arXiv subjects

Sham M. Kakade

Publications and source records attributed to Sham M. Kakade.

At least 19 recordsLinked to original sources

arXiv2026

How Post-Training Shapes Biological Reasoning Models

Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins. These models are built through post-training, yet how each stage shapes reasoning and generalization remains poorly understood. We study when post-training improves performance and when it induces over-specialization. Across genomics, transcriptomics, and proteins, we train and evaluate more than 100 biological reasoning models under controlled variation in backbone, continued pre-training (CPT), supervised fine-tuning (SFT), and reinforcement learning (RL), measuring both in-domain (ID) and out-of-domain (OOD) performance. We find that each post-training stage reshapes generalization in a distinct way rather than contributing uniform gains. CPT improves downstream performance by aligning models with biological language. SFT consistently increases ID performance but causes OOD performance to peak early and decline as models fit the training distribution. RL, when applied to strong SFT checkpoints with aligned rewards, improves OOD performance and partially recovers generalization. These results show that biological reasoning does not improve monotonically with additional supervision or compute. Instead, performance depends on how training stages are composed. Under fixed post-training budgets, the strongest ID-OOD trade-off comes from brief SFT, larger RL allocations, and asymmetric adaptation capacity across stages.

cs.LG↗

arXiv2026

Risk Comparisons in Linear Regression: Implicit Regularization Dominates Explicit Regularization

Existing theory suggests that for linear regression problems categorized by capacity and source conditions, gradient descent (GD) is always minimax optimal, while both ridge regression and online stochastic gradient descent (SGD) are polynomially suboptimal for certain categories of such problems. Moving beyond minimax theory, this work provides instance-wise comparisons of the finite-sample risks for these algorithms on any well-specified linear regression problem. Our analysis yields three key findings. First, GD dominates ridge regression: with comparable regularization, the excess risk of GD is always within a constant factor of that of ridge, but ridge can be polynomially worse even when tuned optimally. Second, GD is incomparable with SGD. While it is known that for certain problems GD can be polynomially better than SGD, the reverse is also true: we construct problems, inspired by benign overfitting theory, where optimally stopped GD is polynomially worse. Finally, GD dominates SGD for a significant subclass of problems -- those with fast and continuously decaying covariance spectra -- which includes all problems satisfying the standard capacity condition.

stat.ML↗

arXiv2026

Evaluating Relational Reasoning in LLMs with REL

Relational reasoning is the ability to infer relations that jointly bind multiple entities, attributes, or variables. This ability is central to scientific reasoning, but existing evaluations of relational reasoning in large language models often focus on structured inputs such as tables, graphs, or synthetic tasks, and do not isolate the difficulty introduced by higher-arity relational binding. We study this problem through the lens of Relational Complexity (RC), which we define as the minimum number of independent entities or operands that must be simultaneously bound to apply a relation. RC provides a principled way to vary reasoning difficulty while controlling for confounders such as input size, vocabulary, and representational choices. Building on RC, we introduce REL, a generative benchmark framework spanning algebra, chemistry, and biology that varies RC within each domain. Across frontier LLMs, performance degrades consistently and monotonically as RC increases, even when the total number of entities is held fixed. This failure mode persists with increased test-time compute and in-context learning, suggesting a limitation tied to the arity of the required relational binding rather than to insufficient inference steps or lack of exposure to examples. Our results identify a regime of higher-arity reasoning in which current models struggle, and motivate re-examining benchmarks through the lens of relational complexity.

cs.AI↗

arXiv2026

Self-Improving Language Models with Bidirectional Evolutionary Search

Search has been proposed as an effective method for self-improving language models and agentic systems, both for post-training sample generation and for inference. However, widely used methods such as best-of-N sampling and tree search face two fundamental limitations: they are guided by sparse verification signals, and they construct candidates primarily through autoregressive expansion, restricting exploration to regions with substantial model probability mass. To address these, we propose Bidirectional Evolutionary Search (BES), a search framework that couples forward candidate evolution with backward goal decomposition. In the forward search, BES augments standard expansion with evolution operators that recombine partial trajectories to generate candidates that are difficult to obtain from a single model rollout. In the backward search, BES recursively decomposes the original task into checkable subgoals, producing dense intermediate feedback that guides forward search. We provide theoretical motivation showing that candidates generated by expansion-only search are confined to a narrow entropy shell while evolutionary operators can escape it, and that backward search can exponentially reduce the number of required samples to find a correct answer. Experiments show that on challenging post-training tasks where mainstream post-training algorithms fail to improve, BES enables consistent gains, and on three open problem solving benchmarks at inference time, BES outperforms existing open-source frameworks in both average and best-case performance. Code and trained models are available at https://github.com/Embodied-Minds-Lab/BES.

cs.CL↗

arXiv2026

Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models

Cross-entropy (CE) training provides dense and scalable supervision for language models, but it optimizes next-token prediction under teacher forcing rather than sequence-level behavior under model rollouts. We introduce a feature-matching objective for language-model fine-tuning that targets sequence-level statistics of the completion distribution, providing dense semantic feedback without requiring a task-specific verifier or preference model. To optimize this objective efficiently, we propose energy-based fine-tuning (EBFT), which uses strided block-parallel sampling to generate multiple rollouts from nested prefixes concurrently, batches feature extraction over these rollouts, and uses the resulting embeddings to perform an on-policy policy-gradient update. We present a theoretical perspective connecting EBFT to KL-regularized feature-matching and energy-based modeling. Empirically, across Q&A coding, unstructured coding, and translation, EBFT matches RLVR and outperforms SFT on downstream accuracy while achieving a lower validation cross-entropy than both methods.

cs.LG↗

arXiv2026

Scaling Reward Modeling without Human Supervision

Learning from feedback is an instrumental process for advancing the capabilities and safety of frontier models, yet its effectiveness is often constrained by cost and scalability. We present a pilot study that explores scaling reward models through unsupervised approaches. We operationalize reward-based scaling (RBS), in its simplest form, as preference learning over document prefixes and suffixes drawn from large-scale web corpora. Its advantage is demonstrated in various aspects: despite using no human annotations, training on 11M tokens of math-focused web data yields steady gains on RewardBench v1 and v2, and these improvements consistently transfer across diverse initialization backbones spanning model families and scales. Across models, our method improves RewardBench v2 accuracy by up to +7.7 points on average, with gains of up to +16.1 on in-domain math subsets and consistent improvements on out-of-domain safety and general subsets. When applied to best-of-N selection and policy optimization, these reward models substantially improve downstream math performance and match or exceed strong supervised reward model baselines of similar size. Overall, we demonstrate the feasibility and promise of training reward models without costly and potentially unreliable human annotations.

cs.LG↗

arXiv2025

The Emergence of Complex Behavior in Large-Scale Ecological Environments

We explore how physical scale and population size shape the emergence of complex behaviors in open-ended ecological environments. In our setting, agents are unsupervised and have no explicit rewards or learning objectives but instead evolve over time according to reproduction, mutation, and selection. As they act, agents also shape their environment and the population around them in an ongoing dynamic ecology. Our goal is not to optimize a single high-performance policy, but instead to examine how behaviors emerge and evolve across large populations due to natural competition and environmental pressures. We use modern hardware along with a new multi-agent simulator to scale the environment and population to sizes much larger than previously attempted, reaching populations of over 60,000 agents, each with their own evolved neural network policy. We identify various emergent behaviors such as long-range resource extraction, vision-based foraging, and predation that arise under competitive and survival pressures. We examine how sensing modalities and environmental scale affect the emergence of these behaviors and find that some of them appear only in sufficiently large environments and populations, and that larger scales increase the stability and consistency of these emergent behaviors. While there is a rich history of research in evolutionary settings, our scaling results on modern hardware provide promising new directions to explore ecology as an instrument of machine learning in an era of increasingly abundant computational resources and efficient machine frameworks. Experimental code is available at https://github.com/jbejjani2022/ecological-emergent-behavior.

cs.MA↗

arXiv2025

Adam or Gauss-Newton? A Comparative Study In Terms of Basis Alignment and SGD Noise

Diagonal preconditioners are computationally feasible approximate to second-order optimizers, which have shown significant promise in accelerating training of deep learning models. Two predominant approaches are based on Adam and Gauss-Newton (GN) methods: the former leverages statistics of current gradients and is the de-factor optimizers for neural networks, and the latter uses the diagonal elements of the Gauss-Newton matrix and underpins some of the recent diagonal optimizers such as Sophia. In this work, we compare these two diagonal preconditioning methods through the lens of two key factors: the choice of basis in the preconditioner, and the impact of gradient noise from mini-batching. To gain insights, we analyze these optimizers on quadratic objectives and logistic regression under all four quadrants. We show that regardless of the basis, there exist instances where Adam outperforms both GN$^{-1}$ and GN$^{-1/2}$ in full-batch settings. Conversely, in the stochastic regime, Adam behaves similarly to GN$^{-1/2}$ for linear regression under a Gaussian data assumption. These theoretical results are supported by empirical studies on both convex and non-convex objectives.

cs.LG↗

arXiv2025

Scaling Laws in Linear Regression: Compute, Parameters, and Data

Empirically, large-scale deep learning models often satisfy a neural scaling law: the test error of the trained model improves polynomially as the model size and data size grow. However, conventional wisdom suggests the test error consists of approximation, bias, and variance errors, where the variance error increases with model size. This disagrees with the general form of neural scaling laws, which predict that increasing model size monotonically improves performance. We study the theory of scaling laws in an infinite dimensional linear regression setup. Specifically, we consider a model with $M$ parameters as a linear function of sketched covariates. The model is trained by one-pass stochastic gradient descent (SGD) using $N$ data. Assuming the optimal parameter satisfies a Gaussian prior and the data covariance matrix has a power-law spectrum of degree $a>1$, we show that the reducible part of the test error is $Θ(M^{-(a-1)} + N^{-(a-1)/a})$. The variance error, which increases with $M$, is dominated by the other errors due to the implicit regularization of SGD, thus disappearing from the bound. Our theory is consistent with the empirical neural scaling laws and verified by numerical simulation.

cs.LG↗

arXiv2025

Eliminating Position Bias of Language Models: A Mechanistic Approach

Position bias has proven to be a prevalent issue of modern language models (LMs), where the models prioritize content based on its position within the given context. This bias often leads to unexpected model failures and hurts performance, robustness, and reliability across various applications. Our mechanistic analysis attributes the position bias to two components employed in nearly all state-of-the-art LMs: causal attention and relative positional encodings. Based on the analyses, we propose to eliminate position bias (e.g., different retrieved documents' orders in QA affect performance) with a training-free zero-shot approach. Our method changes the causal attention to bidirectional attention between documents and utilizes model attention values to decide the relative orders of documents instead of using the order provided in input prompts, therefore enabling Position-INvariant inferencE (PINE) at the document level. By eliminating position bias, models achieve better performance and reliability in downstream tasks, including LM-as-a-judge, retrieval-augmented QA, molecule generation, and math reasoning. Notably, PINE is especially useful when adapting LMs for evaluating reasoning pairs: it consistently provides 8 to 10 percentage points performance gains, making Llama-3-70B-Instruct perform even better than GPT-4-0125-preview and GPT-4o-2024-08-06 on the RewardBench reasoning set.

cs.CL↗

arXiv2025

Mixture of Parrots: Experts improve memorization more than reasoning

The Mixture-of-Experts (MoE) architecture enables a significant increase in the total number of model parameters with minimal computational overhead. However, it is not clear what performance tradeoffs, if any, exist between MoEs and standard dense transformers. In this paper, we show that as we increase the number of experts (while fixing the number of active parameters), the memorization performance consistently increases while the reasoning capabilities saturate. We begin by analyzing the theoretical limitations of MoEs at reasoning. We prove that there exist graph problems that cannot be solved by any number of experts of a certain width; however, the same task can be easily solved by a dense model with a slightly larger width. On the other hand, we find that on memory-intensive tasks, MoEs can effectively leverage a small number of active parameters with a large number of experts to memorize the data. We empirically validate these findings on synthetic graph problems and memory-intensive closed book retrieval tasks. Lastly, we pre-train a series of MoEs and dense transformers and evaluate them on commonly used benchmarks in math and natural language. We find that increasing the number of experts helps solve knowledge-intensive tasks, but fails to yield the same benefits for reasoning tasks.

cs.LG↗

arXiv2025

The Role of Sparsity for Length Generalization in Transformers

Training large language models to predict beyond their training context lengths has drawn much attention in recent years, yet the principles driving such behavior of length generalization remain underexplored. We propose a new theoretical framework to study length generalization for the next-token prediction task, as performed by decoder-only transformers. Conceptually, we show that length generalization occurs as long as each predicted token depends on a small (fixed) number of previous tokens. We formalize such tasks via a notion we call $k$-sparse planted correlation distributions, and show that an idealized model of transformers which generalize attention heads successfully length-generalize on such tasks. As a bonus, our theoretical model justifies certain techniques to modify positional embeddings which have been introduced to improve length generalization, such as position coupling. We support our theoretical results with experiments on synthetic tasks and natural language, which confirm that a key factor driving length generalization is a ``sparse'' dependency structure of each token on the previous ones. Inspired by our theory, we introduce Predictive Position Coupling, which trains the transformer to predict the position IDs used in a positional coupling approach. Predictive Position Coupling thereby allows us to broaden the array of tasks to which position coupling can successfully be applied to achieve length generalization.

cs.LG↗

arXiv2025

Preference-Based Multi-Agent Reinforcement Learning: Data Coverage and Algorithmic Techniques

We initiate the study of Preference-Based Multi-Agent Reinforcement Learning (PbMARL), exploring both theoretical foundations and empirical validations. We define the task as identifying the Nash equilibrium from a preference-only offline dataset in general-sum games, a problem marked by the challenge of sparse feedback signals. Our theory establishes the upper complexity bounds for Nash Equilibrium in effective PbMARL, demonstrating that single-policy coverage is inadequate and highlighting the importance of unilateral dataset coverage. These theoretical insights are verified through comprehensive experiments. To enhance the practical performance, we further introduce two algorithmic techniques. (1) We propose a Mean Squared Error (MSE) regularization along the time axis to achieve a more uniform reward distribution and improve reward learning outcomes. (2) We propose an additional penalty based on the distribution of the dataset to incorporate pessimism, improving stability and effectiveness during training. Our findings underscore the multifaceted approach required for PbMARL, paving the way for effective preference-based multi-agent systems.

cs.LG↗

arXiv2024

Matching the Statistical Query Lower Bound for $k$-Sparse Parity Problems with Sign Stochastic Gradient Descent

The $k$-sparse parity problem is a classical problem in computational complexity and algorithmic theory, serving as a key benchmark for understanding computational classes. In this paper, we solve the $k$-sparse parity problem with sign stochastic gradient descent, a variant of stochastic gradient descent (SGD) on two-layer fully-connected neural networks. We demonstrate that this approach can efficiently solve the $k$-sparse parity problem on a $d$-dimensional hypercube ($k\leq O(\sqrt{d})$) with a sample complexity of $\tilde{O}(d^{k-1})$ using $2^{Θ(k)}$ neurons, matching the established $Ω(d^{k})$ lower bounds of Statistical Query (SQ) models. Our theoretical analysis begins by constructing a good neural network capable of correctly solving the $k$-parity problem. We then demonstrate how a trained neural network with sign SGD can effectively approximate this good network, solving the $k$-parity problem with small statistical errors. To the best of our knowledge, this is the first result that matches the SQ lower bound for solving $k$-sparse parity problem using gradient-based methods.

cs.LG↗

arXiv2024

Superposed Decoding: Multiple Generations from a Single Autoregressive Inference Pass

Many applications today provide users with multiple auto-complete drafts as they type, including GitHub's code completion, Gmail's smart compose, and Apple's messaging auto-suggestions. Under the hood, language models support this by running an autoregressive inference pass to provide a draft. Consequently, providing $k$ drafts to the user requires running an expensive language model $k$ times. To alleviate the computation cost of running $k$ inference passes, we propose Superposed Decoding, a new decoding algorithm that generates $k$ drafts at the computation cost of one autoregressive inference pass. We achieve this by feeding a superposition of the most recent token embeddings from the $k$ drafts as input to the next decoding step of the language model. At every inference step we combine the $k$ drafts with the top-$k$ tokens to get $k^2$ new drafts and cache the $k$ most likely options, using an n-gram interpolation with minimal compute overhead to filter out incoherent generations. Our experiments show that $k$ drafts from Superposed Decoding are at least as coherent and factual as Nucleus Sampling and Greedy Decoding respectively, while being at least $2.44\times$ faster for $k\ge3$. In a compute-normalized setting, user evaluations demonstrably favor text generated by Superposed Decoding over Nucleus Sampling. Superposed Decoding can also be combined with other decoding strategies, resulting in universal coverage gains when scaling inference time compute. Code and more examples open-sourced at https://github.com/RAIVNLab/SuperposedDecoding.

cs.CL↗

arXiv2024

Transcendence: Generative Models Can Outperform The Experts That Train Them

Generative models are trained with the simple objective of imitating the conditional probability distribution induced by the data they are trained on. Therefore, when trained on data generated by humans, we may not expect the artificial model to outperform the humans on their original objectives. In this work, we study the phenomenon of transcendence: when a generative model achieves capabilities that surpass the abilities of the experts generating its data. We demonstrate transcendence by training an autoregressive transformer to play chess from game transcripts, and show that the trained model can sometimes achieve better performance than all players in the dataset. We theoretically prove that transcendence can be enabled by low-temperature sampling, and rigorously assess this claim experimentally. Finally, we discuss other sources of transcendence, laying the groundwork for future investigation of this phenomenon in a broader setting.

cs.LG↗

arXiv2024

Repeat After Me: Transformers are Better than State Space Models at Copying

Transformers are the dominant architecture for sequence modeling, but there is growing interest in models that use a fixed-size latent state that does not depend on the sequence length, which we refer to as "generalized state space models" (GSSMs). In this paper we show that while GSSMs are promising in terms of inference-time efficiency, they are limited compared to transformer models on tasks that require copying from the input context. We start with a theoretical analysis of the simple task of string copying and prove that a two layer transformer can copy strings of exponential length while GSSMs are fundamentally limited by their fixed-size latent state. Empirically, we find that transformers outperform GSSMs in terms of efficiency and generalization on synthetic tasks that require copying the context. Finally, we evaluate pretrained large language models and find that transformer models dramatically outperform state space models at copying and retrieving information from context. Taken together, these results suggest a fundamental gap between transformers and GSSMs on tasks of practical interest.

cs.LG↗

arXiv2024

Learning Hidden Markov Models Using Conditional Samples

This paper is concerned with the computational complexity of learning the Hidden Markov Model (HMM). Although HMMs are some of the most widely used tools in sequential and time series modeling, they are cryptographically hard to learn in the standard setting where one has access to i.i.d. samples of observation sequences. In this paper, we depart from this setup and consider an interactive access model, in which the algorithm can query for samples from the conditional distributions of the HMMs. We show that interactive access to the HMM enables computationally efficient learning algorithms, thereby bypassing cryptographic hardness. Specifically, we obtain efficient algorithms for learning HMMs in two settings: (a) An easier setting where we have query access to the exact conditional probabilities. Here our algorithm runs in polynomial time and makes polynomially many queries to approximate any HMM in total variation distance. (b) A harder setting where we can only obtain samples from the conditional distributions. Here the performance of the algorithm depends on a new parameter, called the fidelity of the HMM. We show that this captures cryptographically hard instances and previously known positive results. We also show that these results extend to a broader class of distributions with latent low rank structure. Our algorithms can be viewed as generalizations and robustifications of Angluin's $L^*$ algorithm for learning deterministic finite automata from membership queries.

cs.LG↗