A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Reinforcement learning after next-token prediction aids in learning from diverse sequence lengths.
problem Learning from sequences of varying lengths and complexity.
method Introducing a framework to study reinforcement learning with autoregressive transformers, focusing on next-token prediction and mixture distributions of short and long sequences.
result Reinforcement learning after next-token prediction enables autoregressive transformers to generalize from long sequences, even when they are rare.
Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model l…
This paper examines how different decoding algorithms for LLMs align with various goals.
problem Consistency of decoding algorithms with different goals in LLMs.
method Analysis of greedy, lookahead, random sampling, and temperature-scaled random sampling algorithms.
result Random sampling is consistent with the true probability distribution, but other goals require optimal algorithms for specific probability distributions.
Study on the structure of classifier boundaries in DNA sequencing.
problem Understanding the structure of boundaries in a Bayes classifier for DNA sequencing.
method Examined the structure of the boundary in a Bayes classifier applied to DNA sequencing data. Introduced a new measure of uncertainty, Neighbor Similarity.
result The boundary is large and complex, and Neighbor Similarity effectively measures classifier uncertainty.
Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurr…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed samples with high resolution. Yet, the noise inherent in the biological processe…
Convolutional Neural Networks (CNNs) have been recently introduced in the domain of session-based next item recommendation. An ordered collection of past items the user has interacted with in a session (or sequence) are embedded into a 2-dimensional latent matrix, and treated as an image. The convolution and pooling op…
Sequence-to-Sequence (seq2seq) modeling has rapidly become an important general-purpose NLP tool that has proven effective for many text-generation and sequence-labeling tasks. Seq2seq builds on deep neural language modeling and inherits its remarkable accuracy in estimating local, next-word distributions. In this work…
This paper proposes an autoregressive (AR) model for sequences of graphs, which generalises traditional AR models. A first novelty consists in formalising the AR model for a very general family of graphs, characterised by a variable topology, and attributes associated with nodes and edges. A graph neural network (GNN) …
Long-term human motion can be represented as a series of motion modes---motion sequences that capture short-term temporal dynamics---with transitions between them. We leverage this structure and present a novel Motion Transformation Variational Auto-Encoders (MT-VAE) for learning motion sequence generation. Our model j…
Neural Machine Translation (NMT) generates target words sequentially in the way of predicting the next word conditioned on the context words. At training time, it predicts with the ground truth words as context while at inference it has to generate the entire sequence from scratch. This discrepancy of the fed context l…
When people learn mathematical patterns or sequences, they are able to identify the concepts (or rules) underlying those patterns. Having learned the underlying concepts, humans are also able to generalize those concepts to other numbers, so far as to even identify previously unseen combinations of those rules. Current…
Let K be a two-periodic braid and let K be its quotient. In this paper we show there is a spectral sequence from the next-to-top winding number grading of the sutured annular Khovanov homology of the closure of K to the next-to-top winding number grading of the sutured annular Khovanov hom…
The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application of next generation sequencing technologies to a tumor sample, followed by the id…
We propose a novel adversarial learning strategy for mixture models of Hawkes processes, leveraging data augmentation techniques of Hawkes process in the framework of self-paced learning. Instead of learning a mixture model directly from a set of event sequences drawn from different Hawkes processes, the proposed metho…
Effectively capturing graph node sequences in the form of vector embeddings is critical to many applications. We achieve this by (i) first learning vector embeddings of single graph nodes and (ii) then composing them to compactly represent node sequences. Specifically, we propose SENSE-S (Semantically Enhanced Node Seq…
Online detection of instantaneous changes in the generative process of a data sequence generally focuses on retrospective inference of such change points without considering their future occurrences. We extend the Bayesian Online Change Point Detection algorithm to also infer the number of time steps until the next cha…
We present a recurrent neural network memory that uses sparse coding to create a combinatoric encoding of sequential inputs. Using several examples, we show that the network can associate distant causes and effects in a discrete stochastic process, predict partially-observable higher-order sequences, and enable a DQN a…
Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…
In this work, we develop a novel regularizer to improve the learning of long-range dependency of sequence data. Applied on language modelling, our regularizer expresses the inductive bias that sequence variables should have high mutual information even though the model might not see abundant observations for complex lo…
Temporal point process is an expressive tool for modeling event sequences over time. In this paper, we take a reinforcement learning view whereby the observed sequences are assumed to be generated from a mixture of latent policies. The purpose is to cluster the sequences with different temporal patterns into the underl…
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from m…
Differential forms on an odd symplectic manifold form a bicomplex: one differential is the wedge product with the symplectic form and the other is de Rham differential. In the corresponding spectral sequence the next differential turns out to be the Batalin-Vilkoviski operator.
We are now witnessing the increasing availability of event stream data, i.e., a sequence of events with each event typically being denoted by the time it occurs and its mark information (e.g., event type). A fundamental problem is to model and predict such kind of marked temporal dynamics, i.e., when the next event wil…
This paper studies the dynamic generator model for spatial-temporal processes such as dynamic textures and action sequences in video data. In this model, each time frame of the video sequence is generated by a generator model, which is a non-linear transformation of a latent state vector, where the non-linear transform…
Traditionally, text generation models take in a sequence of text as input, and iteratively generate the next most probable word using pre-trained parameters. In this work, we propose the architecture to use images instead of text as the input of the text generation model, called StoryGen. In the architecture, we design…
In complex processes, various events can happen in different sequences. The prediction of the next event given an a-priori process state is of importance in such processes. Recent methods have proposed deep learning techniques such as recurrent neural networks, developed on raw event logs, to predict the next event fro…
We introduce the problem of reconstructing a sequence of multidimensional real vectors where some of the data are missing. This problem contains regression and mapping inversion as particular cases where the pattern of missing data is independent of the sequence index. The problem is hard because it involves possibly m…