Issues

• angle_between returns pi (antiparallel) for nearly parallel float32 vectors

  deepchem/deepchem#5211 · Filter by author ChenziqiAdam opened on Oct 11, 2026
  1

• DiskDataset: make_pytorch_dataset duplicates samples with num_workers > 1

  deepchem/deepchem#5198 · Filter by author HESleagacy opened on Oct 6, 2026

• ElectronSampler.log_prob_gaussian returns a wrong log-density unless sigma has one entry per electron

  deepchem/deepchem#5195 · Filter by author ChenziqiAdam opened on Oct 6, 2026

• compute_hydrogen_bonds misses hydrogen bonds depending on fragment order / hydrogen order, and ignores the angle cutoff

  deepchem/deepchem#5194 · Filter by author ChenziqiAdam opened on Oct 6, 2026

• Metric(bedroc_score) returns wrong values (0.51 for a perfect ranking)

  deepchem/deepchem#5191 · Filter by author Zhuoxi2000 opened on Oct 1, 2026
  1

• sequence_utils hhsearch/hhblits never reject an unsupported file type, and the '-M first' branch is dead code

  deepchem/deepchem#5186 · Filter by author aniruddhaadak80 opened on Sep 29, 2026

• FingerprintSplitter raises ZeroDivisionError when int(frac_train * len(dataset)) floors to zero

  deepchem/deepchem#5171 · Filter by author aniruddhaadak80 opened on Sep 28, 2026
  1

• CircularFingerprint.__eq__/__hash__ ignore is_counts_based, so counts and bit-vector featurizers compare equal and collapse in a set

  deepchem/deepchem#5169 · Filter by author aniruddhaadak80 opened on Sep 28, 2026

• load_csv_files() leaves a NaN label with weight 1 when shard_size is None, so shard_size silently changes the training set

  deepchem/deepchem#5167 · Filter by author aniruddhaadak80 opened on Sep 28, 2026
  1

• create_char_to_idx() returns a different char->index mapping in every process (set iteration order leaks into the vocabulary)

  deepchem/deepchem#5165 · Filter by author aniruddhaadak80 opened on Sep 28, 2026

• Placement for a reproducible Tox21 PyTorch example with optional Nebius Jobs instructions

  deepchem/deepchem#5164 · Filter by author SalikovAlex opened on Sep 28, 2026
  1

• RandomSplitter accepts negative split fractions and produces invalid splits

  deepchem/deepchem#5159 · Filter by author MateehUllah opened on Sep 26, 2026
  2

• SpecifiedSplitter allows overlapping validation and test indices

  deepchem/deepchem#5158 · Filter by author MateehUllah opened on Sep 26, 2026
  1

• ScScoreModel accepts score_scale=1 despite requiring it to be greater than 1

  deepchem/deepchem#5157 · Filter by author MateehUllah opened on Sep 26, 2026
  1

• HuggingFaceModel ignores sample weights during supervised training

  deepchem/deepchem#5144 · Filter by author Galax1513 opened on Sep 25, 2026
  3

• Tutorial notebooks reference renamed files: dead Colab badges and stale self-citations

  deepchem/deepchem#5142 · Filter by author oardemalinegv5553-sudo opened on Sep 23, 2026

• https://github.com/deepchem/deepchem/discussions/4703 DFT ideas part

  deepchem/deepchem#5140 · Filter by author supuram opened on Sep 22, 2026
  1

• DiskDataset.itersamples() returns the wrong rows if samples are collected before use

  deepchem/deepchem#5138 · Filter by author RudraDudhat2509 opened on Sep 21, 2026

• FASTALoader silently discards sequences when a FASTA record is empty

  deepchem/deepchem#5132 · Filter by author siddhant-shahhh opened on Sep 13, 2026

• Tests in test_genomics.py error instead of skipping when TensorFlow or simdna are missing

  deepchem/deepchem#5130 · Filter by author siddhant-shahhh opened on Sep 12, 2026

• DAGLayer and DAGGather reject glorot_normal/xavier_normal init

  deepchem/deepchem#5127 · Filter by author sumitjhadev opened on Sep 8, 2026

• Pylance/Pyright does not recognize top-level namespaces such as dc.feat and dc.models

  deepchem/deepchem#5117 · Filter by author behmo opened on Aug 29, 2026
  1

• Documentation search stuck on "Searching" - jQuery is not defined

  deepchem/deepchem#5115 · Filter by author behmo opened on Aug 27, 2026

• PoissonLoss and CategoricalCrossEntropy – log(0) causes -inf / NaN in PyTorch path

  deepchem/deepchem#5099 · Filter by author mishradwaterlaw opened on Aug 19, 2026
  2

• AtomicConv applies dropout during eval, so predict() is nondeterministic

  deepchem/deepchem#5092 · Filter by author chiruu12 opened on Aug 12, 2026
  1