain knowledge into the models by equipped with a KG without pre-training by-self because it is capable of loading model parameters from the pre-trained BERT. Our investigation reveals promising results in twelve NLP tasks. Especially in domain-specific tasks (including finance, law, and medicine), K-BERT significantly outperforms BERT, which demonstrates that K-BERT is an excellent choice for solving the knowledge-driven problems that require experts.

Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.

In order to answer natural language questions over knowledge graphs, most processing pipelines involve entity and relation linking. Traditionally, entity linking and relation linking has been performed either as dependent sequential tasks or independent parallel tasks. In this paper, we propose a framework called "EARL", which performs entity linking and relation linking as a joint single task. EARL uses a graph connection based solution to the problem. We model the linking task as an instance of the Generalised Travelling Salesman Problem (GTSP) and use GTSP approximate algorithm solutions. We later develop EARL which uses a pair-wise graph-distance based solution to the problem.The system determines the best semantic connection between all keywords of the question by referring to a knowledge graph. This is achieved by exploiting the "connection density" between entity candidates and relation candidates. The "connection density" based solution performs at par with the approximate GTSP solution.We have empirically evaluated the framework on a dataset with 5000 questions. Our system surpasses state-of-the-art scores for entity linking task by reporting an accuracy of 0.65 to 0.40 from the next best entity linker.