Neural networks are powered by an implicit bias: a tendency of gradient descent to fit training data in a way that generalizes to unseen data. A recent class of neural network models gaining increasing popularity is structured state space models (SSMs). Prior work argued that the implicit bias of SSMs leads to generalization in a setting where data is generated by a low dimensional teacher. In this paper, we revisit the latter setting, and formally establish a phenomenon entirely undetected by prior work on the implicit bias of SSMs. Namely, we prove that while implicit bias leads to generalization under many choices of training data, there exist special examples whose inclusion in training completely distorts the implicit bias, to a point where generalization fails. This failure occurs despite the special training examples being labeled by the teacher, i.e., having clean labels! We empirically demonstrate the phenomenon, with SSMs trained independently and as part of non-linear neural networks. In the area of adversarial machine learning, disrupting generalization with cleanly labeled training examples is known as clean-label poisoning. Given the proliferation of SSMs, we believe that delineating their susceptibility to clean-label poisoning, and developing methods for overcoming this susceptibility, are critical research directions to pursue.

The Teacher Forcing algorithm trains recurrent networks by supplying observed sequence values as inputs during training and using the network's own one-stepahead predictions to do multi-step sampling. We introduce the Professor Forcing algorithm, which uses adversarial domain adaptation to encourage the dynamics of the recurrent network to be the same when training the network and when sampling from the network over multiple time steps. We apply Professor Forcing to language modeling, vocal synthesis on raw waveforms, handwriting generation, and image generation. Empirically we find that Professor Forcing acts as a regularizer, improving test likelihood on character level Penn Treebank and sequential MNIST. We also find that the model qualitatively improves samples, especially when sampling for a large number of time steps. This is supported by human evaluation of sample quality. Trade-offs between Professor Forcing and Scheduled Sampling are discussed. We produce T-SNEs showing that Professor Forcing successfully makes the dynamics of the network during training and sampling more similar.

Of course, the count function should be fixed.

Psychologists are interested in developing instructional policies that boost student learning. An instructional policy specifies the manner and content of instruction. For example, in the domain of concept learning, a policy might specify the nature of exemplars chosen over a training sequence. Traditional psychological studies compare several hand-selected policies, e.g., contrasting a policy that selects only difficult-to-classify exemplars with a policy that gradually progresses over the training sequence from easy exemplars to more difficult (known as {\em fading}). We propose an alternative to the traditional methodology in which we define a parameterized space of policies and search this space to identify the optimum policy.

Sequential data in our everyday life is often hierarchically structured.

Language models often struggle with cross-mode knowledge retrieval -- the ability to access knowledge learned in one format (mode) when queried in another. We demonstrate that models trained on multiple data sources (e.g., Wikipedia and TinyStories) exhibit significantly reduced accuracy when retrieving knowledge in a format different from its original training mode. This paper quantitatively investigates this phenomenon through a controlled study of random token sequence memorization across different modes. We first explore dataset rewriting as a solution, revealing that effective cross-mode retrieval requires prohibitively extensive rewriting efforts that follow a sigmoid-like relationship. As an alternative, we propose CASCADE, a novel pretraining algorithm that uses cascading datasets with varying sequence lengths and computing losses on only the second half of each training sequence to capture knowledge at different scales. Our experiments demonstrate that CASCADE outperforms dataset rewriting approaches, even when compressed into a single model with a unified loss function. This work provides both qualitative evidence of cross-mode retrieval limitations and a practical solution to enhance language models' ability to access knowledge independently of its presentational format.

Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior knowledge of enzyme catalysis to rationally modulate general protein-molecule features that are misaligned with catalytic patterns. To address this issue, we introduce a two-stage progressive framework, OmniESI, for enzyme-substrate interaction prediction through conditional deep learning. By decomposing the modeling of enzyme-substrate interactions into a two-stage progressive process, OmniESI incorporates two conditional networks that respectively emphasize enzymatic reaction specificity and crucial catalysis-related interactions, facilitating a gradual feature modulation in the latent space from general protein-molecule domain to catalysis-aware domain. On top of this unified architecture, OmniESI can adapt to a variety of downstream tasks, including enzyme kinetic parameter prediction, enzyme-substrate pairing prediction, enzyme mutational effect prediction, and enzymatic active site annotation. Under the multi-perspective performance evaluation of in-distribution and out-of-distribution settings, OmniESI consistently delivered superior performance than state-of-the-art specialized methods across seven benchmarks. More importantly, the proposed conditional networks were shown to internalize the fundamental patterns of catalytic efficiency while significantly improving prediction performance, with only negligible parameter increases (0.16%), as demonstrated by ablation studies on key components. Overall, OmniESI represents a unified predictive approach for enzyme-substrate interactions, providing an effective tool for catalytic mechanism cracking and enzyme engineering with strong generalization and broad applicability.