Daily Papers

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics profiling, we compared drug-response panel (DRP) descriptors against omics features for predictive capacity using gradient boosting tree models across the GDSC and CCLE drug response datasets. DRP descriptors consistently outperformed omics data across key performance metrics, with variable performance across different drugs. Using complementary explainability approaches, we confirmed known MAPK-inhibitor sensitivity signatures, and identified novel potential biomarker candidates for MEK1/2 and BTK/MNK inhibitors. Lastly, to demonstrate the utility of this approach in distinguishing phenotypes, we applied our models to the breast cancer line MCF7 versus the non-tumorigenic MCF10A, and successfully identified compounds that selectively inhibit MCF7 while sparing the non-tumorigenic MCF10A. This methodology, developed using focused drug and cell line panels, supports early-stage drug development by facilitating rational cell line selection and compound prioritisation, enabling more efficient biomarker identification and candidate assessment.

Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.

Compound AI systems that combine multiple LLM calls, such as self-refine and multi-agent-debate, achieve strong performance on many AI tasks. We address a core question in optimizing compound systems: for each LLM call or module in the system, how should one decide which LLM to use? We show that these LLM choices have a large effect on quality, but the search space is exponential. We propose LLMSelector, an efficient framework for model selection in compound systems, which leverages two key empirical insights: (i) end-to-end performance is often monotonic in how well each module performs, with all other modules held fixed, and (ii) per-module performance can be estimated accurately by an LLM. Building upon these insights, LLMSelector iteratively selects one module and allocates to it the model with the highest module-wise performance, as estimated by an LLM, until no further gain is possible. LLMSelector is applicable to any compound system with a bounded number of modules, and its number of API calls scales linearly with the number of modules, achieving high-quality model allocation both empirically and theoretically. Experiments with popular compound systems such as multi-agent debate and self-refine using LLMs such as GPT-4o, Claude 3.5 Sonnet and Gemini 1.5 show that LLMSelector confers 5%-70% accuracy gains compared to using the same LLM for all modules.

Priorities in multi-criteria decision-making (MCDM) convey the relevance preference of one criterion over another, which is usually reflected by imposing the non-negativity and unit-sum constraints. The processing of such priorities is different than other unconstrained data, but this point is often neglected by researchers, which results in fallacious statistical analysis. This article studies three prevalent fallacies in group MCDM along with solutions based on compositional data analysis to avoid misusing statistical operations. First, we use a compositional approach to aggregate the priorities of a group of DMs and show that the outcome of the compositional analysis is identical to the normalized geometric mean, meaning that the arithmetic mean should be avoided. Furthermore, a new aggregation method is developed, which is a robust surrogate for the geometric mean. We also discuss the errors in computing measures of dispersion, including standard deviation and distance functions. Discussing the fallacies in computing the standard deviation, we provide a probabilistic criteria ranking by developing proper Bayesian tests, where we calculate the extent to which a criterion is more important than another. Finally, we explain the errors in computing the distance between priorities, and a clustering algorithm is specially tailored based on proper distance metrics.

Traditional Learning-To-Rank (LETOR) approaches, including pairwise methods like RankNet and LambdaMART, often fall short by solely focusing on pairwise comparisons, leading to sub-optimal global rankings. Conversely, deep learning based listwise methods, while aiming to optimise entire lists, require complex tuning and yield only marginal improvements over robust pairwise models. To overcome these limitations, we introduce Travelling Salesman Problem Rank (TSPRank), a hybrid pairwise-listwise ranking method. TSPRank reframes the ranking problem as a Travelling Salesman Problem (TSP), a well-known combinatorial optimisation challenge that has been extensively studied for its numerous solution algorithms and applications. This approach enables the modelling of pairwise relationships and leverages combinatorial optimisation to determine the listwise ranking. This approach can be directly integrated as an additional component into embeddings generated by existing backbone models to enhance ranking performance. Our extensive experiments across three backbone models on diverse tasks, including stock ranking, information retrieval, and historical events ordering, demonstrate that TSPRank significantly outperforms both pure pairwise and listwise methods. Our qualitative analysis reveals that TSPRank's main advantage over existing methods is its ability to harness global information better while ranking. TSPRank's robustness and superior performance across different domains highlight its potential as a versatile and effective LETOR solution.

In a compound AI system, components such as an LLM call, a retriever, a code interpreter, or tools are interconnected. The system's behavior is primarily driven by parameters such as instructions or tool definitions. Recent advancements enable end-to-end optimization of these parameters using an LLM. Notably, leveraging an LLM as an optimizer is particularly efficient because it avoids gradient computation and can generate complex code and instructions. This paper presents a survey of the principles and emerging trends in LLM-based optimization of compound AI systems. It covers archetypes of compound AI systems, approaches to LLM-based end-to-end optimization, and insights into future directions and broader impacts. Importantly, this survey uses concepts from program analysis to provide a unified view of how an LLM optimizer is prompted to optimize a compound AI system. The exhaustive list of paper is provided at https://github.com/linyuhongg/LLM-based-Optimization-of-Compound-AI-Systems.

Recent advancements in large language models (LLMs) and AI systems have led to a paradigm shift in the design and optimization of complex AI workflows. By integrating multiple components, compound AI systems have become increasingly adept at performing sophisticated tasks. However, as these systems grow in complexity, new challenges arise in optimizing not only individual components but also their interactions. While traditional optimization methods such as supervised fine-tuning (SFT) and reinforcement learning (RL) remain foundational, the rise of natural language feedback introduces promising new approaches, especially for optimizing non-differentiable systems. This paper provides a systematic review of recent progress in optimizing compound AI systems, encompassing both numerical and language-based techniques. We formalize the notion of compound AI system optimization, classify existing methods along several key dimensions, and highlight open research challenges and future directions in this rapidly evolving field. A list of surveyed papers is publicly available at https://github.com/MiuLab/AISysOpt-Survey.

In this study, we propose a multicriteria group decision making (MCGDM) algorithm under uncertainty where data is collected as intervals. The proposed MCGDM algorithm aggregates the data, determines the optimal weights for criteria and ranks alternatives with no further input. The intervals give flexibility to experts in assessing alternatives against criteria and provide an opportunity to gain maximum information. We also propose a novel method to aggregate expert judgements using cloud models. We introduce an experimental approach to check the validity of the aggregation method. After that, we use the aggregation method for an MCGDM problem. Here, we find the optimal weights for each criterion by proposing a bilevel optimisation model. Then, we extend the technique for order of preference by similarity to ideal solution (TOPSIS) for data based on cloud models to prioritise alternatives. As a result, the algorithm can gain information from decision makers with different levels of uncertainty and examine alternatives with no more information from decision-makers. The proposed MCGDM algorithm is implemented on a case study of a cybersecurity problem to illustrate its feasibility and effectiveness. The results verify the robustness and validity of the proposed MCGDM using sensitivity analysis and comparison with other existing algorithms.

Compound AI systems (CASs) that employ LLMs as agents to accomplish knowledge-intensive tasks via interactions with tools and data retrievers have garnered significant interest within database and AI communities. While these systems have the potential to supplement typical analysis workflows of data analysts in enterprise data platforms, unfortunately, CASs are subject to the same data discovery challenges that analysts have encountered over the years -- silos of multimodal data sources, created across teams and departments within an organization, make it difficult to identify appropriate data sources for accomplishing the task at hand. Existing data discovery benchmarks do not model such multimodality and multiplicity of data sources. Moreover, benchmarks of CASs prioritize only evaluating end-to-end task performance. To catalyze research on evaluating the data discovery performance of multimodal data retrievers in CASs within a real-world setting, we propose CMDBench, a benchmark modeling the complexity of enterprise data platforms. We adapt existing datasets and benchmarks in open-domain -- from question answering and complex reasoning tasks to natural language querying over structured data -- to evaluate coarse- and fine-grained data discovery and task execution performance. Our experiments reveal the impact of data retriever design on downstream task performance -- a 46% drop in task accuracy on average -- across various modalities, data sources, and task difficulty. The results indicate the need to develop optimization strategies to identify appropriate LLM agents and retrievers for efficient execution of CASs over enterprise data.

We propose prioritized unit propagation with periodic resetting, which is a simple but surprisingly effective algorithm for solving random SAT instances that are meant to be hard. In particular, an evaluation on the Random Track of the 2017 and 2018 SAT competitions shows that a basic prototype of this simple idea already ranks at second place in both years. We share this observation in the hope that it helps the SAT community better understand the hardness of random instances used in competitions and inspire other interesting ideas on SAT solving.

We study the conditions under which the convex relaxation of a mixed-integer linear programming formulation for ordered optimization problems, where sorting is part of the decision process, yields integral optimal solutions. Thereby solving the problem exactly in polynomial time. Our analysis identifies structural properties of the input data that influence the integrality of the relaxation. We show that incorporating ordered components introduces additional layers of combinatorial complexity that invalidate the exactness observed in classical (non-ordered) settings. In particular, for certain ordered problems such as the min--max case, the linear relaxation never recovers the integral solution. These results clarify the intrinsic hardness introduced by sorting and reveal that the strength of the relaxation depends critically on the ``proximity'' of the ordered problem to its classical counterpart: problems closer to the non-ordered case tend to admit tighter relaxations, while those further away exhibit substantially weaker behavior. Computational experiments on benchmark instances confirm the predictive value of the integrality conditions and demonstrate the practical implications of exact relaxations for ordered location problems.

We define a new class of set functions that in addition to being monotone and subadditive, also admit a very limited form of submodularity defined over a permutation of the ground set. We refer to this permutation as a submodular order. This class of functions includes monotone submodular functions as a sub-family. To understand the importance of this structure in optimization problems we consider the problem of maximizing function value under various types of constraints. To demonstrate the modeling power of submodular order functions we show applications in two different settings. First, we apply our results to the extensively studied problem of assortment optimization. While the objectives in assortment optimization are known to be non-submodular (and non-monotone) even for simple choice models, we show that they are compatible with the notion of submodular order. Consequently, we obtain new and in some cases the first constant factor guarantee for constrained assortment optimization in fundamental choice models. As a second application of submodular order functions, we show an intriguing connection to the maximization of monotone submodular functions in the streaming model. We recover some best known guarantees for this problem as a corollary of our results.

Pairwise re-ranking models predict which of two documents is more relevant to a query and then aggregate a final ranking from such preferences. This is often more effective than pointwise re-ranking models that directly predict a relevance value for each document. However, the high inference overhead of pairwise models limits their practical application: usually, for a set of k documents to be re-ranked, preferences for all k^2-k comparison pairs excluding self-comparisons are aggregated. We investigate whether the efficiency of pairwise re-ranking can be improved by sampling from all pairs. In an exploratory study, we evaluate three sampling methods and five preference aggregation methods. The best combination allows for an order of magnitude fewer comparisons at an acceptable loss of retrieval effectiveness, while competitive effectiveness is already achieved with about one third of the comparisons.

This paper investigates the problem of ensembling multiple strategies for sequential portfolios to outperform individual strategies in terms of long-term wealth. Due to the uncertainty of strategies' performances in the future market, which are often based on specific models and statistical assumptions, investors often mitigate risk and enhance robustness by combining multiple strategies, akin to common approaches in collective learning prediction. However, the absence of a distribution-free and consistent preference framework complicates decisions of combination due to the ambiguous objective. To address this gap, we introduce a novel framework for decision-making in combining strategies, irrespective of market conditions, by establishing the investor's preference between decisions and then forming a clear objective. Through this framework, we propose a combinatorial strategy construction, free from statistical assumptions, for any scale of component strategies, even infinite, such that it meets the determined criterion. Finally, we test the proposed strategy along with its accelerated variant and some other multi-strategies. The numerical experiments show results in favor of the proposed strategies, albeit with small tradeoffs in their Sharpe ratios, in which their cumulative wealths eventually exceed those of the best component strategies while the accelerated strategy significantly improves performance.

We consider non-clairvoyant scheduling with online precedence constraints, where an algorithm is oblivious to any job dependencies and learns about a job only if all of its predecessors have been completed. Given strong impossibility results in classical competitive analysis, we investigate the problem in a learning-augmented setting, where an algorithm has access to predictions without any quality guarantee. We discuss different prediction models: novel problem-specific models as well as general ones, which have been proposed in previous works. We present lower bounds and algorithmic upper bounds for different precedence topologies, and thereby give a structured overview on which and how additional (possibly erroneous) information helps for designing better algorithms. Along the way, we also improve bounds on traditional competitive ratios for existing algorithms.

This paper investigates the extent to which pretrained German BERT encodes knowledge of noun compound semantics. We comprehensively vary combinations of target tokens, layers, and cased vs. uncased models, and evaluate them by predicting the compositionality of 868 gold standard compounds. Looking at representational patterns within the transformer architecture, we observe trends comparable to equivalent prior work on English, with compositionality information most easily recoverable in the early layers. However, our strongest results clearly lag behind those reported for English, suggesting an inherently more difficult task in German. This may be due to the higher productivity of compounding in German than in English and the associated increase in constituent-level ambiguity, including in our target compound set.

Generative Flow Networks (GFlowNets) have been introduced as a method to sample a diverse set of candidates with probabilities proportional to a given reward. However, GFlowNets can only be used with a predefined scalar reward, which can be either computationally expensive or not directly accessible, in the case of multi-objective optimization (MOO) tasks for example. Moreover, to prioritize identifying high-reward candidates, the conventional practice is to raise the reward to a higher exponent, the optimal choice of which may vary across different environments. To address these issues, we propose Order-Preserving GFlowNets (OP-GFNs), which sample with probabilities in proportion to a learned reward function that is consistent with a provided (partial) order on the candidates, thus eliminating the need for an explicit formulation of the reward function. We theoretically prove that the training process of OP-GFNs gradually sparsifies the learned reward landscape in single-objective maximization tasks. The sparsification concentrates on candidates of a higher hierarchy in the ordering, ensuring exploration at the beginning and exploitation towards the end of the training. We demonstrate OP-GFN's state-of-the-art performance in single-objective maximization (totally ordered) and multi-objective Pareto front approximation (partially ordered) tasks, including synthetic datasets, molecule generation, and neural architecture search.

We seek to understand fundamental tradeoffs between the accuracy of prior information that a learner has on a given problem and its learning performance. We introduce the notion of prioritized risk, which differs from traditional notions of minimax and Bayes risk by allowing us to study such fundamental tradeoffs in settings where reality does not necessarily conform to the learner's prior. We present a general reduction-based approach for extending classical minimax lower-bound techniques in order to lower bound the prioritized risk for statistical estimation problems. We also introduce a novel generalization of Fano's inequality (which may be of independent interest) for lower bounding the prioritized risk in more general settings involving unbounded losses. We illustrate the ability of our framework to provide insights into tradeoffs between prior information and learning performance for problems in estimation, regression, and reinforcement learning.

We present SimpleQA, a benchmark that evaluates the ability of language models to answer short, fact-seeking questions. We prioritized two properties in designing this eval. First, SimpleQA is challenging, as it is adversarially collected against GPT-4 responses. Second, responses are easy to grade, because questions are created such that there exists only a single, indisputable answer. Each answer in SimpleQA is graded as either correct, incorrect, or not attempted. A model with ideal behavior would get as many questions correct as possible while not attempting the questions for which it is not confident it knows the correct answer. SimpleQA is a simple, targeted evaluation for whether models "know what they know," and our hope is that this benchmark will remain relevant for the next few generations of frontier models. SimpleQA can be found at https://github.com/openai/simple-evals.

Language models often pre-train on large unsupervised text corpora, then fine-tune on additional task-specific data. However, typical fine-tuning schemes do not prioritize the examples that they tune on. We show that, if you can prioritize informative training data, you can achieve better performance while using fewer labels. To do this we augment a language model with an epinet: a small additional network that helps to estimate model uncertainty and forms an epistemic neural network (ENN). ENNs are neural networks that can know what they don't know. Using an epinet to prioritize uncertain data, we can fine-tune BERT on GLUE tasks to the same performance while using 2x less data than training without prioritization. We also investigate performance in synthetic neural network generative models designed to build understanding. In each setting, using an epinet outperforms heuristic active learning schemes.

Offline paired preference optimization algorithms have become a popular approach for fine-tuning on preference data, outperforming traditional supervised fine-tuning in various tasks. However, traditional implementations often involve redundant computations, especially for tasks with long shared prompts. We introduce prefix sharing for preference tuning, a novel technique that processes chosen and rejected responses as one sequence with a shared prefix. To prevent cross-response contamination, we use a custom block-sparse attention mask. Our method achieves 1.1-1.5times improvement in training throughput on popular DPO datasets, without any effect on convergence. When combined with sequence packing, we observe consistent 1.3-1.6times speedups, benefiting even datasets with smaller sequence lengths. While we focus on Direct Preference Optimization (DPO), our approach is applicable to other paired preference tuning methods. By enhancing computational efficiency, our work contributes to making preference-based fine-tuning more accessible for a wider range of applications and model sizes. We open-source our code at https://github.com/frankxwang/dpo-prefix-sharing.

Direct Preference Optimization (DPO) is an effective technique that leverages pairwise preference data (usually one chosen and rejected response pair per user prompt) to align LLMs to human preferences. In practice, multiple responses can exist for a given prompt with varying quality relative to each other. With availability of such quality ratings for multiple responses, we propose utilizing these responses to create multiple preference pairs for a given prompt. Our work focuses on systematically using the constructed multiple preference pair in DPO training via curriculum learning methodology. In particular, we order these multiple pairs of preference data from easy to hard (emulating curriculum training) according to various criteria. We show detailed comparisons of our proposed approach to the standard single-pair DPO setting. Our method, which we call Curry-DPO consistently shows increased performance gains on MTbench, Vicuna, WizardLM, and the UltraFeedback test set, highlighting its effectiveness. More specifically, Curry-DPO achieves a score of 7.43 on MT-bench with Zephy-7B model outperforming majority of existing LLMs with similar parameter size. Curry-DPO also achieves the highest adjusted win rates on Vicuna, WizardLM, and UltraFeedback test datasets (90.7%, 87.1%, and 87.9% respectively) in our experiments, with notable gains of upto 7.5% when compared to standard DPO technique.

Effective decision-making in Large Language Models (LLMs) is essential for handling intricate tasks. However, existing approaches prioritize performance but often overlook the balance between effectiveness and computational cost. To address this, we first introduce the 3E Criteria to systematically assess the cost-effectiveness of search strategies, revealing that existing methods often trade significant efficiency for marginal performance gains. To improve LLM decision-making while maintaining efficiency, we propose the Speculative Reward Model (SRM), a plug-and-play framework that seamlessly integrates with existing search strategies. Specifically, SRM employs an external reward assigner to predict optimal actions, reducing reliance on LLMs' internal self-evaluation. And a speculative verification mechanism is used to prune suboptimal choices and guide the search toward more promising steps. We evaluate SRM on several complex decision-making tasks including mathematical reasoning, planning and numerical reasoning in specialized domains. Experimental results show that SRM reduces costs to 1/10 of the original search framework on average while maintaining effectiveness.

Current Reinforcement Learning (RL) methods often suffer from sample-inefficiency, resulting from blind exploration strategies that neglect causal relationships among states, actions, and rewards. Although recent causal approaches aim to address this problem, they lack grounded modeling of reward-guided causal understanding of states and actions for goal-orientation, thus impairing learning efficiency. To tackle this issue, we propose a novel method named Causal Information Prioritization (CIP) that improves sample efficiency by leveraging factored MDPs to infer causal relationships between different dimensions of states and actions with respect to rewards, enabling the prioritization of causal information. Specifically, CIP identifies and leverages causal relationships between states and rewards to execute counterfactual data augmentation to prioritize high-impact state features under the causal understanding of the environments. Moreover, CIP integrates a causality-aware empowerment learning objective, which significantly enhances the agent's execution of reward-guided actions for more efficient exploration in complex environments. To fully assess the effectiveness of CIP, we conduct extensive experiments across 39 tasks in 5 diverse continuous control environments, encompassing both locomotion and manipulation skills learning with pixel-based and sparse reward settings. Experimental results demonstrate that CIP consistently outperforms existing RL methods across a wide range of scenarios.

In recent years, large-scale data collection efforts have prioritized the amount of data collected in order to improve the modeling capabilities of large language models. This prioritization, however, has resulted in concerns with respect to the rights of data subjects represented in data collections, particularly when considering the difficulty in interrogating these collections due to insufficient documentation and tools for analysis. Mindful of these pitfalls, we present our methodology for a documentation-first, human-centered data collection project as part of the BigScience initiative. We identified a geographically diverse set of target language groups (Arabic, Basque, Chinese, Catalan, English, French, Indic languages, Indonesian, Niger-Congo languages, Portuguese, Spanish, and Vietnamese, as well as programming languages) for which to collect metadata on potential data sources. To structure this effort, we developed our online catalogue as a supporting tool for gathering metadata through organized public hackathons. We present our development process; analyses of the resulting resource metadata, including distributions over languages, regions, and resource types; and our lessons learned in this endeavor.