Daily Papers

Convolutional Neural Networks (CNN) have gained great success in many artificial intelligence tasks. However, finding a good set of hyperparameters for a CNN remains a challenging task. It usually takes an expert with deep knowledge, and trials and errors. Genetic algorithms have been used in hyperparameter optimizations. However, traditional genetic algorithms with fixed-length chromosomes may not be a good fit for optimizing deep learning hyperparameters, because deep learning models have variable number of hyperparameters depending on the model depth. As the depth increases, the number of hyperparameters grows exponentially, and searching becomes exponentially harder. It is important to have an efficient algorithm that can find a good model in reasonable time. In this article, we propose to use a variable length genetic algorithm (GA) to systematically and automatically tune the hyperparameters of a CNN to improve its performance. Experimental results show that our algorithm can find good CNN hyperparameters efficiently. It is clear from our experiments that if more time is spent on optimizing the hyperparameters, better results could be achieved. Theoretically, if we had unlimited time and CPU power, we could find the optimized hyperparameters and achieve the best results in the future.

The Unmanned Aerial Vehicle (UAV) path planning problem is a complex optimization problem in the field of robotics. In this paper, we investigate the possible utilization of this problem in benchmarking global optimization methods. We devise a problem instance generator and pick 56 representative instances, which we compare to established benchmarking suits through Exploratory Landscape Analysis to show their uniqueness. For the computational comparison, we select twelve well-performing global optimization techniques from both subfields of stochastic algorithms (evolutionary computation methods) and deterministic algorithms (Dividing RECTangles, or DIRECT-type methods). The experiments were conducted in settings with varying dimensionality and computational budgets. The results were analyzed through several criteria (number of best-found solutions, mean relative error, Friedman ranks) and utilized established statistical tests. The best-ranking methods for the UAV problems were almost universally the top-performing evolutionary techniques from recent competitions on numerical optimization at the Institute of Electrical and Electronics Engineers Congress on Evolutionary Computation. Lastly, we discussed the variable dimension characteristics of the studied UAV problems that remain still largely under-investigated.

We study the problem of efficiently generating differentially private synthetic data that approximate the statistical properties of an underlying sensitive dataset. In recent years, there has been a growing line of work that approaches this problem using first-order optimization techniques. However, such techniques are restricted to optimizing differentiable objectives only, severely limiting the types of analyses that can be conducted. For example, first-order mechanisms have been primarily successful in approximating statistical queries only in the form of marginals for discrete data domains. In some cases, one can circumvent such issues by relaxing the task's objective to maintain differentiability. However, even when possible, these approaches impose a fundamental limitation in which modifications to the minimization problem become additional sources of error. Therefore, we propose Private-GSD, a private genetic algorithm based on zeroth-order optimization heuristics that do not require modifying the original objective. As a result, it avoids the aforementioned limitations of first-order optimization. We empirically evaluate Private-GSD against baseline algorithms on data derived from the American Community Survey across a variety of statistics--otherwise known as statistical queries--both for discrete and real-valued attributes. We show that Private-GSD outperforms the state-of-the-art methods on non-differential queries while matching accuracy in approximating differentiable ones.

This paper introduces PyGAD, an open-source easy-to-use Python library for building the genetic algorithm. PyGAD supports a wide range of parameters to give the user control over everything in its life cycle. This includes, but is not limited to, population, gene value range, gene data type, parent selection, crossover, and mutation. PyGAD is designed as a general-purpose optimization library that allows the user to customize the fitness function. Its usage consists of 3 main steps: build the fitness function, create an instance of the pygad.GA class, and calling the pygad.GA.run() method. The library supports training deep learning models created either with PyGAD itself or with frameworks like Keras and PyTorch. Given its stable state, PyGAD is also in active development to respond to the user's requested features and enhancement received on GitHub https://github.com/ahmedfgad/GeneticAlgorithmPython. PyGAD comes with documentation https://pygad.readthedocs.io for further details and examples.

Multi-objective evolutionary algorithms (MOEAs) are among the most widely and successfully applied optimizers for multi-objective problems. However, to store many optimal trade-offs (the Pareto optima) at once, MOEAs are typically run with a large, static population of solution candidates, which can slow down the algorithm. We propose the dynamic NSGA-II (dNSGA-II), which is based on the popular NSGA-II and features a non-static population size. The dNSGA-II starts with a small initial population size of four and doubles it after a user-specified number tau of function evaluations, up to a maximum size of mu. Via a mathematical runtime analysis, we prove that the dNSGA-II with parameters mu geq 4(n + 1) and tau geq 256{50} e n computes the full Pareto front of the OneMinMax benchmark of size n in O(log(mu) tau + mu log(n)) function evaluations, both in expectation and with high probability. For an optimal choice of mu and tau, the resulting O(n log(n)) runtime improves the optimal expected runtime of the classic NSGA-II by a factor of Theta(n). In addition, we show that the parameter tau can be removed when utilizing concurrent runs of the dNSGA-II. This approach leads to a mild slow-down by a factor of O(log(n)) compared to an optimal choice of tau for the dNSGA-II, which is still a speed-up of Theta(n / log(n)) over the classic NSGA-II.

This paper proposes a novel admission and routing scheme which takes into account arbitrarily assigned priorities for network flows. The presented approach leverages the centralized Software Defined Networking (SDN) capabilities in order to do so. Exact and heuristic approaches to the stated Priority Flow Admission and Routing (PFAR) problem are provided. The exact approach which provides an optimal solution is based on Integer Linear Programming (ILP). Given the potentially long running time required to find an exact and optimal solution, a heuristic approach is proposed; this approach is based on Genetic Algorithms (GAs). In order to effectively estimate the performance of the proposed approaches, a simulator that is capable of generating semi-random network topologies and flows has been developed. Experimental results for large problem instances (up 50 network nodes and thousands of network flows), show that: i) an optimal solution can be often found in few seconds (even milliseconds), and ii) the heuristic approach yields close-to-optimal solutions (approximately 95\% of the optimal) in a fixed amount of time; these experimental results demonstrate the pertinence of the proposed approaches.

Optimization can be found in many real-life applications. Designing an effective algorithm for a specific optimization problem typically requires a tedious amount of effort from human experts with domain knowledge and algorithm design skills. In this paper, we propose a novel approach called Algorithm Evolution using Large Language Model (AEL). It utilizes a large language model (LLM) to automatically generate optimization algorithms via an evolutionary framework. AEL does algorithm-level evolution without model training. Human effort and requirements for domain knowledge can be significantly reduced. We take constructive methods for the salesman traveling problem as a test example, we show that the constructive algorithm obtained by AEL outperforms simple hand-crafted and LLM-generated heuristics. Compared with other domain deep learning model-based algorithms, these methods exhibit excellent scalability across different problem sizes. AEL is also very different from previous attempts that utilize LLMs as search operators in algorithms.

The study of hardest and easiest fitness landscapes is an active area of research. Recently, Kaufmann, Larcher, Lengler and Zou conjectured that for the self-adjusting (1,lambda)-EA, Adversarial Dynamic BinVal (ADBV) is the hardest dynamic monotone function to optimize. We introduce the function Switching Dynamic BinVal (SDBV) which coincides with ADBV whenever the number of remaining zeros in the search point is strictly less than n/2, where n denotes the dimension of the search space. We show, using a combinatorial argument, that for the (1+1)-EA with any mutation rate p in [0,1], SDBV is drift-minimizing among the class of dynamic monotone functions. Our construction provides the first explicit example of an instance of the partially-ordered evolutionary algorithm (PO-EA) model with parameterized pessimism introduced by Colin, Doerr and F\'erey, building on work of Jansen. We further show that the (1+1)-EA optimizes SDBV in Theta(n^{3/2}) generations. Our simulations demonstrate matching runtimes for both static and self-adjusting (1,lambda) and (1+lambda)-EA. We further show, using an example of fixed dimension, that drift-minimization does not equal maximal runtime.

This paper presents a strategy to allocate services on a Cloud system without overloading nodes and maintaining the system stability with minimum cost. We specify an abstract model of cloud resources utilization, including multiple types of resources as well as considerations for the service migration costs. A prototype meta-heuristic load balancer is demonstrated and experimental results are presented and discussed. We also propose a novel genetic algorithm, where population is seeded with the outputs of other meta-heuristic algorithms.

We study the problem of estimating the time delay between two signals representing delayed, irregularly sampled and noisy versions of the same underlying pattern. We propose and demonstrate an evolutionary algorithm for the (hyper)parameter estimation of a kernel-based technique in the context of an astronomical problem, namely estimating the time delay between two gravitationally lensed signals from a distant quasar. Mixed types (integer and real) are used to represent variables within the evolutionary algorithm. We test the algorithm on several artificial data sets, and also on real astronomical observations of quasar Q0957+561. By carrying out a statistical analysis of the results we present a detailed comparison of our method with the most popular methods for time delay estimation in astrophysics. Our method yields more accurate and more stable time delay estimates: for Q0957+561, we obtain 419.6 days for the time delay between images A and B. Our methodology can be readily applied to current state-of-the-art optical monitoring data in astronomy, but can also be applied in other disciplines involving similar time series data.

A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the algorithm is suitable for searching vast chemical space, it is difficult to optimize pharmacological properties while maintaining molecular substructure. To solve this issue, we introduce a genetic algorithm featuring a constrained molecular inverse design. The proposed algorithm successfully produces valid molecules for crossover and mutation. Furthermore, it optimizes specific properties while adhering to structural constraints using a two-phase optimization. Experiments prove that our algorithm effectively finds molecules that satisfy specific properties while maintaining structural constraints.

This paper presents a reinforced genetic approach to a defined d-resource system optimization problem. The classical evolution schema was ineffective due to a very strict feasibility function in the studied problem. Hence, the presented strategy has introduced several modifications and adaptations to standard genetic routines, e.g.: a migration operator which is an analogy to the biological random genetic drift.

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face limitations such as suboptimal solutions from greedy methods or prohibitive computational costs and limited applicability of exact optimization approaches. To address these challenges, we propose an evolutionary optimization method for decision tree induction based on genetic programming (GP). Our key innovation is the integration of semantic priors and domain-specific knowledge about the search space into the optimization algorithm. To this end, we introduce LLEGO, a framework that incorporates semantic priors into genetic search operators through the use of Large Language Models (LLMs), thereby enhancing search efficiency and targeting regions of the search space that yield decision trees with superior generalization performance. This is operationalized through novel genetic operators that work with structured natural language prompts, effectively utilizing LLMs as conditional generative models and sources of semantic knowledge. Specifically, we introduce fitness-guided crossover to exploit high-performing regions, and diversity-guided mutation for efficient global exploration of the search space. These operators are controlled by corresponding hyperparameters that enable a more nuanced balance between exploration and exploitation across the search space. Empirically, we demonstrate across various benchmarks that LLEGO evolves superior-performing trees compared to existing tree induction methods, and exhibits significantly more efficient search performance compared to conventional GP approaches.

Although large pre-trained models of code have delivered significant advancements in various code processing tasks, there is an impediment to the wide and fluent adoption of these powerful models in software developers' daily workflow: these large models consume hundreds of megabytes of memory and run slowly on personal devices, which causes problems in model deployment and greatly degrades the user experience. It motivates us to propose Compressor, a novel approach that can compress the pre-trained models of code into extremely small models with negligible performance sacrifice. Our proposed method formulates the design of tiny models as simplifying the pre-trained model architecture: searching for a significantly smaller model that follows an architectural design similar to the original pre-trained model. Compressor proposes a genetic algorithm (GA)-based strategy to guide the simplification process. Prior studies found that a model with higher computational cost tends to be more powerful. Inspired by this insight, the GA algorithm is designed to maximize a model's Giga floating-point operations (GFLOPs), an indicator of the model computational cost, to satisfy the constraint of the target model size. Then, we use the knowledge distillation technique to train the small model: unlabelled data is fed into the large model and the outputs are used as labels to train the small model. We evaluate Compressor with two state-of-the-art pre-trained models, i.e., CodeBERT and GraphCodeBERT, on two important tasks, i.e., vulnerability prediction and clone detection. We use our method to compress pre-trained models to a size (3 MB), which is 160times smaller than the original size. The results show that compressed CodeBERT and GraphCodeBERT are 4.31times and 4.15times faster than the original model at inference, respectively. More importantly, ...

Reasoning language models have shown an uncanny ability to improve performance at test-time by ``thinking longer''-that is, by generating longer chain-of-thought sequences and hence using more compute. However, the length of their chain-of-thought reasoning is not controllable, making it impossible to allocate test-time compute to achieve a desired level of performance. We introduce Length Controlled Policy Optimization (LCPO), a simple reinforcement learning method that optimizes for accuracy and adherence to user-specified length constraints. We use LCPO to train L1, a reasoning language model that produces outputs satisfying a length constraint given in its prompt. L1's length control allows for smoothly trading off computational cost and accuracy on a wide range of tasks, and outperforms the state-of-the-art S1 method for length control. Furthermore, we uncover an unexpected short chain-of-thought capability in models trained with LCPO. For instance, our 1.5B L1 model surpasses GPT-4o at equal reasoning lengths. Overall, LCPO enables precise control over reasoning length, allowing for fine-grained allocation of test-time compute and accuracy. We release code and models at https://www.cmu-l3.github.io/l1

Automatic music generation systems have gained in popularity and sophistication as advances in cloud computing have enabled large-scale complex computations such as deep models and optimization algorithms on personal devices. Yet, they still face an important challenge, that of long-term structure, which is key to conveying a sense of musical coherence. We present the MorpheuS music generation system designed to tackle this problem. MorpheuS' novel framework has the ability to generate polyphonic pieces with a given tension profile and long- and short-term repeated pattern structures. A mathematical model for tonal tension quantifies the tension profile and state-of-the-art pattern detection algorithms extract repeated patterns in a template piece. An efficient optimization metaheuristic, variable neighborhood search, generates music by assigning pitches that best fit the prescribed tension profile to the template rhythm while hard constraining long-term structure through the detected patterns. This ability to generate affective music with specific tension profile and long-term structure is particularly useful in a game or film music context. Music generated by the MorpheuS system has been performed live in concerts.

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large combinatorial and unstructured spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose GameOpt, a novel game-theoretical approach to combinatorial BO. GameOpt establishes a cooperative game between the different optimization variables, and selects points that are game equilibria of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate- analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making GameOpt scalable to large combinatorial spaces. We demonstrate the application of GameOpt to the challenging protein design problem and validate its performance on four real-world protein datasets. Each protein can take up to 20^{X} possible configurations, where X is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.

Heuristic design with large language models (LLMs) has emerged as a promising approach for tackling combinatorial optimization problems (COPs). However, existing approaches often rely on manually predefined evolutionary computation (EC) optimizers and single-task training schemes, which may constrain the exploration of diverse heuristic algorithms and hinder the generalization of the resulting heuristics. To address these issues, we propose Meta-Optimization of Heuristics (MoH), a novel framework that operates at the optimizer level, discovering effective optimizers through the principle of meta-learning. Specifically, MoH leverages LLMs to iteratively refine a meta-optimizer that autonomously constructs diverse optimizers through (self-)invocation, thereby eliminating the reliance on a predefined EC optimizer. These constructed optimizers subsequently evolve heuristics for downstream tasks, enabling broader heuristic exploration. Moreover, MoH employs a multi-task training scheme to promote its generalization capability. Experiments on classic COPs demonstrate that MoH constructs an effective and interpretable meta-optimizer, achieving state-of-the-art performance across various downstream tasks, particularly in cross-size settings.

Deep artificial neural networks (DNNs) are typically trained via gradient-based learning algorithms, namely backpropagation. Evolution strategies (ES) can rival backprop-based algorithms such as Q-learning and policy gradients on challenging deep reinforcement learning (RL) problems. However, ES can be considered a gradient-based algorithm because it performs stochastic gradient descent via an operation similar to a finite-difference approximation of the gradient. That raises the question of whether non-gradient-based evolutionary algorithms can work at DNN scales. Here we demonstrate they can: we evolve the weights of a DNN with a simple, gradient-free, population-based genetic algorithm (GA) and it performs well on hard deep RL problems, including Atari and humanoid locomotion. The Deep GA successfully evolves networks with over four million free parameters, the largest neural networks ever evolved with a traditional evolutionary algorithm. These results (1) expand our sense of the scale at which GAs can operate, (2) suggest intriguingly that in some cases following the gradient is not the best choice for optimizing performance, and (3) make immediately available the multitude of neuroevolution techniques that improve performance. We demonstrate the latter by showing that combining DNNs with novelty search, which encourages exploration on tasks with deceptive or sparse reward functions, can solve a high-dimensional problem on which reward-maximizing algorithms (e.g.\ DQN, A3C, ES, and the GA) fail. Additionally, the Deep GA is faster than ES, A3C, and DQN (it can train Atari in {raise.17ex\scriptstyle\sim}4 hours on one desktop or {raise.17ex\scriptstyle\sim}1 hour distributed on 720 cores), and enables a state-of-the-art, up to 10,000-fold compact encoding technique.

Large Language Models (LLMs) excel at generating synthetic data, but ensuring its quality and diversity remains challenging. We propose Genetic Prompt, a novel framework that combines genetic algorithms with LLMs to augment synthetic data generation. Our approach treats semantic text attributes as gene sequences and leverages the LLM to simulate crossover and mutation operations. This genetic process enhances data quality and diversity by creating novel attribute combinations, yielding synthetic distributions closer to real-world data. To optimize parent selection, we also integrate an active learning scheme that expands the offspring search space. Our experiments on multiple NLP tasks reveal several key findings: Genetic Prompt not only significantly outperforms state-of-the-art baselines but also shows robust performance across various generator model sizes and scales. Moreover, we demonstrate that fusing our synthetic data with the original training set significantly boosts downstream model performance, particularly for class-imbalanced scenarios. Our findings validate that Genetic Prompt is an effective method for producing high-quality synthetic data for a wide range of NLP applications.

Large Language Models (LLMs) rely on instruction samples for alignment, but creating these datasets poses challenges, particularly in expert-dependent tasks like coding, which can be cost-prohibitive. One approach to mitigate these challenges is synthesizing data using another LLM. In this paper, we introduce a scalable method for generating synthetic instructions to enhance the code generation capability of LLMs. The proposed algorithm, Genetic-Instruct, mimics evolutionary processes, utilizing self-instruction to create numerous synthetic samples from a limited number of seeds. Genetic-Instruct is designed for efficient scaling of the generation process. Fine-tuning multiple coding LLMs with the synthetic samples demonstrates a significant improvement in their code generation accuracy compared to the baselines.

Large Language Models (LLMs) have shown impressive capabilities in many scenarios, but their performance depends, in part, on the choice of prompt. Past research has focused on optimizing prompts specific to a task. However, much less attention has been given to optimizing the general instructions included in a prompt, known as a system prompt. To address this gap, we propose SPRIG, an edit-based genetic algorithm that iteratively constructs prompts from prespecified components to maximize the model's performance in general scenarios. We evaluate the performance of system prompts on a collection of 47 different types of tasks to ensure generalizability. Our study finds that a single optimized system prompt performs on par with task prompts optimized for each individual task. Moreover, combining system and task-level optimizations leads to further improvement, which showcases their complementary nature. Experiments also reveal that the optimized system prompts generalize effectively across model families, parameter sizes, and languages. This study provides insights into the role of system-level instructions in maximizing LLM potential.

Since the emergence of large language models, prompt learning has become a popular method for optimizing and customizing these models. Special prompts, such as Chain-of-Thought, have even revealed previously unknown reasoning capabilities within these models. However, the progress of discovering effective prompts has been slow, driving a desire for general prompt optimization methods. Unfortunately, few existing prompt learning methods satisfy the criteria of being truly "general", i.e., automatic, discrete, black-box, gradient-free, and interpretable all at once. In this paper, we introduce metaheuristics, a branch of discrete non-convex optimization methods with over 100 options, as a promising approach to prompt learning. Within our paradigm, we test six typical methods: hill climbing, simulated annealing, genetic algorithms with/without crossover, tabu search, and harmony search, demonstrating their effectiveness in black-box prompt learning and Chain-of-Thought prompt tuning. Furthermore, we show that these methods can be used to discover more human-understandable prompts that were previously unknown, opening the door to a cornucopia of possibilities in prompt optimization. We release all the codes in https://github.com/research4pan/Plum.

Discovering efficient algorithms for solving complex problems has been an outstanding challenge in mathematics and computer science, requiring substantial human expertise over the years. Recent advancements in evolutionary search with large language models (LLMs) have shown promise in accelerating the discovery of algorithms across various domains, particularly in mathematics and optimization. However, existing approaches treat the LLM as a static generator, missing the opportunity to update the model with the signal obtained from evolutionary exploration. In this work, we propose to augment LLM-based evolutionary search by continuously refining the search operator - the LLM - through reinforcement learning (RL) fine-tuning. Our method leverages evolutionary search as an exploration strategy to discover improved algorithms, while RL optimizes the LLM policy based on these discoveries. Our experiments on three combinatorial optimization tasks - bin packing, traveling salesman, and the flatpack problem - show that combining RL and evolutionary search improves discovery efficiency of improved algorithms, showcasing the potential of RL-enhanced evolutionary strategies to assist computer scientists and mathematicians for more efficient algorithm design.

Selecting the best code solution from multiple generated ones is an essential task in code generation, which can be achieved by using some reliable validators (e.g., developer-written test cases) for assistance. Since reliable test cases are not always available and can be expensive to build in practice, researchers propose to automatically generate test cases to assess code solutions. However, when both code solutions and test cases are plausible and not reliable, selecting the best solution becomes challenging. Although some heuristic strategies have been proposed to tackle this problem, they lack a strong theoretical guarantee and it is still an open question whether an optimal selection strategy exists. Our work contributes in two ways. First, we show that within a Bayesian framework, the optimal selection strategy can be defined based on the posterior probability of the observed passing states between solutions and tests. The problem of identifying the best solution is then framed as an integer programming problem. Second, we propose an efficient approach for approximating this optimal (yet uncomputable) strategy, where the approximation error is bounded by the correctness of prior knowledge. We then incorporate effective prior knowledge to tailor code generation tasks. Both theoretical and empirical studies confirm that existing heuristics are limited in selecting the best solutions with plausible test cases. Our proposed approximated optimal strategy B4 significantly surpasses existing heuristics in selecting code solutions generated by large language models (LLMs) with LLM-generated tests, achieving a relative performance improvement by up to 50% over the strongest heuristic and 246% over the random selection in the most challenging scenarios. Our code is publicly available at https://github.com/ZJU-CTAG/B4.

In this study we explore the optimization of laser pulse duration to obtain the shortest possible pulse. We do this by employing a feedback loop between a pulse shaper and pulse duration measurements. We apply to this problem several iterative algorithms including gradient descent, Bayesian Optimization and genetic algorithms, using a simulation of the actual laser represented via a semi-physical model of the laser based on the process of linear and non-linear phase accumulation.

In practice, we usually need to build variable-sized models adapting for diverse resource constraints in different application scenarios, where weight initialization is an important step prior to training. The Learngene framework, introduced recently, firstly learns one compact part termed as learngene from a large well-trained model, after which learngene is expanded to initialize variable-sized models. In this paper, we start from analysing the importance of guidance for the expansion of well-trained learngene layers, inspiring the design of a simple but highly effective Learngene approach termed SWS (Stage-wise Weight Sharing), where both learngene layers and their learning process critically contribute to providing knowledge and guidance for initializing models at varying scales. Specifically, to learn learngene layers, we build an auxiliary model comprising multiple stages where the layer weights in each stage are shared, after which we train it through distillation. Subsequently, we expand these learngene layers containing stage information at their corresponding stage to initialize models of variable depths. Extensive experiments on ImageNet-1K demonstrate that SWS achieves consistent better performance compared to many models trained from scratch, while reducing around 6.6x total training costs. In some cases, SWS performs better only after 1 epoch tuning. When initializing variable-sized models adapting for different resource constraints, SWS achieves better results while reducing around 20x parameters stored to initialize these models and around 10x pre-training costs, in contrast to the pre-training and fine-tuning approach.

A modified LAB algorithm is introduced in this paper. It builds upon the original LAB algorithm (Reddy et al. 2023), which is a socio-inspired algorithm that models competitive and learning behaviours within a group, establishing hierarchical roles. The proposed algorithm incorporates the roulette wheel approach and a reduction factor introducing inter-group competition and iteratively narrowing down the sample space. The algorithm is validated by solving the benchmark test problems from CEC 2005 and CEC 2017. The solutions are validated using standard statistical tests such as two-sided and pairwise signed rank Wilcoxon test and Friedman rank test. The algorithm exhibited improved and superior robustness as well as search space exploration capabilities. Furthermore, a Clustering-Based Search Space Reduction (C-SSR) method is proposed, making the algorithm capable to solve constrained problems. The C-SSR method enables the algorithm to identify clusters of feasible regions, satisfying the constraints and contributing to achieve the optimal solution. This method demonstrates its effectiveness as a potential alternative to traditional constraint handling techniques. The results obtained using the Modified LAB algorithm are then compared with those achieved by other recent metaheuristic algorithms.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

We consider a class of assortment optimization problems in an offline data-driven setting. A firm does not know the underlying customer choice model but has access to an offline dataset consisting of the historically offered assortment set, customer choice, and revenue. The objective is to use the offline dataset to find an optimal assortment. Due to the combinatorial nature of assortment optimization, the problem of insufficient data coverage is likely to occur in the offline dataset. Therefore, designing a provably efficient offline learning algorithm becomes a significant challenge. To this end, we propose an algorithm referred to as Pessimistic ASsortment opTimizAtion (PASTA for short) designed based on the principle of pessimism, that can correctly identify the optimal assortment by only requiring the offline data to cover the optimal assortment under general settings. In particular, we establish a regret bound for the offline assortment optimization problem under the celebrated multinomial logit model. We also propose an efficient computational procedure to solve our pessimistic assortment optimization problem. Numerical studies demonstrate the superiority of the proposed method over the existing baseline method.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

Length generalization refers to the ability to extrapolate from short training sequences to long test sequences and is a challenge for current large language models. While prior work has proposed some architecture or data format changes to achieve length generalization, these proposals typically apply to a limited set of tasks. Building on prior scratchpad and Chain-of-Thought (CoT) techniques, we propose Turing Programs, a novel CoT strategy that decomposes an algorithmic task into steps mimicking the computation of a Turing Machine. This framework is both universal, as it can accommodate any algorithmic task, and simple, requiring only copying text from the context with small modifications. We show that by using Turing Programs, we obtain robust length generalization on a range of algorithmic tasks: addition, multiplication and in-context SGD. We then demonstrate that transformers achieve length generalization on random Turing Programs, suggesting that length generalization is possible for any algorithmic task. Finally, we theoretically prove that transformers can implement Turing Programs, constructing a simple RASP (Weiss et al.) program that simulates an arbitrary Turing machine.

LLM-based auto-annotators have become a key component of the LLM development process due to their cost-effectiveness and scalability compared to human-based evaluation. However, these auto-annotators can introduce complex biases that are hard to remove. Even simple, known confounders such as preference for longer outputs remain in existing automated evaluation metrics. We propose a simple regression analysis approach for controlling biases in auto-evaluations. As a real case study, we focus on reducing the length bias of AlpacaEval, a fast and affordable benchmark for chat LLMs that uses LLMs to estimate response quality. Despite being highly correlated with human preferences, AlpacaEval is known to favor models that generate longer outputs. We introduce a length-controlled AlpacaEval that aims to answer the counterfactual question: "What would the preference be if the model's and baseline's output had the same length?". To achieve this, we first fit a generalized linear model to predict the biased output of interest (auto-annotator preferences) based on the mediators we want to control for (length difference) and other relevant features. We then obtain length-controlled preferences by predicting preferences while conditioning the GLM with a zero difference in lengths. Length-controlling not only improves the robustness of the metric to manipulations in model verbosity, we also find that it increases the Spearman correlation with LMSYS' Chatbot Arena from 0.94 to 0.98. We release the code and leaderboard at https://tatsu-lab.github.io/alpaca_eval/ .

A ubiquitous feature of data of our era is their extra-large sizes and dimensions. Analyzing such high-dimensional data poses significant challenges, since the feature dimension is often much larger than the sample size. This thesis introduces robust and computationally efficient methods to address several common challenges associated with high-dimensional data. In my first manuscript, I propose a coherent approach to variable screening that accommodates nonlinear associations. I develop a novel variable screening method that transcends traditional linear assumptions by leveraging mutual information, with an intended application in neuroimaging data. This approach allows for accurate identification of important variables by capturing nonlinear as well as linear relationships between the outcome and covariates. Building on this foundation, I develop new optimization methods for sparse estimation using nonconvex penalties in my second manuscript. These methods address notable challenges in current statistical computing practices, facilitating computationally efficient and robust analyses of complex datasets. The proposed method can be applied to a general class of optimization problems. In my third manuscript, I contribute to robust modeling of high-dimensional correlated observations by developing a mixed-effects model based on Tsallis power-law entropy maximization and discussed the theoretical properties of such distribution. This model surpasses the constraints of conventional Gaussian models by accommodating a broader class of distributions with enhanced robustness to outliers. Additionally, I develop a proximal nonlinear conjugate gradient algorithm that accelerates convergence while maintaining numerical stability, along with rigorous statistical properties for the proposed framework.

Retrieval-augmented generation (RAG) systems enhance large language models by incorporating external knowledge, addressing issues like outdated internal knowledge and hallucination. However, their reliance on external knowledge bases makes them vulnerable to corpus poisoning attacks, where adversarial passages can be injected to manipulate retrieval results. Existing methods for crafting such passages, such as random token replacement or training inversion models, are often slow and computationally expensive, requiring either access to retriever's gradients or large computational resources. To address these limitations, we propose Dynamic Importance-Guided Genetic Algorithm (DIGA), an efficient black-box method that leverages two key properties of retrievers: insensitivity to token order and bias towards influential tokens. By focusing on these characteristics, DIGA dynamically adjusts its genetic operations to generate effective adversarial passages with significantly reduced time and memory usage. Our experimental evaluation shows that DIGA achieves superior efficiency and scalability compared to existing methods, while maintaining comparable or better attack success rates across multiple datasets.

Recent progress in generative models, especially in text-guided diffusion models, has enabled the production of aesthetically-pleasing imagery resembling the works of professional human artists. However, one has to carefully compose the textual description, called the prompt, and augment it with a set of clarifying keywords. Since aesthetics are challenging to evaluate computationally, human feedback is needed to determine the optimal prompt formulation and keyword combination. In this paper, we present a human-in-the-loop approach to learning the most useful combination of prompt keywords using a genetic algorithm. We also show how such an approach can improve the aesthetic appeal of images depicting the same descriptions.

Is the lottery ticket phenomenon an idiosyncrasy of gradient-based training or does it generalize to evolutionary optimization? In this paper we establish the existence of highly sparse trainable initializations for evolution strategies (ES) and characterize qualitative differences compared to gradient descent (GD)-based sparse training. We introduce a novel signal-to-noise iterative pruning procedure, which incorporates loss curvature information into the network pruning step. This can enable the discovery of even sparser trainable network initializations when using black-box evolution as compared to GD-based optimization. Furthermore, we find that these initializations encode an inductive bias, which transfers across different ES, related tasks and even to GD-based training. Finally, we compare the local optima resulting from the different optimization paradigms and sparsity levels. In contrast to GD, ES explore diverse and flat local optima and do not preserve linear mode connectivity across sparsity levels and independent runs. The results highlight qualitative differences between evolution and gradient-based learning dynamics, which can be uncovered by the study of iterative pruning procedures.

Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to some form of self-adaptive selection mechanism. In nature, genetic diversity can be the consequence of many different factors, but when considering reproduction Sexual Selection can have an impact on promoting variety within a species. Specifically, Mate Choice often results in different selective pressures between sexes, which in turn may trigger evolutionary differences among them. Although some mechanisms of Sexual Selection have been applied to Genetic Programming in the past, the literature is scarce when it comes to mate choice. Recently, a way of modelling mating preferences by ideal mate representations was proposed, achieving good results when compared to a standard approach. These mating preferences evolve freely in a self-adaptive fashion, creating an evolutionary driving force of its own alongside fitness pressure. The inner mechanisms of this approach operate from personal choice, as each individual has its own representation of a perfect mate which affects the mate to be selected. In this paper, we compare this method against a random mate choice to assess whether there are advantages in evolving personal preferences. We conducted experiments using three symbolic regression problems and different mutation rates. The results show that self-adaptive mating preferences are able to create a more diverse set of solutions when compared to the traditional approach and a random mate approach (with statistically significant differences) and have a higher success rate in three of the six instances tested.

We propose Delta L Normalization, a simple yet effective loss aggregation method tailored to the characteristic of dynamic generation lengths in Reinforcement Learning with Verifiable Rewards (RLVR). Recently, RLVR has demonstrated strong potential in improving the reasoning capabilities of large language models (LLMs), but a major challenge lies in the large variability of response lengths during training, which leads to high gradient variance and unstable optimization. Although previous methods such as GRPO, DAPO, and Dr. GRPO introduce different loss normalization terms to address this issue, they either produce biased estimates or still suffer from high gradient variance. By analyzing the effect of varying lengths on policy loss both theoretically and empirically, we reformulate the problem as finding a minimum-variance unbiased estimator. Our proposed Delta L Normalization not only provides an unbiased estimate of the true policy loss but also minimizes gradient variance in theory. Extensive experiments show that it consistently achieves superior results across different model sizes, maximum lengths, and tasks. Our code will be made public at https://github.com/zerolllin/Delta-L-Normalization.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Speculative decoding reduces the inference latency of a target large language model via utilizing a smaller and faster draft model. Its performance depends on a hyperparameter K -- the candidate length, i.e., the number of candidate tokens for the target model to verify in each round. However, previous methods often use simple heuristics to choose K, which may result in sub-optimal performance. We study the choice of the candidate length K and formulate it as a Markov Decision Process. We theoretically show that the optimal policy of this Markov decision process takes the form of a threshold policy, i.e., the current speculation should stop and be verified when the probability of getting a rejection exceeds a threshold value. Motivated by this theory, we propose SpecDec++, an enhanced version of speculative decoding that adaptively determines the candidate length on the fly. We augment the draft model with a trained acceptance prediction head to predict the conditional acceptance probability of the candidate tokens. SpecDec++ will stop the current speculation when the predicted probability that at least one token gets rejected exceeds a threshold. We implement SpecDec++ and apply it to the llama-2-chat 7B & 70B model pair. Our adaptive method achieves a 2.04x speedup on the Alpaca dataset (an additional 7.2% improvement over the baseline speculative decoding). On the GSM8K and HumanEval datasets, our method achieves a 2.26x speedup (9.4% improvement) and 2.23x speedup (11.1% improvement), respectively.

Any optimization algorithm programming interface can be seen as a black-box function with additional free parameters. In this spirit, simulated annealing (SA) can be implemented in pseudo-code within the dimensions of a single slide with free parameters relating to the annealing schedule. Such an implementation, however, necessarily neglects much of the structure necessary to take advantage of advances in computing resources and algorithmic breakthroughs. Simulated annealing is often introduced in myriad disciplines, from discrete examples like the Traveling Salesman Problem (TSP) to molecular cluster potential energy exploration or even explorations of a protein's configurational space. Theoretical guarantees also demand a stricter structure in terms of statistical quantities, which cannot simply be left to the user. We will introduce several standard paradigms and demonstrate how these can be "lifted" into a unified framework using object-oriented programming in Python. We demonstrate how clean, interoperable, reproducible programming libraries can be used to access and rapidly iterate on variants of Simulated Annealing in a manner which can be extended to serve as a best practices blueprint or design pattern for a data-driven optimization library.

Neural architecture search (NAS), the study of automating the discovery of optimal deep neural network architectures for tasks in domains such as computer vision and natural language processing, has seen rapid growth in the machine learning research community. While there have been many recent advancements in NAS, there is still a significant focus on reducing the computational cost incurred when validating discovered architectures by making search more efficient. Evolutionary algorithms, specifically genetic algorithms, have a history of usage in NAS and continue to gain popularity versus other optimization approaches as a highly efficient way to explore the architecture objective space. Most NAS research efforts have centered around computer vision tasks and only recently have other modalities, such as the rapidly growing field of natural language processing, been investigated in depth. In this work, we show how genetic algorithms can be paired with lightly trained objective predictors in an iterative cycle to accelerate multi-objective architectural exploration in a way that works in the modalities of both machine translation and image classification.

Communications satellite network (CSN), as an integral component of the next generation of communication systems, has the capability to offer services globally. Data transmission in this network primarily relies on two modes: inter-satellite communication and satellite-to-ground station communication. The latter directly impacts the successful reception of data by users. However, due to resource and task limitations, finding a satisfactory solution poses a significant challenge. The communication satellite-ground station network scheduling problem (CS-GSNSP) aims to optimize CSN effectiveness by devising a plan that maximizes link construction time while considering constraints associated with satellite operation modes. The large number of tasks and numerous constraints in the problem result in a time-consuming evaluation of fitness function values. To address this issue, we propose a fuzzy fitness evaluation method (FFEM) that employs fuzzy or real evaluation methods based on individual similarity degrees. Additionally, we introduce an evolutionary algorithm based on FFEM, called evolutionary algorithm based on FFEM (FFEEA), for iteratively searching high-quality network construction schemes. In FFEEA, an adaptive crossover approach is used for efficient population search. Finally, extensive experiments are conducted to demonstrate that our proposed fuzzy fitness evaluation method and other improvement strategies significantly enhance satellite network service time. The study introduces a novel approach to enhance the efficiency of solving combinatorial optimization problems, such as CS-GSNSP, by mitigating the complexity associated with fitness evaluation.

Length generalization, the ability to solve problems of longer sequences than those observed during training, poses a core challenge of Transformer-based large language models (LLM). Although existing studies have predominantly focused on data-driven approaches for arithmetic operations and symbolic manipulation tasks, these approaches tend to be task-specific with limited overall performance. To pursue a more general solution, this paper focuses on a broader case of reasoning problems that are computable, i.e., problems that algorithms can solve, thus can be solved by the Turing Machine. From this perspective, this paper proposes Turing MAchine Imitation Learning (TAIL) to improve the length generalization ability of LLMs. TAIL synthesizes chain-of-thoughts (CoT) data that imitate the execution process of a Turing Machine by computer programs, which linearly expands the reasoning steps into atomic states to alleviate shortcut learning and explicit memory fetch mechanism to reduce the difficulties of dynamic and long-range data access in elementary operations. To validate the reliability and universality of TAIL, we construct a challenging synthetic dataset covering 8 classes of algorithms and 18 tasks. Without bells and whistles, TAIL significantly improves the length generalization ability as well as the performance of Qwen2.5-7B on various tasks using only synthetic data, surpassing previous methods and DeepSeek-R1. The experimental results reveal that the key concepts in the Turing Machine, instead of the thinking styles, are indispensable for TAIL for length generalization, through which the model exhibits read-and-write behaviors consistent with the properties of the Turing Machine in their attention layers. This work provides a promising direction for future research in the learning of LLM reasoning from synthetic data.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

Within the field of causal inference, we consider the problem of estimating heterogeneous treatment effects from data. We propose and validate a novel approach for learning feature representations to aid the estimation of the conditional average treatment effect or CATE. Our method focuses on an intermediate layer in a neural network trained to predict the outcome from the features. In contrast to previous approaches that encourage the distribution of representations to be treatment-invariant, we leverage a genetic algorithm that optimizes over representations useful for predicting the outcome to select those less useful for predicting the treatment. This allows us to retain information within the features useful for predicting outcome even if that information may be related to treatment assignment. We validate our method on synthetic examples and illustrate its use on a real life dataset.

Choosing automatically the right algorithm using problem descriptors is a classical component of combinatorial optimization. It is also a good tool for making evolutionary algorithms fast, robust and versatile. We present Shiwa, an algorithm good at both discrete and continuous, noisy and noise-free, sequential and parallel, black-box optimization. Our algorithm is experimentally compared to competitors on YABBOB, a BBOB comparable testbed, and on some variants of it, and then validated on several real world testbeds.

Vehicle Routing Problems (VRP) are an extension of the Traveling Salesperson Problem and are a fundamental NP-hard challenge in combinatorial optimization. Solving VRP in real-time at large scale has become critical in numerous applications, from growing markets like last-mile delivery to emerging use-cases like interactive logistics planning. Such applications involve solving similar problem instances repeatedly, yet current state-of-the-art solvers treat each instance on its own without leveraging previous examples. We introduce a novel optimization framework that uses a reinforcement learning agent - trained on prior instances - to quickly generate initial solutions, which are then further optimized by genetic algorithms. Our framework, Evolutionary Algorithm with Reinforcement Learning Initialization (EARLI), consistently outperforms current state-of-the-art solvers across various time scales. For example, EARLI handles vehicle routing with 500 locations within 1s, 10x faster than current solvers for the same solution quality, enabling applications like real-time and interactive routing. EARLI can generalize to new data, as demonstrated on real e-commerce delivery data of a previously unseen city. Our hybrid framework presents a new way to combine reinforcement learning and genetic algorithms, paving the road for closer interdisciplinary collaboration between AI and optimization communities towards real-time optimization in diverse domains.

Bayesian optimization is an approach to optimizing objective functions that take a long time (minutes or hours) to evaluate. It is best-suited for optimization over continuous domains of less than 20 dimensions, and tolerates stochastic noise in function evaluations. It builds a surrogate for the objective and quantifies the uncertainty in that surrogate using a Bayesian machine learning technique, Gaussian process regression, and then uses an acquisition function defined from this surrogate to decide where to sample. In this tutorial, we describe how Bayesian optimization works, including Gaussian process regression and three common acquisition functions: expected improvement, entropy search, and knowledge gradient. We then discuss more advanced techniques, including running multiple function evaluations in parallel, multi-fidelity and multi-information source optimization, expensive-to-evaluate constraints, random environmental conditions, multi-task Bayesian optimization, and the inclusion of derivative information. We conclude with a discussion of Bayesian optimization software and future research directions in the field. Within our tutorial material we provide a generalization of expected improvement to noisy evaluations, beyond the noise-free setting where it is more commonly applied. This generalization is justified by a formal decision-theoretic argument, standing in contrast to previous ad hoc modifications.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Learning heuristics for vehicle routing problems (VRPs) has gained much attention due to the less reliance on hand-crafted rules. However, existing methods are typically trained and tested on the same task with a fixed size and distribution (of nodes), and hence suffer from limited generalization performance. This paper studies a challenging yet realistic setting, which considers generalization across both size and distribution in VRPs. We propose a generic meta-learning framework, which enables effective training of an initialized model with the capability of fast adaptation to new tasks during inference. We further develop a simple yet efficient approximation method to reduce the training overhead. Extensive experiments on both synthetic and benchmark instances of the traveling salesman problem (TSP) and capacitated vehicle routing problem (CVRP) demonstrate the effectiveness of our method. The code is available at: https://github.com/RoyalSkye/Omni-VRP.

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources pair problems with solutions, but omit the intermediate thought process that guides coding. To close this gap, we present a scalable synthetic data generation pipeline that produces nearly 800k instruction-reasoning-code-test quadruplets. Each sample combines a task, a step-by-step reasoning trace, a working solution, and executable tests, enabling models to learn not just the what but also the how of problem solving. Our pipeline combines four key components: curated contest problems, web-mined content filtered by relevance classifiers, data expansion guided by reasoning patterns, and multi-stage execution-based validation. A genetic mutation algorithm further increases task diversity while maintaining consistency between reasoning traces and code implementations. Our key finding is that fine-tuning LLMs on this dataset yields consistent improvements on coding benchmarks. Beyond raw accuracy, reasoning-aware data can substitute for model scaling, generalize across architectures, and outperform leading open-source alternatives under identical sample budgets. Our work establishes reasoning-centered synthetic data generation as an efficient approach for advancing coding capabilities in LLMs. We publish our dataset and generation pipeline to facilitate further research.

Large language models (LLMs) like ChatGPT and GPT-4 have attracted great attention given their surprising performance on a wide range of NLP tasks. Length controlled generation of LLMs emerges as an important topic, which enables users to fully leverage the capability of LLMs in more real-world scenarios like generating a proper answer or essay of a desired length. In addition, the autoregressive generation in LLMs is extremely time-consuming, while the ability of controlling this generated length can reduce the inference cost by limiting the length. Therefore, we propose a prompt-based length control method to achieve high-accuracy length controlled generation. In particular, we adopt reinforcement learning with the reward signal given by either trainable or rule-based reward models, which further enhances the length-control ability of LLMs by rewarding outputs that follows pre-defined control instruction. To enable rule-based inference, we also introduce standard prompt extractor to collect the standard control information from users' input. Experiments show that our method significantly improves the accuracy of prompt-based length control for summarization task on popular datasets like CNNDM and NYT. Both the standard prompt extractor and the RL-tuned model have show strong generalization ability to unseen control prompt templates.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

Feature selection is one of the most challenging issues in machine learning, especially while working with high dimensional data. In this paper, we address the problem of feature selection and propose a new approach called Evolving Fast and Slow. This new approach is based on using two parallel genetic algorithms having high and low mutation rates, respectively. Evolving Fast and Slow requires a new parallel architecture combining an automatic system that evolves fast and an effortful system that evolves slow. With this architecture, exploration and exploitation can be done simultaneously and in unison. Evolving fast, with high mutation rate, can be useful to explore new unknown places in the search space with long jumps; and Evolving Slow, with low mutation rate, can be useful to exploit previously known places in the search space with short movements. Our experiments show that Evolving Fast and Slow achieves very good results in terms of both accuracy and feature elimination.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

The success of Deepseek-R1 has drawn the LLM community's attention to reinforcement learning (RL) methods like GRPO. However, such rule-based 0/1 outcome reward methods lack the capability to regulate the intermediate reasoning processes during chain-of-thought (CoT) generation, leading to severe overthinking phenomena. In response, recent studies have designed reward functions to reinforce models' behaviors in producing shorter yet correct completions. Nevertheless, we observe that these length-penalty reward functions exacerbate RL training instability: as the completion length decreases, model accuracy abruptly collapses, often occurring early in training. To address this issue, we propose a simple yet effective solution GRPO-lambda, an efficient and stabilized variant of GRPO, which dynamically adjusts the reward strategy by monitoring the correctness ratio among completions within each query-sampled group. A low correctness ratio indicates the need to avoid length penalty that compromises CoT quality, triggering a switch to length-agnostic 0/1 rewards that prioritize reasoning capability. A high ratio maintains length penalties to boost efficiency. Experimental results show that our approach avoids training instability caused by length penalty while maintaining the optimal accuracy-efficiency trade-off. On the GSM8K, GPQA, MATH-500, AMC 2023, and AIME 2024 benchmarks, it improves average accuracy by 1.48% while reducing CoT sequence length by 47.3%.

Scientists often infer abstract procedures from specific instances of problems and use the abstractions to generate new, related instances. For example, programs encoding the formal rules and properties of a system have been useful in fields ranging from RL (procedural environments) to physics (simulation engines). These programs can be seen as functions which execute to different outputs based on their parameterizations (e.g., gridworld configuration or initial physical conditions). We introduce the term EFA (Executable Functional Abstraction) to denote such programs for math problems. EFA-like constructs have been shown to be useful for math reasoning as problem generators for stress-testing models. However, prior work has been limited to abstractions for grade-school math (whose simple rules are easy to encode in programs), while generating EFAs for advanced math has thus far required human engineering. We explore the automatic construction of EFAs for advanced math problems. We operationalize the task of automatically constructing EFAs as a program synthesis task, and develop EFAGen, which conditions an LLM on a seed math problem and its step-by-step solution to generate candidate EFA programs that are faithful to the generalized problem and solution class underlying the seed problem. Furthermore, we formalize properties any valid EFA must possess in terms of executable unit tests, and show how the tests can be used as verifiable rewards to train LLMs to become better writers of EFAs. We demonstrate that EFAs constructed by EFAGen behave rationally by remaining faithful to seed problems, produce learnable problem variations, and that EFAGen can infer EFAs across multiple diverse sources of competition-level math problems. Finally, we show downstream uses of model-written EFAs e.g. finding problem variations that are harder or easier for a learner to solve, as well as data generation.

In this paper, we present a novel approach to accelerate the Bayesian inference process, focusing specifically on the nested sampling algorithms. Bayesian inference plays a crucial role in cosmological parameter estimation, providing a robust framework for extracting theoretical insights from observational data. However, its computational demands can be substantial, primarily due to the need for numerous likelihood function evaluations. Our proposed method utilizes the power of deep learning, employing feedforward neural networks to approximate the likelihood function dynamically during the Bayesian inference process. Unlike traditional approaches, our method trains neural networks on-the-fly using the current set of live points as training data, without the need for pre-training. This flexibility enables adaptation to various theoretical models and datasets. We perform simple hyperparameter optimization using genetic algorithms to suggest initial neural network architectures for learning each likelihood function. Once sufficient accuracy is achieved, the neural network replaces the original likelihood function. The implementation integrates with nested sampling algorithms and has been thoroughly evaluated using both simple cosmological dark energy models and diverse observational datasets. Additionally, we explore the potential of genetic algorithms for generating initial live points within nested sampling inference, opening up new avenues for enhancing the efficiency and effectiveness of Bayesian inference methods.

Interpretability of Deep Learning (DL) is a barrier to trustworthy AI. Despite great efforts made by the Explainable AI (XAI) community, explanations lack robustness -- indistinguishable input perturbations may lead to different XAI results. Thus, it is vital to assess how robust DL interpretability is, given an XAI method. In this paper, we identify several challenges that the state-of-the-art is unable to cope with collectively: i) existing metrics are not comprehensive; ii) XAI techniques are highly heterogeneous; iii) misinterpretations are normally rare events. To tackle these challenges, we introduce two black-box evaluation methods, concerning the worst-case interpretation discrepancy and a probabilistic notion of how robust in general, respectively. Genetic Algorithm (GA) with bespoke fitness function is used to solve constrained optimisation for efficient worst-case evaluation. Subset Simulation (SS), dedicated to estimate rare event probabilities, is used for evaluating overall robustness. Experiments show that the accuracy, sensitivity, and efficiency of our methods outperform the state-of-the-arts. Finally, we demonstrate two applications of our methods: ranking robust XAI methods and selecting training schemes to improve both classification and interpretation robustness.

We study the problem of constrained efficient global optimization, where both the objective and constraints are expensive black-box functions that can be learned with Gaussian processes. We propose CONFIG (CONstrained efFIcient Global Optimization), a simple and effective algorithm to solve it. Under certain regularity assumptions, we show that our algorithm enjoys the same cumulative regret bound as that in the unconstrained case and similar cumulative constraint violation upper bounds. For commonly used Matern and Squared Exponential kernels, our bounds are sublinear and allow us to derive a convergence rate to the optimal solution of the original constrained problem. In addition, our method naturally provides a scheme to declare infeasibility when the original black-box optimization problem is infeasible. Numerical experiments on sampled instances from the Gaussian process, artificial numerical problems, and a black-box building controller tuning problem all demonstrate the competitive performance of our algorithm. Compared to the other state-of-the-art methods, our algorithm significantly improves the theoretical guarantees, while achieving competitive empirical performance.

The core challenge of high-dimensional and expensive black-box optimization (BBO) is how to obtain better performance faster with little function evaluation cost. The essence of the problem is how to design an efficient optimization strategy tailored to the target task. This paper designs a powerful optimization framework to automatically learn the optimization strategies from the target or cheap surrogate task without human intervention. However, current methods are weak for this due to poor representation of optimization strategy. To achieve this, 1) drawing on the mechanism of genetic algorithm, we propose a deep neural network framework called B2Opt, which has a stronger representation of optimization strategies based on survival of the fittest; 2) B2Opt can utilize the cheap surrogate functions of the target task to guide the design of the efficient optimization strategies. Compared to the state-of-the-art BBO baselines, B2Opt can achieve multiple orders of magnitude performance improvement with less function evaluation cost. We validate our proposal on high-dimensional synthetic functions and two real-world applications. We also find that deep B2Opt performs better than shallow ones.

Since the release of Deepseek-R1, reinforcement learning with verifiable rewards (RLVR) has become a central approach for training large language models (LLMs) on reasoning tasks. Recent work has largely focused on modifying loss functions to make RLVR more efficient and effective. In this paper, motivated by studies of overthinking in LLMs, we propose Length-aware Sampling for Policy Optimization (LSPO), a novel meta-RLVR algorithm that dynamically selects training data at each step based on the average response length. We evaluate LSPO across multiple base models and datasets, demonstrating that it consistently improves learning effectiveness. In addition, we conduct a detailed ablation study to examine alternative ways of incorporating length signals into dynamic sampling, offering further insights and highlighting promising directions for future research.

Heuristics are widely used for dealing with complex search and optimization problems. However, manual design of heuristics can be often very labour extensive and requires rich working experience and knowledge. This paper proposes Evolution of Heuristic (EoH), a novel evolutionary paradigm that leverages both Large Language Models (LLMs) and Evolutionary Computation (EC) methods for Automatic Heuristic Design (AHD). EoH represents the ideas of heuristics in natural language, termed thoughts. They are then translated into executable codes by LLMs. The evolution of both thoughts and codes in an evolutionary search framework makes it very effective and efficient for generating high-performance heuristics. Experiments on three widely studied combinatorial optimization benchmark problems demonstrate that EoH outperforms commonly used handcrafted heuristics and other recent AHD methods including FunSearch. Particularly, the heuristic produced by EoH with a low computational budget (in terms of the number of queries to LLMs) significantly outperforms widely-used human hand-crafted baseline algorithms for the online bin packing problem.

The performance of an algorithm often critically depends on its parameter configuration. While a variety of automated algorithm configuration methods have been proposed to relieve users from the tedious and error-prone task of manually tuning parameters, there is still a lot of untapped potential as the learned configuration is static, i.e., parameter settings remain fixed throughout the run. However, it has been shown that some algorithm parameters are best adjusted dynamically during execution, e.g., to adapt to the current part of the optimization landscape. Thus far, this is most commonly achieved through hand-crafted heuristics. A promising recent alternative is to automatically learn such dynamic parameter adaptation policies from data. In this article, we give the first comprehensive account of this new field of automated dynamic algorithm configuration (DAC), present a series of recent advances, and provide a solid foundation for future research in this field. Specifically, we (i) situate DAC in the broader historical context of AI research; (ii) formalize DAC as a computational problem; (iii) identify the methods used in prior-art to tackle this problem; (iv) conduct empirical case studies for using DAC in evolutionary optimization, AI planning, and machine learning.

The instruction-following ability of large language models enables humans to interact with AI agents in a natural way. However, when required to generate responses of a specific length, large language models often struggle to meet users' needs due to their inherent difficulty in accurately perceiving numerical constraints. To explore the ability of large language models to control the length of generated responses, we propose the Target Length Generation Task (TLG) and design two metrics, Precise Match (PM) and Flexible Match (FM) to evaluate the model's performance in adhering to specified response lengths. Furthermore, we introduce a novel, model-agnostic approach called Ruler, which employs Meta Length Tokens (MLTs) to enhance the instruction-following ability of large language models under length-constrained instructions. Specifically, Ruler equips LLMs with the ability to generate responses of a specified length based on length constraints within the instructions. Moreover, Ruler can automatically generate appropriate MLT when length constraints are not explicitly provided, demonstrating excellent versatility and generalization. Comprehensive experiments show the effectiveness of Ruler across different LLMs on Target Length Generation Task, e.g., at All Level 27.97 average gain on PM, 29.57 average gain on FM. In addition, we conduct extensive ablation experiments to further substantiate the efficacy and generalization of Ruler. Our code and data is available at https://github.com/Geaming2002/Ruler.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

In this work, we consider and analyze the sample complexity of model-free reinforcement learning with a generative model. Particularly, we analyze mirror descent value iteration (MDVI) by Geist et al. (2019) and Vieillard et al. (2020a), which uses the Kullback-Leibler divergence and entropy regularization in its value and policy updates. Our analysis shows that it is nearly minimax-optimal for finding an varepsilon-optimal policy when varepsilon is sufficiently small. This is the first theoretical result that demonstrates that a simple model-free algorithm without variance-reduction can be nearly minimax-optimal under the considered setting.

Compression is at the heart of intelligence. A theoretically optimal way to compress any sequence of data is to find the shortest program that outputs that sequence and then halts. However, such 'Kolmogorov compression' is uncomputable, and code generating LLMs struggle to approximate this theoretical ideal, as it requires reasoning, planning and search capabilities beyond those of current models. In this work, we introduce the KoLMogorov-Test (KT), a compression-as-intelligence test for code generating LLMs. In KT a model is presented with a sequence of data at inference time, and asked to generate the shortest program that produces the sequence. We identify several benefits of KT for both evaluation and training: an essentially infinite number of problem instances of varying difficulty is readily available, strong baselines already exist, the evaluation metric (compression) cannot be gamed, and pretraining data contamination is highly unlikely. To evaluate current models, we use audio, text, and DNA data, as well as sequences produced by random synthetic programs. Current flagship models perform poorly - both GPT4-o and Llama-3.1-405B struggle on our natural and synthetic sequences. On our synthetic distribution, we are able to train code generation models with lower compression rates than previous approaches. Moreover, we show that gains on synthetic data generalize poorly to real data, suggesting that new innovations are necessary for additional gains on KT.

Large reasoning models (LRMs) achieve higher performance on challenging reasoning tasks by generating more tokens at inference time, but this verbosity often wastes computation on easy problems. Existing solutions, including supervised finetuning on shorter traces, user-controlled budgets, or RL with uniform penalties, either require data curation, manual configuration, or treat all problems alike regardless of difficulty. We introduce Adaptive Length Penalty (ALP), a reinforcement learning objective tailoring generation length to per-prompt solve rate. During training, ALP monitors each prompt's online solve rate through multiple rollouts and adds a differentiable penalty whose magnitude scales inversely with that rate, so confident (easy) prompts incur a high cost for extra tokens while hard prompts remain unhindered. Posttraining DeepScaleR-1.5B with ALP cuts average token usage by 50\% without significantly dropping performance. Relative to fixed-budget and uniform penalty baselines, ALP redistributes its reduced budget more intelligently by cutting compute on easy prompts and reallocating saved tokens to difficult ones, delivering higher accuracy on the hardest problems with higher cost.

AlphaEvolve is a generic evolutionary coding agent that combines the generative capabilities of LLMs with automated evaluation in an iterative evolutionary framework that proposes, tests, and refines algorithmic solutions to challenging scientific and practical problems. In this paper we showcase AlphaEvolve as a tool for autonomously discovering novel mathematical constructions and advancing our understanding of long-standing open problems. To demonstrate its breadth, we considered a list of 67 problems spanning mathematical analysis, combinatorics, geometry, and number theory. The system rediscovered the best known solutions in most of the cases and discovered improved solutions in several. In some instances, AlphaEvolve is also able to generalize results for a finite number of input values into a formula valid for all input values. Furthermore, we are able to combine this methodology with Deep Think and AlphaProof in a broader framework where the additional proof-assistants and reasoning systems provide automated proof generation and further mathematical insights. These results demonstrate that large language model-guided evolutionary search can autonomously discover mathematical constructions that complement human intuition, at times matching or even improving the best known results, highlighting the potential for significant new ways of interaction between mathematicians and AI systems. We present AlphaEvolve as a powerful new tool for mathematical discovery, capable of exploring vast search spaces to solve complex optimization problems at scale, often with significantly reduced requirements on preparation and computation time.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

In online algorithm selection (OAS), instances of an algorithmic problem class are presented to an agent one after another, and the agent has to quickly select a presumably best algorithm from a fixed set of candidate algorithms. For decision problems such as satisfiability (SAT), quality typically refers to the algorithm's runtime. As the latter is known to exhibit a heavy-tail distribution, an algorithm is normally stopped when exceeding a predefined upper time limit. As a consequence, machine learning methods used to optimize an algorithm selection strategy in a data-driven manner need to deal with right-censored samples, a problem that has received little attention in the literature so far. In this work, we revisit multi-armed bandit algorithms for OAS and discuss their capability of dealing with the problem. Moreover, we adapt them towards runtime-oriented losses, allowing for partially censored data while keeping a space- and time-complexity independent of the time horizon. In an extensive experimental evaluation on an adapted version of the ASlib benchmark, we demonstrate that theoretically well-founded methods based on Thompson sampling perform specifically strong and improve in comparison to existing methods.

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training data that includes sequential changes and modifications, they can approximate likely changes that humans would make. To highlight the breadth of implications of such evolution through large models (ELM), in the main experiment ELM combined with MAP-Elites generates hundreds of thousands of functional examples of Python programs that output working ambulating robots in the Sodarace domain, which the original LLM had never seen in pre-training. These examples then help to bootstrap training a new conditional language model that can output the right walker for a particular terrain. The ability to bootstrap new models that can output appropriate artifacts for a given context in a domain where zero training data was previously available carries implications for open-endedness, deep learning, and reinforcement learning. These implications are explored here in depth in the hope of inspiring new directions of research now opened up by ELM.

Computing a Gaussian process (GP) posterior has a computational cost cubical in the number of historical points. A reformulation of the same GP posterior highlights that this complexity mainly depends on how many unique historical points are considered. This can have important implication in active learning settings, where the set of historical points is constructed sequentially by the learner. We show that sequential black-box optimization based on GPs (GP-Opt) can be made efficient by sticking to a candidate solution for multiple evaluation steps and switch only when necessary. Limiting the number of switches also limits the number of unique points in the history of the GP. Thus, the efficient GP reformulation can be used to exactly and cheaply compute the posteriors required to run the GP-Opt algorithms. This approach is especially useful in real-world applications of GP-Opt with high switch costs (e.g. switching chemicals in wet labs, data/model loading in hyperparameter optimization). As examples of this meta-approach, we modify two well-established GP-Opt algorithms, GP-UCB and GP-EI, to switch candidates as infrequently as possible adapting rules from batched GP-Opt. These versions preserve all the theoretical no-regret guarantees while improving practical aspects of the algorithms such as runtime, memory complexity, and the ability of batching candidates and evaluating them in parallel.

To address the challenges of limited Battery Swap Stations datasets, high operational costs, and fluctuating user charging demand, this research proposes a probability estimation model based on charging pile data and constructs nine scenario-specific battery swap demand datasets. In addition, this study combines Least Recently Used strategy with Genetic Algorithm and incorporates a guided search mechanism, which effectively enhances the global optimization capability. Thus, a dual-factor decision-making based charging schedule optimization system is constructed. Experimental results show that the constructed datasets exhibit stable trend characteristics, adhering to 24-hour and 168-hour periodicity patterns, with outlier ratios consistently below 3.26%, confirming data validity. Compared to baseline, the improved algorithm achieves better fitness individuals in 80% of test regions under the same iterations. When benchmarked against immediate swap-and-charge strategy, our algorithm achieves a peak cost reduction of 13.96%. Moreover, peak user satisfaction reaches 98.57%, while the average iteration time remains below 0.6 seconds, demonstrating good computational efficiency. The complete datasets and optimization algorithm are open-sourced at https://github.com/qingshufan/GA-EVLRU.

Solving NP-hard problems traditionally relies on heuristics, yet manually designing effective heuristics for complex problems remains a significant challenge. While recent advancements like FunSearch have shown that large language models (LLMs) can be integrated into evolutionary algorithms (EAs) for heuristic design, their potential is hindered by limitations in balancing exploitation and exploration. We introduce Quality-Uncertainty Balanced Evolution (QUBE), a novel approach that enhances LLM+EA methods by redefining the priority criterion within the FunSearch framework. QUBE employs the Quality-Uncertainty Trade-off Criterion (QUTC), based on our proposed Uncertainty-Inclusive Quality metric, to evaluate and guide the evolutionary process. Through extensive experiments on challenging NP-complete problems, QUBE demonstrates significant performance improvements over FunSearch and baseline methods. Our code are available at https://github.com/zzjchen/QUBE\_code.

Recent work on enhancing the reasoning abilities of large language models (LLMs) has introduced explicit length control as a means of constraining computational cost while preserving accuracy. However, existing approaches rely on fixed-length training budgets, which do not take advantage of the natural progression from exploration to compression during learning. In this work, we propose a curriculum learning strategy for length-controlled reasoning using Group Relative Policy Optimization (GRPO). Our method starts with generous token budgets and gradually tightens them over training, encouraging models to first discover effective solution strategies and then distill them into more concise reasoning traces. We augment GRPO with a reward function that balances three signals: task correctness (via verifier feedback), length efficiency, and formatting adherence (via structural tags). Experiments on GSM8K, MATH500, SVAMP, College Math, and GSM+ demonstrate that curriculum-based training consistently outperforms fixed-budget baselines at the same final budget, achieving higher accuracy and significantly improved token efficiency. We further ablate the impact of reward weighting and decay schedule design, showing that progressive constraint serves as a powerful inductive bias for training efficient reasoning models. Our code and checkpoints are released at: https://github.com/hammoudhasan/curriculum_grpo.

We present a novel application of evolutionary algorithms to automate the creation of powerful foundation models. While model merging has emerged as a promising approach for LLM development due to its cost-effectiveness, it currently relies on human intuition and domain knowledge, limiting its potential. Here, we propose an evolutionary approach that overcomes this limitation by automatically discovering effective combinations of diverse open-source models, harnessing their collective intelligence without requiring extensive additional training data or compute. Our approach operates in both parameter space and data flow space, allowing for optimization beyond just the weights of the individual models. This approach even facilitates cross-domain merging, generating models like a Japanese LLM with Math reasoning capabilities. Surprisingly, our Japanese Math LLM achieved state-of-the-art performance on a variety of established Japanese LLM benchmarks, even surpassing models with significantly more parameters, despite not being explicitly trained for such tasks. Furthermore, a culturally-aware Japanese VLM generated through our approach demonstrates its effectiveness in describing Japanese culture-specific content, outperforming previous Japanese VLMs. This work not only contributes new state-of-the-art models back to the open-source community, but also introduces a new paradigm for automated model composition, paving the way for exploring alternative, efficient approaches to foundation model development.

We propose a novel approach to scaling LLM inference for code generation. We frame code generation as a black box optimization problem within the code space, and employ optimization-inspired techniques to enhance exploration. Specifically, we introduce Scattered Forest Search to enhance solution diversity while searching for solutions. Our theoretical analysis illustrates how these methods avoid local optima during optimization. Extensive experiments on HumanEval, MBPP, APPS, CodeContests, and Leetcode reveal significant performance improvements. For instance, our method achieves a pass@1 rate of 67.1% on HumanEval+ and 87.2% on HumanEval with GPT-3.5, marking improvements of 8.6% and 4.3% over the state-of-the-art, while also halving the iterations needed to find the correct solution. Furthermore, our method scales more efficiently than existing search techniques, including tree search, line search, and repeated sampling.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Population-based search has recently emerged as a possible alternative to Reinforcement Learning (RL) for black-box neural architecture search (NAS). It performs well in practice even though it is not theoretically well understood. In particular, whereas traditional population-based search methods such as evolutionary algorithms (EAs) draw much power from crossover operations, it is difficult to take advantage of them in NAS. The main obstacle is believed to be the permutation problem: The mapping between genotype and phenotype in traditional graph representations is many-to-one, leading to a disruptive effect of standard crossover. This paper presents the first theoretical analysis of the behaviors of mutation, crossover and RL in black-box NAS, and proposes a new crossover operator based on the shortest edit path (SEP) in graph space. The SEP crossover is shown theoretically to overcome the permutation problem, and as a result, have a better expected improvement compared to mutation, standard crossover and RL. Further, it empirically outperform these other methods on state-of-the-art NAS benchmarks. The SEP crossover therefore allows taking full advantage of population-based search in NAS, and the underlying theory can serve as a foundation for deeper understanding of black-box NAS methods in general.

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier---AmoebaNet-A---that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-the-art 83.9% / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.

Large language models have transformed natural language processing, yet supervised fine-tuning (SFT) remains computationally intensive. This paper formally proves that capabilities acquired through SFT can be approximated by a base transformer model using inference-time techniques, specifically in-context learning (ICL), without altering model parameters, under idealized assumptions including unbounded computational resources and access to the fine-tuning dataset. We extend these results to practical scenarios with finite context lengths and partial dataset access. For text generation tasks with fixed output length l, datasets of size Oleft( m V{varepsilon^2} log m{delta} right) or, with bounded context, Oleft( l log V{varepsilon^2} log 1{delta} right) suffice to approximate fine-tuned behavior across m contexts within error varepsilon, where V is the vocabulary size and delta is the failure probability. For linear classification, datasets of size Oleft( d{varepsilon} right) or, with fixed context, Oleft( 1{varepsilon^2} log 1{delta} right) are sufficient, where d is the input dimension. Grounded in the Turing completeness of transformers, these results provide a theoretical foundation for resource-efficient deployment of large language models, with practical techniques like retrieval-augmented generation bridging theory to real-world applications.

Solving a linear system Ax=b is a fundamental scientific computing primitive for which numerous solvers and preconditioners have been developed. These come with parameters whose optimal values depend on the system being solved and are often impossible or too expensive to identify; thus in practice sub-optimal heuristics are used. We consider the common setting in which many related linear systems need to be solved, e.g. during a single numerical simulation. In this scenario, can we sequentially choose parameters that attain a near-optimal overall number of iterations, without extra matrix computations? We answer in the affirmative for Successive Over-Relaxation (SOR), a standard solver whose parameter omega has a strong impact on its runtime. For this method, we prove that a bandit online learning algorithm--using only the number of iterations as feedback--can select parameters for a sequence of instances such that the overall cost approaches that of the best fixed omega as the sequence length increases. Furthermore, when given additional structural information, we show that a contextual bandit method asymptotically achieves the performance of the instance-optimal policy, which selects the best omega for each instance. Our work provides the first learning-theoretic treatment of high-precision linear system solvers and the first end-to-end guarantees for data-driven scientific computing, demonstrating theoretically the potential to speed up numerical methods using well-understood learning algorithms.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

This study proposes a hybrid deep-learning-metaheuristic framework with a bi-level architecture for road network design problems (NDPs). We train a graph neural network (GNN) to approximate the solution of the user equilibrium (UE) traffic assignment problem and use inferences made by the trained model to calculate fitness function evaluations of a genetic algorithm (GA) to approximate solutions for NDPs. Using three test networks, two NDP variants and an exact solver as benchmark, we show that on average, our proposed framework can provide solutions within 1.5% gap of the best results in less than 0.5% of the time used by the exact solution procedure. Our framework can be utilized within an expert system for infrastructure planning to determine the best infrastructure planning and management decisions under different scenarios. Given the flexibility of the framework, it can easily be adapted to many other decision problems that can be modeled as bi-level problems on graphs. Moreover, we foreseen interesting future research directions, thus we also put forward a brief research agenda for this topic. The key observation from our research that can shape future research is that the fitness function evaluation time using the inferences made by the GNN model was in the order of milliseconds, which points to an opportunity and a need for novel heuristics that 1) can cope well with noisy fitness function values provided by deep learning models, and 2) can use the significantly enlarged efficiency of the evaluation step to explore the search space effectively (rather than efficiently). This opens a new avenue for a modern class of metaheuristics that are crafted for use with AI-powered predictors.

Effective training of today's large language models (LLMs) depends on large batches and long sequences for throughput and accuracy. To handle variable-length sequences on hardware accelerators, it is common practice to introduce padding tokens, so that all sequences in a batch have the same length. We show in this paper that the variation in sequence lengths in common NLP datasets is such that up to 50% of all tokens can be padding. In less common, but not extreme, cases (e.g. GLUE-cola with sequence length 128), the ratio is up to 89%. Existing methods to address the resulting inefficiency are complicated by the need to avoid cross-contamination in self-attention, by a reduction in accuracy when sequence ordering information is lost, or by customized kernel implementations only valid for specific accelerators. This paper introduces a new formalization of sequence packing in the context of the well-studied bin packing problem, and presents new algorithms based on this formulation which, for example, confer a 2x speedup for phase 2 pre-training in BERT. We show how existing models can be adapted to ensure mathematical equivalence between the original and packed models, meaning that packed models can be trained with existing pre-training and fine-tuning practices.

Large Language Models have achieved remarkable success in natural language processing tasks, with Reinforcement Learning playing a key role in adapting them to specific applications. However, obtaining ground truth answers for training LLMs in mathematical problem-solving is often challenging, costly, and sometimes unfeasible. This research delves into the utilization of format and length as surrogate signals to train LLMs for mathematical problem-solving, bypassing the need for traditional ground truth answers.Our study shows that a reward function centered on format correctness alone can yield performance improvements comparable to the standard GRPO algorithm in early phases. Recognizing the limitations of format-only rewards in the later phases, we incorporate length-based rewards. The resulting GRPO approach, leveraging format-length surrogate signals, not only matches but surpasses the performance of the standard GRPO algorithm relying on ground truth answers in certain scenarios, achieving 40.0\% accuracy on AIME2024 with a 7B base model. Through systematic exploration and experimentation, this research not only offers a practical solution for training LLMs to solve mathematical problems and reducing the dependence on extensive ground truth data collection, but also reveals the essence of why our label-free approach succeeds: base model is like an excellent student who has already mastered mathematical and logical reasoning skills, but performs poorly on the test paper, it simply needs to develop good answering habits to achieve outstanding results in exams , in other words, to unlock the capabilities it already possesses.

Diffusion models are emerging expressive generative models, in which a large number of time steps (inference steps) are required for a single image generation. To accelerate such tedious process, reducing steps uniformly is considered as an undisputed principle of diffusion models. We consider that such a uniform assumption is not the optimal solution in practice; i.e., we can find different optimal time steps for different models. Therefore, we propose to search the optimal time steps sequence and compressed model architecture in a unified framework to achieve effective image generation for diffusion models without any further training. Specifically, we first design a unified search space that consists of all possible time steps and various architectures. Then, a two stage evolutionary algorithm is introduced to find the optimal solution in the designed search space. To further accelerate the search process, we employ FID score between generated and real samples to estimate the performance of the sampled examples. As a result, the proposed method is (i).training-free, obtaining the optimal time steps and model architecture without any training process; (ii). orthogonal to most advanced diffusion samplers and can be integrated to gain better sample quality. (iii). generalized, where the searched time steps and architectures can be directly applied on different diffusion models with the same guidance scale. Experimental results show that our method achieves excellent performance by using only a few time steps, e.g. 17.86 FID score on ImageNet 64 times 64 with only four steps, compared to 138.66 with DDIM. The code is available at https://github.com/lilijiangg/AutoDiffusion.

We address the challenge of exploration in reinforcement learning (RL) when the agent operates in an unknown environment with sparse or no rewards. In this work, we study the maximum entropy exploration problem of two different types. The first type is visitation entropy maximization previously considered by Hazan et al.(2019) in the discounted setting. For this type of exploration, we propose a game-theoretic algorithm that has mathcal{O}(H^3S^2A/varepsilon^2) sample complexity thus improving the varepsilon-dependence upon existing results, where S is a number of states, A is a number of actions, H is an episode length, and varepsilon is a desired accuracy. The second type of entropy we study is the trajectory entropy. This objective function is closely related to the entropy-regularized MDPs, and we propose a simple algorithm that has a sample complexity of order mathcal{O}(poly(S,A,H)/varepsilon). Interestingly, it is the first theoretical result in RL literature that establishes the potential statistical advantage of regularized MDPs for exploration. Finally, we apply developed regularization techniques to reduce sample complexity of visitation entropy maximization to mathcal{O}(H^2SA/varepsilon^2), yielding a statistical separation between maximum entropy exploration and reward-free exploration.

Several recent advances in AI systems (e.g., Tree-of-Thoughts and Program-Aided Language Models) solve problems by providing a "scaffolding" program that structures multiple calls to language models to generate better outputs. A scaffolding program is written in a programming language such as Python. In this work, we use a language-model-infused scaffolding program to improve itself. We start with a seed "improver" that improves an input program according to a given utility function by querying a language model several times and returning the best solution. We then run this seed improver to improve itself. Across a small set of downstream tasks, the resulting improved improver generates programs with significantly better performance than its seed improver. Afterward, we analyze the variety of self-improvement strategies proposed by the language model, including beam search, genetic algorithms, and simulated annealing. Since the language models themselves are not altered, this is not full recursive self-improvement. Nonetheless, it demonstrates that a modern language model, GPT-4 in our proof-of-concept experiments, is capable of writing code that can call itself to improve itself. We critically consider concerns around the development of self-improving technologies and evaluate the frequency with which the generated code bypasses a sandbox.

This project proposes and compares a new way to optimise Super Mario Bros. (SMB) environment where the control is in hand of two approaches, namely, Genetic Algorithm (MarioGA) and NeuroEvolution (MarioNE). Not only we learn playing SMB using these techniques, but also optimise it with constrains of collection of coins and finishing levels. Firstly, we formalise the SMB agent to maximize the total value of collected coins (reward) and maximising the total distance traveled (reward) in order to finish the level faster (time penalty) for both the algorithms. Secondly, we study MarioGA and its evaluation function (fitness criteria) including its representation methods, crossover used, mutation operator formalism, selection method used, MarioGA loop, and few other parameters. Thirdly, MarioNE is applied on SMB where a population of ANNs with random weights is generated, and these networks control Marios actions in the game. Fourth, SMB is further constrained to complete the task within the specified time, rebirths (deaths) within the limit, and performs actions or moves within the maximum allowed moves, while seeking to maximize the total coin value collected. This ensures an efficient way of finishing SMB levels. Finally, we provide a fivefold comparative analysis by plotting fitness plots, ability to finish different levels of world 1, and domain adaptation (transfer learning) of the trained models.

The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: https://github.com/kirjner/GGS

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

This work proposes a simple yet effective sampling framework for combinatorial optimization (CO). Our method builds on discrete Langevin dynamics (LD), an efficient gradient-guided generative paradigm. However, we observe that directly applying LD often leads to limited exploration. To overcome this limitation, we propose the Regularized Langevin Dynamics (RLD), which enforces an expected distance between the sampled and current solutions, effectively avoiding local minima. We develop two CO solvers on top of RLD, one based on simulated annealing (SA), and the other one based on neural network (NN). Empirical results on three classic CO problems demonstrate that both of our methods can achieve comparable or better performance against the previous state-of-the-art (SOTA) SA- and NN-based solvers. In particular, our SA algorithm reduces the runtime of the previous SOTA SA method by up to 80\%, while achieving equal or superior performance. In summary, RLD offers a promising framework for enhancing both traditional heuristics and NN models to solve CO problems. Our code is available at https://github.com/Shengyu-Feng/RLD4CO.

The performance of Convolutional Neural Networks (CNNs) highly relies on their architectures. In order to design a CNN with promising performance, extended expertise in both CNNs and the investigated problem is required, which is not necessarily held by every user interested in CNNs or the problem domain. In this paper, we propose to automatically evolve CNN architectures by using a genetic algorithm based on ResNet blocks and DenseNet blocks. The proposed algorithm is completely automatic in designing CNN architectures, particularly, neither pre-processing before it starts nor post-processing on the designed CNN is needed. Furthermore, the proposed algorithm does not require users with domain knowledge on CNNs, the investigated problem or even genetic algorithms. The proposed algorithm is evaluated on CIFAR10 and CIFAR100 against 18 state-of-the-art peer competitors. Experimental results show that it outperforms state-of-the-art CNNs hand-crafted and CNNs designed by automatic peer competitors in terms of the classification accuracy, and achieves the competitive classification accuracy against semi-automatic peer competitors. In addition, the proposed algorithm consumes much less time than most peer competitors in finding the best CNN architectures.

We propose a new uncertainty estimator for gradient-free optimisation of black-box simulators using deep generative surrogate models. Optimisation of these simulators is especially challenging for stochastic simulators and higher dimensions. To address these issues, we utilise a deep generative surrogate approach to model the black box response for the entire parameter space. We then leverage this knowledge to estimate the proposed uncertainty based on the Wasserstein distance - the Wasserstein uncertainty. This approach is employed in a posterior agnostic gradient-free optimisation algorithm that minimises regret over the entire parameter space. A series of tests were conducted to demonstrate that our method is more robust to the shape of both the black box function and the stochastic response of the black box than state-of-the-art methods, such as efficient global optimisation with a deep Gaussian process surrogate.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

Despite the remarkable capabilities, Large Language Models (LLMs) face deployment challenges due to their extensive size. Pruning methods drop a subset of weights to accelerate, but many of them require retraining, which is prohibitively expensive and computationally demanding. Recently, post-training pruning approaches introduced novel metrics, enabling the pruning of LLMs without retraining. However, these metrics require the involvement of human experts and tedious trial and error. To efficiently identify superior pruning metrics, we develop an automatic framework for searching symbolic pruning metrics using genetic programming. In particular, we devise an elaborate search space encompassing the existing pruning metrics to discover the potential symbolic pruning metric. We propose an opposing operation simplification strategy to increase the diversity of the population. In this way, Pruner-Zero allows auto-generation of symbolic pruning metrics. Based on the searched results, we explore the correlation between pruning metrics and performance after pruning and summarize some principles. Extensive experiments on LLaMA and LLaMA-2 on language modeling and zero-shot tasks demonstrate that our Pruner-Zero obtains superior performance than SOTA post-training pruning methods. Code at: https://github.com/pprp/Pruner-Zero.

Multiobjective combinatorial optimization (MOCO) problems can be found in many real-world applications. However, exactly solving these problems would be very challenging, particularly when they are NP-hard. Many handcrafted heuristic methods have been proposed to tackle different MOCO problems over the past decades. In this work, we generalize the idea of neural combinatorial optimization, and develop a learning-based approach to approximate the whole Pareto set for a given MOCO problem without further search procedure. We propose a single preference-conditioned model to directly generate approximate Pareto solutions for any trade-off preference, and design an efficient multiobjective reinforcement learning algorithm to train this model. Our proposed method can be treated as a learning-based extension for the widely-used decomposition-based multiobjective evolutionary algorithm (MOEA/D). It uses a single model to accommodate all the possible preferences, whereas other methods use a finite number of solutions to approximate the Pareto set. Experimental results show that our proposed method significantly outperforms some other methods on the multiobjective traveling salesman problem, multiobjective vehicle routing problem, and multiobjective knapsack problem in terms of solution quality, speed, and model efficiency.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

As a sub-discipline of evolutionary and computational linguistics, emergent communication (EC) studies communication protocols, called emergent languages, arising in simulations where agents communicate. A key goal of EC is to give rise to languages that share statistical properties with natural languages. In this paper, we reinterpret Lewis's signaling game, a frequently used setting in EC, as beta-VAE and reformulate its objective function as ELBO. Consequently, we clarify the existence of prior distributions of emergent languages and show that the choice of the priors can influence their statistical properties. Specifically, we address the properties of word lengths and segmentation, known as Zipf's law of abbreviation (ZLA) and Harris's articulation scheme (HAS), respectively. It has been reported that the emergent languages do not follow them when using the conventional objective. We experimentally demonstrate that by selecting an appropriate prior distribution, more natural segments emerge, while suggesting that the conventional one prevents the languages from following ZLA and HAS.

Active learning (AL) algorithms may achieve better performance with fewer data because the model guides the data selection process. While many algorithms have been proposed, there is little study on what the optimal AL algorithm looks like, which would help researchers understand where their models fall short and iterate on the design. In this paper, we present a simulated annealing algorithm to search for this optimal oracle and analyze it for several tasks. We present qualitative and quantitative insights into the behaviors of this oracle, comparing and contrasting them with those of various heuristics. Moreover, we are able to consistently improve the heuristics using one particular insight. We hope that our findings can better inform future active learning research. The code is available at https://github.com/YilunZhou/optimal-active-learning.

Recent large reasoning models (LRMs) driven by reinforcement learning algorithms (e.g., GRPO) have achieved remarkable performance on challenging reasoning tasks. However, these models suffer from overthinking, generating unnecessarily long and redundant reasoning even for simple questions, which substantially increases computational cost and response latency. While existing methods incorporate length rewards to GRPO to promote concise reasoning, they incur significant performance degradation. We identify the root cause: when rewards for correct but long rollouts are penalized, GRPO's group-relative advantage function can assign them negative advantages, actively discouraging valid reasoning. To overcome this, we propose Decoupled Reward Policy Optimization (DRPO), a novel framework that decouples the length-based learning signal of correct rollouts from incorrect ones. DRPO ensures that reward signals for correct rollouts are normalized solely within the positive group, shielding them from interference by negative samples. The DRPO's objective is grounded in integrating an optimized positive data distribution, which maximizes length-based rewards under a KL regularization, into a discriminative objective. We derive a closed-form solution for this distribution, enabling efficient computation of the objective and its gradients using only on-policy data and importance weighting. Of independent interest, this formulation is general and can incorporate other preference rewards of positive data beyond length. Experiments on mathematical reasoning tasks demonstrate DRPO's significant superiority over six efficient reasoning baselines. Notably, with a 1.5B model, our method achieves 77\% length reduction with only 1.1\% performance loss on simple questions like GSM8k dataset, while the follow-up baseline sacrifices 4.3\% for 68\% length reduction.

Large language models (LLMs) have demonstrated impressive performance on reasoning tasks, including mathematical reasoning. However, the current evaluation mostly focuses on carefully constructed benchmarks and neglects the consideration of real-world reasoning problems that present missing or contradictory conditions, known as ill-defined problems. To further study this problem, we develop a largescale benchmark called Problems with Missing and Contradictory conditions ( PMC) containing over 5,000 validated ill-defined mathematical problems. Our preliminary experiments through PMC reveal two challenges about existing methods: (1) traditional methods exhibit a trade-off between solving accuracy and rejection capabilities, and (2) formal methods struggle with modeling complex problems. To address these challenges, We develop Variable-Constraint Search (VCSEARCH), a trainingfree framework that leverages formal language to detect ill-defined problems, where a variableconstraint pair search strategy is incorporated to improve the modeling capability of formal language. Extensive experiments demonstrate that VCSEARCH improves the accuracy of identifying unsolvable problems by at least 12% across different LLMs, thus achieving stronger robust mathematical reasoning ability.

Aligned instruction following models can better fulfill user requests than their unaligned counterparts. However, it has been shown that there is a length bias in evaluation of such models, and that training algorithms tend to exploit this bias by learning longer responses. In this work we show how to train models that can be controlled at inference time with instructions containing desired length constraints. Such models are superior in length instructed evaluations, outperforming standard instruction following models such as GPT4, Llama 3 and Mixtral.

We investigate the potential of bio-inspired evolutionary algorithms for designing quantum circuits with specific goals, focusing on two particular tasks. The first one is motivated by the ideas of Artificial Life that are used to reproduce stochastic cellular automata with given rules. We test the robustness of quantum implementations of the cellular automata for different numbers of quantum gates The second task deals with the sampling of quantum circuits that generate highly entangled quantum states, which constitute an important resource for quantum computing. In particular, an evolutionary algorithm is employed to optimize circuits with respect to a fitness function defined with the Mayer-Wallach entanglement measure. We demonstrate that, by balancing the mutation rate between exploration and exploitation, we can find entangling quantum circuits for up to five qubits. We also discuss the trade-off between the number of gates in quantum circuits and the computational costs of finding the gate arrangements leading to a strongly entangled state. Our findings provide additional insight into the trade-off between the complexity of a circuit and its performance, which is an important factor in the design of quantum circuits.

We propose an evolution strategies-based algorithm for estimating gradients in unrolled computation graphs, called ES-Single. Similarly to the recently-proposed Persistent Evolution Strategies (PES), ES-Single is unbiased, and overcomes chaos arising from recursive function applications by smoothing the meta-loss landscape. ES-Single samples a single perturbation per particle, that is kept fixed over the course of an inner problem (e.g., perturbations are not re-sampled for each partial unroll). Compared to PES, ES-Single is simpler to implement and has lower variance: the variance of ES-Single is constant with respect to the number of truncated unrolls, removing a key barrier in applying ES to long inner problems using short truncations. We show that ES-Single is unbiased for quadratic inner problems, and demonstrate empirically that its variance can be substantially lower than that of PES. ES-Single consistently outperforms PES on a variety of tasks, including a synthetic benchmark task, hyperparameter optimization, training recurrent neural networks, and training learned optimizers.

In machine learning applications, it is well known that carefully designed learning rate (step size) schedules can significantly improve the convergence of commonly used first-order optimization algorithms. Therefore how to set step size adaptively becomes an important research question. A popular and effective method is the Polyak step size, which sets step size adaptively for gradient descent or stochastic gradient descent without the need to estimate the smoothness parameter of the objective function. However, there has not been a principled way to generalize the Polyak step size for algorithms with momentum accelerations. This paper presents a general framework to set the learning rate adaptively for first-order optimization methods with momentum, motivated by the derivation of Polyak step size. It is shown that the resulting methods are much less sensitive to the choice of momentum parameter and may avoid the oscillation of the heavy-ball method on ill-conditioned problems. These adaptive step sizes are further extended to the stochastic settings, which are attractive choices for stochastic gradient descent with momentum. Our methods are demonstrated to be more effective for stochastic gradient methods than prior adaptive step size algorithms in large-scale machine learning tasks.

Task allocation is a key combinatorial optimization problem, crucial for modern applications such as multi-robot cooperation and resource scheduling. Decision makers must allocate entities to tasks reasonably across different scenarios. However, traditional methods assume static attributes and numbers of tasks and entities, often relying on dynamic programming and heuristic algorithms for solutions. In reality, task allocation resembles Markov decision processes, with dynamically changing task and entity attributes. Thus, algorithms must dynamically allocate tasks based on their states. To address this issue, we propose a two-stage task allocation algorithm based on similarity, utilizing reinforcement learning to learn allocation strategies. The proposed pre-assign strategy allows entities to preselect appropriate tasks, effectively avoiding local optima and thereby better finding the optimal allocation. We also introduce an attention mechanism and a hyperparameter network structure to adapt to the changing number and attributes of entities and tasks, enabling our network structure to generalize to new tasks. Experimental results across multiple environments demonstrate that our algorithm effectively addresses the challenges of dynamic task allocation in practical applications. Compared to heuristic algorithms like genetic algorithms, our reinforcement learning approach better solves dynamic allocation problems and achieves zero-shot generalization to new tasks with good performance. The code is available at https://github.com/yk7333/TaskAllocation.

We explore efficient neural architecture search methods and show that a simple yet powerful evolutionary algorithm can discover new architectures with excellent performance. Our approach combines a novel hierarchical genetic representation scheme that imitates the modularized design pattern commonly adopted by human experts, and an expressive search space that supports complex topologies. Our algorithm efficiently discovers architectures that outperform a large number of manually designed models for image classification, obtaining top-1 error of 3.6% on CIFAR-10 and 20.3% when transferred to ImageNet, which is competitive with the best existing neural architecture search approaches. We also present results using random search, achieving 0.3% less top-1 accuracy on CIFAR-10 and 0.1% less on ImageNet whilst reducing the search time from 36 hours down to 1 hour.

In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine learning model in order to decide whether to pause training and start a new model, or resume the training of a previously-considered model. We specifically tailor our method to machine learning problems by developing a novel positive-definite covariance kernel to capture a variety of training curves. Furthermore, we develop a Gaussian process prior that scales gracefully with additional temporal observations. Finally, we provide an information-theoretic framework to automate the decision process. Experiments on several common machine learning models show that our approach is extremely effective in practice.

In this work, we introduce CodeEvolve, an open-source evolutionary coding agent that unites Large Language Models (LLMs) with genetic algorithms to solve complex computational problems. Our framework adapts powerful evolutionary concepts to the LLM domain, building upon recent methods for generalized scientific discovery. CodeEvolve employs an island-based genetic algorithm to maintain population diversity and increase throughput, introduces a novel inspiration-based crossover mechanism that leverages the LLMs context window to combine features from successful solutions, and implements meta-prompting strategies for dynamic exploration of the solution space. We conduct a rigorous evaluation of CodeEvolve on a subset of the mathematical benchmarks used to evaluate Google DeepMind's closed-source AlphaEvolve. Our findings show that our method surpasses AlphaEvolve's performance on several challenging problems. To foster collaboration and accelerate progress, we release our complete framework as an open-source repository.

Domain Generation Algorithms (DGAs) are frequently used to generate numerous domains for use by botnets. These domains are often utilized as rendezvous points for servers that malware has command and control over. There are many algorithms that are used to generate domains, however many of these algorithms are simplistic and easily detected by traditional machine learning techniques. In this paper, three variants of Generative Adversarial Networks (GANs) are optimized to generate domains which have similar characteristics of benign domains, resulting in domains which greatly evade several state-of-the-art deep learning based DGA classifiers. We additionally provide a detailed analysis into offensive usability for each variant with respect to repeated and existing domain collisions. Finally, we fine-tune the state-of-the-art DGA classifiers by adding GAN generated samples to their original training datasets and analyze the changes in performance. Our results conclude that GAN based DGAs are superior in evading DGA classifiers in comparison to traditional DGAs, and of the variants, the Wasserstein GAN with Gradient Penalty (WGANGP) is the highest performing DGA for uses both offensively and defensively.

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.